R5 Peptides Constitute Condensed Phases with Liquid-Like Properties in Biomimetic Silica Capsules

Biomimetic silica-peptide nanocomposites are promising materials for applications in drug delivery and enzyme encapsulation due to their biocompatibility, tunable morphologies, and unique structural characteristics. However, the structural dynamics of the peptide scaffold remain largely elusive, impeding rational biomimetic materials design. This shortcoming is not the least due to a lack of methods that can access such heterogeneous systems with dynamics on a wide range of time scales. Among the most studied candidates are silica particles templated by the diatom-derived peptide R5, known for its ability to guide silica precipitation under mild, toxicologically friendly conditions, leading to silica capsules filled with a peptide scaffold. Here, we describe the structural dynamics of R5 within its self-assemblies and the silica particles it templates with a combination of advanced magnetic resonance methods, including 13C-direct detected NMR, site-directive spin-labeling EPR, and sensitivity-enhanced solid-state NMR. We provide evidence that R5 self-assemblies form condensed phases with liquid-like dynamics both before and after silica encapsulation. Our suite of methods allowed us to access R5/silica composites over a comprehensive range of time scales. These results demonstrate that R5 retains a remarkable degree of internal dynamics, with distinct regions of solid-like and liquid-like behavior even within the silica particles. Specifically, the peptide scaffold comprises three dynamic species: (i) solid-like at the peptide-silica interface, (ii) liquid-like mobility within the scaffold core, and (iii) intermediate dynamics at the boundary regions between core and interface species. Our findings rationalize the high mobility of guest molecules, such as drugs or enzyme substrates, within R5-silica nanoparticles, which is crucial for their functionality in controlled release and catalytic applications. This understanding paves the way for improved rational design considerations for advanced nanomaterials and expands our knowledge of biomimetic mineralization mechanisms. At the same time, the methodological approach can be useful for many types of peptide-guided biominerals, bridging fundamental biochemistry with biotechnological innovation.

Silica-binding peptides: physical chemistry and emerging biomaterials applications

Silica-binding peptides (SBPs) are increasingly recognized as versatile tools for various applications spanning biosensing, biocatalysis, and environmental remediation. This review explores the interaction between these peptides and silica surfaces, offering insights into how variables such as surface silanol density, peptide sequence and composition, and solution conditions influence binding affinity. Key advancements in SBP applications are discussed, including their roles in protein purification, biocatalysis, biosensing, and biomedical engineering. By examining the underlying binding mechanisms and exploring their practical potential, this work provides a comprehensive understanding of how SBPs can drive innovations in materials science and biotechnology.

Morphology-Dependent Interaction of Silica Nanoparticles with Intestinal Cells: Connecting Shape to Barrier Function

The intestinal compartment ensures nutrient absorption and barrier function against pathogens. Despite decades of research on the complexity of the gut, the adaptive potential to physical cues, such as those derived from interaction with particles of different shapes, remains less understood. Taking advantage of the technological versatility of silica nanoparticles, spherical, rod-shaped, and virus-like materials were synthesized. Morphology-dependent interactions were studied on differentiated Caco-2/HT29-MTX-E12 cells. Contributions of shape, aspect ratio, surface roughness, and size were evaluated considering the influence of the mucus layer and intracellular uptake pathways. Small particle size and surface roughness favored the highest penetration through the mucus but limited interaction with the cell monolayer and efficient internalization. Particles of a larger aspect ratio (rod-shaped) seemed to privilege paracellular permeation and increased cell-cell distances, albeit without hampering barrier integrity. Inhibition of clathrin-mediated endocytosis and chemical modulation of cell junctions effectively tuned these responses, confirming morphology-specific interactions elicited by bioinspired silica nanomaterials.

Understanding Self-Assembly of Silica-Precipitating Peptides to Control Silica Particle Morphology

The most advanced materials are those found in nature. These evolutionary optimized substances provide highest efficiencies, e.g., in harvesting solar energy or providing extreme stability, and are intrinsically biocompatible. However, the mimicry of biological materials is limited to a few successful applications since there is still a lack of the tools to recreate natural materials. Herein, such means are provided based on a peptide library derived from the silaffin protein R5 that enables rational biomimetic materials design. It is now evident that biomaterials do not form via mechanisms observed in vitro. Instead, the material's function and morphology are predetermined by precursors that self-assemble in solution, often from a combination of protein and salts. These assemblies act as templates for biomaterials. The RRIL peptides used here are a small part of the silica-precipitation machinery in diatoms. By connecting RRIL motifs via varying central bi- or trifunctional residues, a library of stereoisomers is generated, which allows characterization of different template structures in the presence of phosphate ions by combining residue-resolved real-time NMR spectroscopy and molecular dynamics (MD) simulations. Understanding these templates in atomistic detail, the morphology of silica particles is controlled via manipulation of the template precursors.

