Engineering the Interface between Inorganic Nanoparticles and Biological Systems through Ligand Design

Nano-Engineering Strategies for Tumor-Specific Therapy

Nanodelivery systems (NDSs) provide promising prospects for decreasing drug doses, reducing side effects, and improving therapeutic effects. However, the bioapplications of NDSs are still compromised by their fast clearance, indiscriminate biodistribution, and limited tumor accumulation. Hence, engineering modification of NDSs aiming at promoting tumor-specific therapy and avoiding systemic toxicity is usually needed. An NDS integrating various functionalities, including flexible camouflage, specific biorecognition, and sensitive stimuli-responsiveness, into one sequence would be "smart" and highly effective. Herein, we systematically summarize the related principles, methods, and progress. At the end of the review, we predict the obstacles to precise nanoengineering and prospects for the future application of NDSs.

The Molecular Footprint of Peptides on the Surface of Ultrasmall Gold Nanoparticles (2 nm) Is Governed by Steric Demand

Ultrasmall gold nanoparticles were functionalized with peptides of two to seven amino acids that contained one cysteine molecule as anchor via a thiol-gold bond and a number of alanine residues as nonbinding amino acid. The cysteine was located either in the center of the molecule or at the end (C-terminus). For comparison, gold nanoparticles were also functionalized with cysteine alone. The particles were characterized by UV spectroscopy, differential centrifugal sedimentation (DCS), high-resolution transmission electron microscopy (HRTEM), and small-angle X-ray scattering (SAXS). This confirmed the uniform metal core (2 nm diameter). The hydrodynamic diameter was probed by 1H-DOSY NMR spectroscopy and showed an increase in thickness of the hydrated peptide layer with increasing peptide size (up to 1.4 nm for heptapeptides; 0.20 nm per amino acid in the peptide). 1H NMR spectroscopy of water-dispersed nanoparticles showed the integrity of the peptides and the effect of the metal core on the peptide. Notably, the NMR signals were very broad near the metal surface and became increasingly narrow in a distance. In particular, the methyl groups of alanine can be used as probe for the resolution of the NMR spectra. The number of peptide ligands on each nanoparticle was determined using quantitative 1H NMR spectroscopy. It decreased with increasing peptide length from about 100 for a dipeptide to about 12 for a heptapeptide, resulting in an increase of the molecular footprint from about 0.1 to 1.1 nm2.

Modular Fabrication of Bioorthogonal Nanozymes for Biomedical Applications

The incorporation of transition metal catalysts (TMCs) into nanoscaffolds generates nanocatalysts that replicate key aspects of enzymatic behavior. The TMCs can access bioorthogonal chemistry unavailable to living systems. These bioorthogonal nanozymes can be employed as in situ "factories" for generating bioactive molecules where needed. The generation of effective bioorthogonal nanozymes requires co-engineering of the TMC and the nanometric scaffold. This review presents an overview of recent advances in the field of bioorthogonal nanozymes, focusing on modular design aspects of both nanomaterial and catalyst and how they synergistically work together for in situ uncaging of imaging and therapeutic agents.

Ligand Lipophilicity Determines Molecular Mechanisms of Nanoparticle Adsorption to Lipid Bilayers

The interactions of ligand-functionalized nanoparticles with the cell membrane affect cellular uptake, cytotoxicity, and related behaviors, but relating these interactions to ligand properties remains challenging. In this work, we perform coarse-grained molecular dynamics simulations to study how the adsorption of ligand-functionalized cationic gold nanoparticles (NPs) to a single-component lipid bilayer (as a model cell membrane) is influenced by ligand end group lipophilicity. A set of 2 nm diameter NPs, each coated with a monolayer of organic ligands that differ only in their end groups, was simulated to mimic NPs recently studied experimentally. Metadynamics calculations were performed to determine key features of the free energy landscape for adsorption as a function of the distance of the NP from the bilayer and the number of NP-lipid contacts. These simulations revealed that NP adsorption is thermodynamically favorable for all NPs due to the extraction of lipids from the bilayer and into the NP monolayer. To resolve ligand-dependent differences in adsorption behavior, string method calculations were performed to compute minimum free energy pathways for adsorption. These calculations revealed a surprising nonmonotonic dependence of the free energy barrier for adsorption on ligand end group lipophilicity. Large free energy barriers are predicted for the least lipophilic end groups because favorable NP-lipid contacts are initiated only through the unfavorable protrusion of lipid tail groups out of the bilayer. The smallest free energy barriers are predicted for end groups of intermediate lipophilicity which promote NP-lipid contacts by intercalating within the bilayer. Unexpectedly, large free energy barriers are also predicted for the most lipophilic end groups which remain sequestered within the ligand monolayer rather than intercalating within the bilayer. These trends are broadly in agreement with past experimental measurements and reveal how subtle variations in ligand lipophilicity dictate adsorption mechanisms and associated kinetics by influencing the interplay of lipid-ligand interactions.

