Mixed Fluorinated/Hydrogenated Self-Assembled Monolayer-Protected Gold Nanoparticles: In Silico and In Vitro Behavior

Chemical Information Processing by a Responsive Chemical System

Nature has an extraordinary capacity to precisely regulate the chemical reactivity in a highly complex mixture of molecules that is present in the cell. External stimuli lead to transient up- and downregulation of chemical reactions and provide a means for a cell to process information arriving from the environment. The development of synthetic chemical systems with life-like properties requires strategies that allow likewise control over chemical reactivity in a complex environment. Here, we show a synthetic system that mimics the initial steps that take place when a natural signal transduction pathway is activated. Monophosphate nucleosides act as chemical triggers for the self-assembly of nanoreactors that upregulate chemical reactions between reagents present at low micromolar concentrations. Different nucleotides template different assemblies and hence activate different pathways, thus establishing a distinct connection between input and output molecules. Trigger-induced upregulation of chemical reactivity occurs for only a limited amount of time because the chemical triggers are gradually removed from the system by enzymes. It is shown that the same system transiently produces different output molecules depending on the chemical input that is provided.

Molecular Modeling of the Fluorination Effect on the Penetration of Nanoparticles across Lipid Bilayers

The fluorinated decorations have recently been widely used in many biomedical applications. However, the potential mechanism of the fluorination effect on the cellular delivery of nanoparticles (NPs) still remains elusive. In this work, we systemically explore the penetration of a perfluoro-octanethiol-coated gold NP (PF-Au NP) and, for comparison, an octanethiol-coated gold NP (OT-Au NP) across lipid bilayers. We also investigated the effect of these two types of NPs on the properties of lipid bilayers. Our findings indicate that the lipid type and the surface tension of the lipid bilayer significantly impact the penetration capabilities of the fluorinated gold NP. By examining the distribution of ligands on the surface of the two types of NPs in water and during the penetration process, we unveil their distinct penetration characteristics. Specifically, the PF-Au NP exhibits amphiphobic behavior (both hydrophobic and lipophobic), while the OT-Au NP exhibits solely hydrophobic characteristics. Finally, we observe that the penetration capabilities can be increased by adjusting the degree of fluorination of the ligands on the NP surface. Overall, this study provides useful physical insights into the unique properties of the fluorinated decorations in NP permeation.

Relating Molecular Dynamics Simulations to Functional Activity for Gly-Rich Membranolytic Helical Kiadin Peptides

Kiadins are in silico designed peptides with a strong similarity to diPGLa-H, a tandem sequence of PGLa-H (KIAKVALKAL) and with single, double or quadruple glycine substitutions. They were found to show high variability in their activity and selectivity against Gram-negative and Gram-positive bacteria, as well as cytotoxicity against host cells, which are influenced by the number and placing of glycine residues along the sequence. The conformational flexibility introduced by these substitutions contributes differently peptide structuring and to their interactions with the model membranes, as observed by molecular dynamics simulations. We relate these results to experimentally determined data on the structure of kiadins and their interactions with liposomes having a phospholipid membrane composition similar to simulation membrane models, as well as to their antibacterial and cytotoxic activities, and also discuss the challenges in interpreting these multiscale experiments and understanding why the presence of glycine residues in the sequence affected the antibacterial potency and toxicity towards host cells in a different manner.

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.

Thiolate end-group regulates ligand arrangement, hydration and affinity for small compounds in monolayer-protected gold nanoparticles

The ability to control the properties of monolayer protected gold nanoparticles (MPNPs) discloses unrevealed features stemming from collective properties of the ligands forming the monolayer and presents opportunities to design new materials. To date, the influence of ligand end-group size and capacity to form hydrogen bonds on structure and hydration of small MPNPs (<5 nm) has been poorly studied. Here, we show that both features determine ligands order, solvent accessibility, capacity to host hydrophobic compounds and interfacial properties of MPNPs. The polarity perceived by a radical probe and its binding constant with the monolayer investigated by electron spin resonance is rationalized by molecular dynamics simulations, which suggest that larger space-filling groups - trimethylammonium, zwitterionic and short polyethylene glycol - favor a radial organization of the thiolates, whereas smaller groups - as sulfonate - promote the formation of bundles. Zwitterionic ligands create a surface network of hydrogen bonds, which affects nanoparticle hydrophobicity and maximize the partition equilibrium constant of the probe. This study discloses the role of the chemistry of the end-group on monolayer features with effects that span from molecular- to nano-scale and opens the door to a shift in the conception of new MPNPs exploiting the end-group as a novel design motif.