Biomedical applications of solid-binding peptides and proteins

Over the past decades, solid-binding peptides (SBPs) have found multiple applications in materials science. In non-covalent surface modification strategies, solid-binding peptides are a simple and versatile tool for the immobilization of biomolecules on a vast variety of solid surfaces. Especially in physiological environments, SBPs can increase the biocompatibility of hybrid materials and offer tunable properties for the display of biomolecules with minimal impact on their functionality. All these features make SBPs attractive for the manufacturing of bioinspired materials in diagnostic and therapeutic applications. In particular, biomedical applications such as drug delivery, biosensing, and regenerative therapies have benefited from the introduction of SBPs. Here, we review recent literature on the use of solid-binding peptides and solid-binding proteins in biomedical applications. We focus on applications where modulating the interactions between solid materials and biomolecules is crucial. In this review, we describe solid-binding peptides and proteins, providing background on sequence design and binding mechanism. We then discuss their application on materials relevant for biomedicine (calcium phosphates, silicates, ice crystals, metals, plastics, and graphene). Although the limited characterization of SBPs still represents a challenge for their design and widespread application, our review shows that SBP-mediated bioconjugation can be easily introduced into complex designs and on nanomaterials with very different surface chemistries.

A Biomimetic, Silaffin R5-Based Antigen Delivery Platform

Nature offers a wide range of evolutionary optimized materials that combine unique properties with intrinsic biocompatibility and that can be exploited as biomimetic materials. The R5 and RRIL peptides employed here are derived from silaffin proteins that play a crucial role in the biomineralization of marine diatom silica shells and are also able to form silica materials in vitro. Here, we demonstrate the application of biomimetic silica particles as a vaccine delivery and adjuvant platform by linking the precipitating peptides R5 and the RRIL motif to a variety of peptide antigens. The resulting antigen-loaded silica particles combine the advantages of biomaterial-based vaccines with the proven intracellular uptake of silica particles. These particles induce NETosis in human neutrophils as well as IL-6 and TNF-α secretion in murine bone marrow-derived dendritic cells.

Delivery of Natural Agents by Means of Mesoporous Silica Nanospheres as a Promising Anticancer Strategy

Natural prodrugs derived from different natural origins (e.g., medicinal plants, microbes, animals) have a long history in traditional medicine. They exhibit a broad range of pharmacological activities, including anticancer effects in vitro and in vivo. They have potential as safe, cost-effective treatments with few side effects, but are lacking in solubility, bioavailability, specific targeting and have short half-lives. These are barriers to clinical application. Nanomedicine has the potential to offer solutions to circumvent these limitations and allow the use of natural pro-drugs in cancer therapy. Mesoporous silica nanoparticles (MSNs) of various morphology have attracted considerable attention in the search for targeted drug delivery systems. MSNs are characterized by chemical stability, easy synthesis and functionalization, large surface area, tunable pore sizes and volumes, good biocompatibility, controlled drug release under different conditions, and high drug-loading capacity, enabling multifunctional purposes. In vivo pre-clinical evaluations, a significant majority of results indicate the safety profile of MSNs if they are synthesized in an optimized way. Here, we present an overview of synthesis methods, possible surface functionalization, cellular uptake, biodistribution, toxicity, loading strategies, delivery designs with controlled release, and cancer targeting and discuss the future of anticancer nanotechnology-based natural prodrug delivery systems.

Biomimetic and bioinspired silicifications: Recent advances for biomaterial design and applications

The rational design and controllable synthesis of functional silica-based materials have gained increased interest in a variety of biomedical and biotechnological applications due to their unique properties. The current review shows that marine organisms, such as siliceous sponges and diatoms, could be the inspiration for the fabrication of advanced biohybrid materials. Several biomolecules were involved in the molecular mechanism of biosilicification in vivo. Mimicking their behavior, functional silica-based biomaterials have been generated via biomimetic and bioinspired silicification in vitro. Additionally, several advanced technologies were developed for in vitro and in vivo immobilization of biomolecules with potential applications in biocatalysis, biosensors, bioimaging, and immunoassays. A thin silica layer could coat a single living cell or virus as a protective shell offering new opportunities in biotechnology and nanomedicine fields. Promising nanotechnologies have been developed for drug encapsulation and delivery in a targeted and controlled manner, in particular for poorly soluble hydrophobic drugs. Moreover, biomimetic silica, as a morphogenetically active biocompatible material, has been utilized in the field of bone regeneration and in the development of biomedical implantable devices. STATEMENT OF SIGNIFICANCE: In nature, silica-based biomaterials, such as diatom frustules and sponge spicules, with high mechanical and physical properties were created under biocompatible conditions. The fundamental knowledge underlying the molecular mechanisms of biosilica formation could inspire engineers and chemists to design novel hybrid biomaterials using molecular biomimetic strategies. The production of such biohybrid materials brings the biosilicification field closer to practical applications. This review starts with the biosilicification process of sponges and diatoms with recently updated researches. Then, this article covers recent advances in the design of silica-based biomaterials and their potential applications in the fields of biotechnology and nanomedicine, highlighting several promising technologies for encapsulation of functional proteins and living cells, drug delivery and the preparation of scaffolds for bone regeneration.

Incorporating Thiourea into Fluorescent Probes: A Reliable Strategy for Mitochondrion-Targeted Imaging and Superoxide Anion Tracking in Living Cells

Three aggregation-induced emission active fluorescent compounds, TPA-Pyr-Octane, TPA-Pyr-Br, and TPA-Pyr-Thiourea (TPA = triphenylamine pyridinium), are synthesized; their tiny differences in chemical structures result in a huge difference in cell-imaging applications. Especially, incorporating thiourea into fluorescent probes is found as a reliable strategy for mitochondrion-targeted imaging and superoxide anion tracking in living cells, which is possibly due to the presence of hydrogen bonding between thiourea and mitochondrion proteins. This finding is very useful for the design of biosensors and delivery carriers in disease treatment.