Modulation of Gold Nanoparticle Ligand Structure-Dynamic Relationships Probed Using Solution NMR

Ligand dynamics plays a critical role in the chemical and biological properties of gold nanoparticles (AuNPs). In this study, ligands featuring hydrophobic alkanethiol interiors and hydrophilic shells were used to systematically examine the effects of ligand headgroups on the ligand dynamics. Solution nuclear magnetic resonance (NMR) spectroscopy provided quantitative insight into the monolayer ligand dynamics. Notably, the introduction of hydrophobic moieties to the cationic headgroups significantly decreased ligand conformational mobility; however, variations in hydrophobicity among these moieties had a limited effect on this reduction. Further examination of ligand dynamics under various physiological conditions, including ionic strength and temperature, showed that ligands bound to the AuNP surface become less conformationally mobile with an increase in ionic strength or decreasing temperature. This exploration of ligand dynamics provides insight into designing nanoparticles tailored to specific biological applications.

The Why and How of Ultrasmall Nanoparticles

ConspectusIn this Account, we describe our research into ultrasmall nanoparticles, including their unique properties, and outline some of the new opportunities they offer. We will summarize our perspective on the current state of the field and highlight what we see as key questions that remain to be solved. First, there are several nanostructure size-scale regimes, with qualitatively distinct functional biological attributes. Broadly generalized, larger particles (e.g., larger than 300 nm) tend to be more efficiently swept away by the first line of the immune system (for example macrophages). In the "middle-sized" regime (20-300 nm), nanoparticle surfaces and shapes can be recognized by energy-dependent cellular reorganizations, then organized locally in a spatial and temporally coherent way. That energy is gated and made available by specific cellular recognition processes. The relationship between particle surface design, endogenously derived nonspecific biomolecular corona, and architectural features recognized by the cell is complex and only purposefully and very precisely designed nanoparticle architectures are able to navigate to specific targets. At sufficiently small sizes (<10 nm including the ligand shell, associated with a core diameter of a few nm at most) we enter the "quasi-molecular regime" in which the endogenous biomolecular environment exchanges so rapidly with the ultrasmall particle surface that larger scale cellular and immune recognition events are often greatly simplified. As an example, ultrasmall particles can penetrate cellular and biological barriers within tissue architectures via passive diffusion, in much the same way as small molecule drugs do. An intriguing question arises: what happens at the interface of cellular recognition and ultrasmall quasi-molecular size regimes? Succinctly put, ultrasmall conjugates can evade defense mechanisms driven by larger scale cellular nanoscale recognition, enabling them to flexibly exploit molecular interaction motifs to interact with specific targets. Numerous advances in control of architecture that take advantage of these phenomena have taken place or are underway. For instance, syntheses can now be sufficiently controlled that it is possible to make nanoparticles of a few hundreds of atoms or metalloid clusters of several tens of atoms that can be characterized by single crystal X-ray structure analysis. While the synthesis of atomically precise clusters in organic solvents presents challenges, water-based syntheses of ultrasmall nanoparticles can be upscaled and lead to well-defined particle populations. The surface of ultrasmall nanoparticles can be covalently modified with a wide variety of ligands to control the interactions of these particles with biosystems, as well as drugs and fluorophores. And, in contrast to larger particles, many advanced molecular analytical and separation tools can be applied to understand their structure. For example, NMR spectroscopy allows us to obtain a detailed image of the particle surface and the attached ligands. These are considerable advantages that allow further elaboration of the level of architectural control and characterization of the ultrasmall structures required to access novel functional regimes and outcomes. The ultrasmall nanoparticle regime has a unique status and provides a potentially very interesting direction for development.