Molecular Recognition by Gold Nanoparticle-Based Receptors as Defined through Surface Morphology and Pockets Fingerprint

Ligand shell-protected gold nanoparticles can form nanoreceptors that recognize and bind to specific molecules in solution, with numerous potential innovative applications in science and industry. At this stage, the challenge is to rationally design such nanoreceptors to optimize their performance and boost their further development. Toward this aim, we have developed a new computational tool, Nanotron. This allows the analysis of molecular dynamics simulations of ligand shell-protected nanoparticles to define their exact surface morphology and pocket fingerprints of binding cavities in the coating monolayer. Importantly, from dissecting the well-characterized pairing formed by the guest salicylate molecule and specific host nanoreceptors, our work reveals that guest binding at such nanoreceptors occurs via preformed deep pockets in the host. Upon the interaction with the guest, such pockets undergo an induced-fit-like structural optimization for best host-guest fitting. Our findings and methodological advancement will accelerate the rational design of new-generation nanoreceptors.

Probing Multiscale Factors Affecting the Reactivity of Nanoparticle-Bound Molecules

The structures and physicochemical properties of surface-stabilizing molecules play a critical role in defining the properties, interactions, and functionality of hybrid nanomaterials such as monolayer-stabilized nanoparticles. Concurrently, the distinct surface-bound interfacial environment imposes very specific conditions on molecular reactivity and behavior in this setting. Our ability to probe hybrid nanoscale systems experimentally remains limited, yet understanding the consequences of surface confinement on molecular reactivity is crucial for enabling predictive nanoparticle synthon approaches for postsynthesis engineering of nanoparticle surface chemistry and construction of devices and materials from nanoparticle components. Here, we have undertaken an integrated experimental and computational study of the reaction kinetics for nanoparticle-bound hydrazones, which provide a prototypical platform for understanding chemical reactivity in a nanoconfined setting. Systematic variation of just one molecular-scale structural parameter-the distance between reactive site and nanoparticle surface-showed that the surface-bound reactivity is influenced by multiscale effects. Nanoparticle-bound reactions were tracked in situ using ¹⁹F NMR spectroscopy, allowing direct comparison to the reactions of analogous substrates in bulk solution. The surface-confined reactions proceed more slowly than their solution-phase counterparts, and kinetic inhibition becomes more significant for reactive sites positioned closer to the nanoparticle surface. Molecular dynamics simulations allowed us to identify distinct supramolecular architectures and unexpected dynamic features of the surface-bound molecules that underpin the experimentally observed trends in reactivity. This study allows us to draw general conclusions regarding interlinked structural and dynamical features across several length scales that influence interfacial reactivity in monolayer-confined environments.

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

Nanoparticles (NPs) provide multipurpose platforms for a wide range of biological applications. These applications are enabled through molecular design of surface coverages, modulating NP interactions with biosystems. In this review, we highlight approaches to functionalize nanoparticles with "small" organic ligands (Mw < 1000), providing insight into how organic synthesis can be used to engineer NPs for nanobiology and nanomedicine.

Mixed-monolayer functionalized gold nanoparticles for cancer treatment: Atomistic molecular dynamics simulations study

Gold nanoparticles (AuNPs) are employed as drug carriers due to their inertness, non-toxicity, and ease of synthesis. An experimental search for the optimal AuNP design would require a systematic variation of physico-chemical properties which is time-consuming and expensive. Computational methods provide quicker and cheaper approach to complement experiments and provide useful guidelines. In this paper, we performed atomistic molecular dynamics simulations to study how the size, hydrophobicity, and concentration of the drug affect the structure of functionalized AuNPs in the aqueous environment. We simulated two groups of nano-systems functionalized with a zwitterionic background ligand, and a ligand carrying a drug (Quinolinol or Panobinostat). Results indicate that in the case of a hydrophobic drug (Quinolinol), the hydrophobicity drives the conformation changes of the coating layer. The tendency of the hydrophobic drug to reduce its solvent-accessible surface results in a decrease of the coating thickness and the overall NP size. Although the amount of accessible drug can be increased by increasing its initial concentration, it will compromise the solubility of the system. In the case of a hydrophilic drug (Panobinostat), the ligand in excess has a dominant influence on the final structure of the coating conformations. The percentage of accessible drug is significantly higher than in the hydrophobic systems for any given ratio. It implies that for hydrophilic systems we can generally expect higher biological efficiency. Our results highlight the importance of taking into account physico-chemical properties of drugs and ligands when developing gold-based nanosystems, especially in the case of hydrophobic drugs.

An ICP-MS-based assay for characterization of gold nanoparticles with potential biomedical use

Most of potential diagnostic and therapeutic nanoparticles fail to reach clinical trials because assessment of their 'drug-like' properties is often overlooked during the discovery stage. This compromises the results of cell culture and animal experiments, making them insufficient to evaluate the lead candidates for testing on patients. In this study, we demonstrate the potential of high-resolution inductively coupled plasma mass spectrometry (ICP-MS) as a nanoparticle qualification tool. Using novel gold nanoparticles stabilized by N-heterocyclic carbenes as test nanoparticles, it was shown that important prerequisites for biomedical applications, such as resistance to the action of human serum milieu or reactivity toward serum biomolecules, can be reliably assessed by recording the signals of gold or sulfur isotopes. Implemented during the screening stage, the method would provide benefits in shortening timelines and reducing cost for selection and initial testing of medicinal nanoparticle candidates.

Knowledge gaps in immune response and immunotherapy involving nanomaterials: Databases and artificial intelligence for material design

Exploring the interactions between the immune system and nanomaterials (NMs) is critical for designing effective and safe NMs, but large knowledge gaps remain to be filled prior to clinical applications (e.g., immunotherapy). The lack of databases on interactions between the immune system and NMs affects the discovery of new NMs for immunotherapy. Complement activation and inhibition by NMs have been widely studied, but the general rules remain unclear. Biomimetic nanocoating to promote the clearance of NMs by the immune system is an alternative strategy for the immune response mediation of the biological corona. Immune response predictions based on NM properties can facilitate the design of NMs for immunotherapy, and artificial intelligences deserve much attention in the field. This review addresses the knowledge gaps regarding immune response and immunotherapy in relation to NMs, effective immunotherapy and material design without adverse immune responses.

One Peptide for Them All: Gold Nanoparticles of Different Sizes Are Stabilized by a Common Peptide Amphiphile

The functionalization of gold nanoparticles (GNPs) with peptidic moieties can prevent their aggregation and facilitate their use for applications both in vitro and in vivo. To date, no peptide-based coating has been shown to stabilize GNPs larger than 30 nm in diameter; such particles are of interest for applications including vaccine development, drug delivery, and sensing. Here, GNPs with diameters of 20, 40, and 100 nm are functionalized with peptide amphiphiles. Using a combination of transmission electron microscopy, UV-vis spectroscopy, and dynamic light scattering, we show that GNPs up to 100 nm in size can be stabilized by these molecules. Moreover, we demonstrate that these peptide amphiphiles form curvature-dependent, ordered structures on the surface of the GNPs and that the GNPs remain disperse at high-salt concentrations and in the presence of competing thiol-containing molecules. These results represent the development of a peptide amphiphile-based coating system for GNPs which has the potential to be beneficial for a wide range of biological applications, in addition to image enhancement and catalysis.

Functionalized Gold Nanoparticles as Contrast Agents for Proton and Dual Proton/Fluorine MRI

Gold nanoparticles carrying fluorinated ligands in their monolayer are, by themselves, contrast agents for 19F magnetic resonance imaging displaying high sensitivity because of the high density of fluorine nuclei achievable by grafting suitable ligands on the gold core surface. Functionalization of these nanoparticles with Gd(III) chelates allows adding a further functional activity to these systems, developing materials also acting as contrast agents for proton magnetic resonance imaging. These dual mode contrast agents may allow capitalizing on the benefits of 1H and 19F magnetic resonance imaging in a single diagnostic session. In this work, we describe a proof of principle of this approach by studying these nanoparticles in a high field preclinical scanner. The Gd(III) centers within the nanoparticles monolayer shorten considerably the 19F T1 of the ligands but, nevertheless, these systems display strong and sharp NMR signals which allow recording good quality 19F MRI phantom images at nanoparticle concentration of 20 mg/mL after proper adjustment of the imaging sequence. The Gd(III) centers also influence the T1 relaxation time of the water protons and high quality 1H MRI images could be obtained. Gold nanoparticles protected by hydrogenated ligands and decorated with Gd(III) chelates are reported for comparison as 1H MRI contrast agents.