Deconstructing Electrostatics of Functionalized Metal Nanoparticles from Molecular Dynamics Simulations

Gold nanoparticles (NPs) with different surface functionalizations can selectively interact with specific proteins, allowing a wide range of possible applications in biotechnology and biomedicine. To prevent their tendency to aggregate and to modulate their interaction with charged biomolecules or substrates (e.g., for biosensing applications), they can be functionalized with charged groups, introducing a mutual interaction which can be modulated by changing the ionic strength of the solvent. In silico modeling of these systems is often addressed with low-resolution models, which must account for these effects in the, often implicit, solvent representation. Here, we present a systematic conformational dynamic characterization of ligand-coated gold nanoparticles with different sizes, charges, and functionalizations by means of atomistic molecular dynamics simulations. Based on these, we deconstruct their electrostatic properties and propose a general representation of their average-long-range interactions extendable to different sizes, charges, and ionic strengths. This study clarifies in detail the role of the different features of the NP (charge, size, structure) and of the ionic strength in determining the details of the interparticle interaction and represents the first step toward a general strategy for the parametrization of NP coarse-grained models able to account for varying ionic strengths.

Inorganic nanoparticles as scaffolds for bioorthogonal catalysts

Bioorthogonal transition metal catalysts (TMCs) transform therapeutically inactive molecules (pro-drugs) into active drug compounds. Inorganic nanoscaffolds protect and solubilize catalysts while offering a flexible design space for decoration with targeting elements and stimuli-responsive activity. These "drug factories" can activate pro-drugs in situ, localizing treatment to the disease site and minimizing off-target effects. Inorganic nanoscaffolds provide structurally diverse scaffolds for encapsulating TMCs. This ability to define the catalyst environment can be employed to enhance the stability and selectivity of the TMC, providing access to enzyme-like bioorthogonal processes. The use of inorganic nanomaterials as scaffolds TMCs and the use of these bioorthogonal nanozymes in vitro and in vivo applications will be discussed in this review.

Biodegradable Antibacterial Bioorthogonal Polymeric Nanocatalysts Prepared by Flash Nanoprecipitation

Bioorthogonal activation of pro-dyes and prodrugs using transition-metal catalysts (TMCs) provides a promising strategy for imaging and therapeutic applications. TMCs can be loaded into polymeric nanoparticles through hydrophobic encapsulation to generate polymeric nanocatalysts with enhanced solubility and stability. However, biomedical use of these nanostructures faces challenges due to unwanted tissue accumulation of nonbiodegradable nanomaterials and cytotoxicity of heavy-metal catalysts. We report here the creation of fully biodegradable nanocatalysts based on an engineered FDA-approved polymer and the naturally existing catalyst hemin. Stable nanocatalysts were generated through kinetic stabilization using flash nanoprecipitation. The therapeutic potential of these nanocatalysts was demonstrated through effective treatment of bacterial biofilms through the bioorthogonal activation of a pro-antibiotic.

Spotting Local Environments in Self-Assembled Monolayer-Protected Gold Nanoparticles

Organic-inorganic (O-I) nanomaterials are versatile platforms for an incredible high number of applications, ranging from heterogeneous catalysis to molecular sensing, cell targeting, imaging, and cancer diagnosis and therapy, just to name a few. Much of their potential stems from the unique control of organic environments around inorganic sites within a single O-I nanomaterial, which allows for new properties that were inaccessible using purely organic or inorganic materials. Structural and mechanistic characterization plays a key role in understanding and rationally designing such hybrid nanoconstructs. Here, we introduce a general methodology to identify and classify local (supra)molecular environments in an archetypal class of O-I nanomaterials, i.e., self-assembled monolayer-protected gold nanoparticles (SAM-AuNPs). By using an atomistic machine-learning guided workflow based on the Smooth Overlap of Atomic Positions (SOAP) descriptor, we analyze a collection of chemically different SAM-AuNPs and detect and compare local environments in a way that is agnostic and automated, i.e., with no need of a priori information and minimal user intervention. In addition, the computational results coupled with experimental electron spin resonance measurements prove that is possible to have more than one local environment inside SAMs, being the thickness of the organic shell and solvation primary factors in the determining number and nature of multiple coexisting environments. These indications are extended to complex mixed hydrophilic-hydrophobic SAMs. This work demonstrates that it is possible to spot and compare local molecular environments in SAM-AuNPs exploiting atomistic machine-learning approaches, establishes ground rules to control them, and holds the potential for the rational design of O-I nanomaterials instructed from data.

All-natural gelatin-based bioorthogonal catalysts for efficient eradication of bacterial biofilms

Bioorthogonal catalysis mediated by transition metal catalysts (TMCs) presents a versatile tool for in situ generation of diagnostic and therapeutic agents. The use of 'naked' TMCs in complex media faces numerous obstacles arising from catalyst deactivation and poor water solubility. The integration of TMCs into engineered inorganic scaffolds provides 'nanozymes' with enhanced water solubility and stability, offering potential applications in biomedicine. However, the clinical translation of nanozymes remains challenging due to their side effects including the genotoxicity of heavy metal catalysts and unwanted tissue accumulation of the non-biodegradable nanomaterials used as scaffolds. We report here the creation of an all-natural catalytic "polyzyme", comprised of gelatin-eugenol nanoemulsion engineered to encapsulate catalytically active hemin, a non-toxic iron porphyrin. These polyzymes penetrate biofilms and eradicate mature bacterial biofilms through bioorthogonal activation of a pro-antibiotic, providing a highly biocompatible platform for antimicrobial therapeutics.

Role of Ionic Strength in the Formation of Stable Supramolecular Nanoparticle-Protein Conjugates for Biosensing

Monolayer-protected gold nanoparticles (AuNPs) exhibit distinct physical and chemical properties depending on the nature of the ligand chemistry. A commonly employed NP monolayer comprises hydrophobic molecules linked to a shell of PEG and terminated with functional end group, which can be charged or neutral. Different layers of the ligand shell can also interact in different manners with proteins, expanding the range of possible applications of these inorganic nanoparticles. AuNP-fluorescent Green Fluorescent Protein (GFP) conjugates are gaining increasing attention in sensing applications. Experimentally, their stability is observed to be maintained at low ionic strength conditions, but not at physiologically relevant conditions of higher ionic strength, limiting their applications in the field of biosensors. While a significant amount of fundamental work has been done to quantify electrostatic interactions of colloidal nanoparticle at the nanoscale, a theoretical description of the ion distribution around AuNPs still remains relatively unexplored. We perform extensive atomistic simulations of two oppositely charged monolayer-protected AuNPs interacting with fluorescent supercharged GFPs co-engineered to have complementary charges. These simulations were run at different ionic strengths to disclose the role of the ionic environment on AuNP–GFP binding. The results highlight the capability of both AuNPs to intercalate ions and water molecules within the gold–sulfur inner shell and the different tendency of ligands to bend inward allowing the protein to bind not only with the terminal ligands but also the hydrophobic alkyl chains. Different binding stability is observed in the two investigated cases as a function of the ligand chemistry.

Nanobiotechnology and Immunotherapy: Two Powerful and Cooperative Allies against Cancer

A number of novel cancer therapies have recently emerged that have rapidly moved from the bench to the clinic. Onco-immunotherapies, such as immune checkpoint blockade inhibitors and adoptive cell therapies, have revolutionized the field, since they provide a way to induce strong anti-tumor immune responses, which are able to fight cancer effectively. However, despite showing great efficacy in hematological and some solid tumors, unresponsiveness, development of therapy resistance and the development of serious adverse effects, limit their capacity to impact the vast majority of tumors. Nanoparticle-based delivery systems are versatile vehicles for a wide variety of molecular cargoes and provide an innovative strategy to improve conventional onco-immunotherapies. They can be finely tuned to release their contents in the tumor microenvironment, or to deliver combinations of adjuvants and antigens in the case of nanovaccines. In this review, we summarize the recent advancements in the field of nanobiotechnology, to remodel the tumor microenvironment and to enhance immunotherapies.