Cell Adhesion on RGD-Displaying Knottins with Varying Numbers of Tryptophan Amino Acids to Tune the Affinity for Assembly on Cucurbit[8]uril Surfaces

Influence of Surface Chemistry on Host/Guest Interactions: A Model Study on Redox-Sensitive β-Cyclodextrin/Ferrocene Complexes

While host/guest interactions are widely used to control molecular assembly on surfaces, quantitative information on the effect of surface chemistry on their efficiency is lacking. To address this question, we combined electrochemical characterization with quartz crystal microbalance with dissipation monitoring to study host/guest interactions between surface-attached ferrocene (Fc) guests and soluble β-cyclodextrin (β-CD) hosts. We identified several parameters that influence the redox response, β-CD complexation ability, and repellent properties of Fc monolayers, including the method of Fc grafting, the linker connecting Fc with the surface, and the diluting molecule used to tune Fc surface density. The study on monovalent β-CD/Fc complexation was completed by the characterization of multivalent interactions between Fc monolayers and β-CD-functionalized polymers, with new insights being obtained on the interplay between the surface chemistry, binding efficiency, and reversibility under electrochemical stimulus. These results should facilitate the design of well-defined functional interfaces and their implementation in stimuli-responsive materials and sensing devices.

Development of Mesoporous Silica Nanoparticle-Based Films with Tunable Arginine-Glycine-Aspartate Peptide Global Density and Clustering Levels to Study Stem Cell Adhesion and Differentiation

Stem cell adhesion is mediated via the binding of integrin receptors to adhesion motifs present in the extracellular matrix (ECM). The spatial organization of adhesion ligands plays an important role in stem cell integrin-mediated adhesion. In this study, we developed a series of biointerfaces using arginine-glycine-aspartate (RGD)-functionalized mesoporous silica nanoparticles (MSN-RGD) to study the effect of RGD adhesion ligand global density (ligand coverage over the surface), spacing, and RGD clustering levels on stem cell adhesion and differentiation. To prepare the biointerface, MSNs were chemically functionalized with RGD peptides via an antifouling poly(ethylene glycol) (PEG) linker. The RGD surface functionalization ratio could be controlled to create MSNs with high and low RGD ligand clustering levels. MSN films with varying RGD global densities could be created by blending different ratios of MSN-RGD and non-RGD-functionalized MSNs together. A computational simulation study was performed to analyze nanoparticle distribution and RGD spacing on the resulting surfaces to determine experimental conditions. Enhanced cell adhesion and spreading were observed when RGD global density increased from 1.06 to 5.32 nmol cm-2 using highly clustered RGD-MSN-based films. Higher RGD ligand clustering levels led to larger cell spreading and increased formation of focal adhesions. Moreover, a higher RGD ligand clustering level promoted the expression of alkaline phosphatase in hMSCs. Overall, these findings indicate that both RGD global density and clustering levels are crucial variables in regulating stem cell behaviors. This study provides important information about ligand-integrin interactions, which could be implemented into biomaterial design to achieve optimal performance of adhesive functional peptides.

DNA modified MSN-films as versatile biointerfaces to study stem cell adhesion processes

A significant bottleneck in the clinical translation of stem cells remains eliciting the desired stem cell behavior once transplanted in the body. In their natural environment, stem cell fate is regulated by their interaction with extracellular matrix (ECM), mainly through integrin-mediated cell adhesion. 2D biointerfaces that selectively present ECM-derived ligands can be used as valuable tools to study and improve our understanding on how stem cells interact with their environment. Here we developed a new type of biointerface based on mesoporous silica nanoparticles (MSN) which are interesting nanomaterials for biointerface engineering because they allow close control over surface physiochemical properties. To create the platform, DNA functionalized MSN (MSN-ssDNA) with varying PEG linker length were developed. Cell adhesion tripeptide RGD was conjugated to a complementary DNA strand, which could specifically bind to MSN-ssDNA to create MSN-dsDNA-RGD films. We showed that MSN-dsDNA-RGD films could promote hMSCs adhesion and spreading, whereas MSN-dsDNA films without RGD resulted in poor cell spreading with round morphology, and low cell adhesion. In addition, we showed that cell adhesion to the films is PEG length-dependent. The design of the platform allows easy incorporation of other and multiple ECM ligands, as well as soluble cues, making MSN-ssDNA based biointerfaces a novel tool to study ligand-stem cell interactions.

Biomolecular Electron Controller Composed of Nanobiohybrid with Electrically Released Complex for Spatiotemporal Control of Neuronal Differentiation

In vitro spatiotemporal control of cell differentiation is a critical issue in several biomedical fields such as stem cell therapy and regenerative medicine, as it enables the generation of heterogeneous tissue structures similar to those of their native counterparts. However, the simultaneous control of both spatial and temporal cell differentiation poses important challenges, and therefore no previous studies have achieved this goal. Here, the authors develop a cell differentiation biomolecular electron controller ("Biomoletron") composed of recombinant proteins, DNA, Au nanoparticles, peptides, and an electrically released complex with retinoic acid (RA) to spatiotemporally control SH-SY5Y cell differentiation. RA is only released from the Biomoletron when the complex is electrically stimulated, thus demonstrating the temporal control of SH-SY5Y cell differentiation. Furthermore, by introducing a patterned Au substrate that allows controlling the area where the Biomoletron is immobilized, spatiotemporal differentiation of the SH-SY5Y cell is successfully achieved. Therefore, the proposed Biomoletron-mediated differentiation method provides a promising strategy for spatiotemporal cell differentiation control with applications in regenerative medicine and cell therapy.

2D biointerfaces to study stem cell-ligand interactions

Stem cells have great potential in the field of tissue engineering and regenerative medicine due to their inherent regenerative capabilities. However, an ongoing challenge within their clinical translation is to elicit or predict the desired stem cell behavior once transplanted. Stem cell behavior and function are regulated by their interaction with biophysical and biochemical signals present in their natural environment (i.e., stem cell niches). To increase our understanding about the interplay between stem cells and their resident microenvironments, biointerfaces have been developed as tools to study how these substrates can affect stem cell behaviors. This article aims to review recent developments on fabricating cell-instructive interfaces to control cell adhesion processes towards directing stem cell behavior. After an introduction on stem cells and their natural environment, static surfaces exhibiting predefined biochemical signals to probe the effect of chemical features on stem cell behaviors are discussed. In the third section, we discuss more complex dynamic platforms able to display biochemical cues with spatiotemporal control using on-off ligand display, reversible ligand display, and ligand mobility. In the last part of the review, we provide the reader with an outlook on future designs of biointerfaces. STATEMENT OF SIGNIFICANCE: Stem cells have great potential as treatments for many degenerative disorders prevalent in our aging societies. However, an ongoing challenge within their clinical translation is to promote stem cell mediated regeneration once they are transplanted in the body. Stem cells reside within our bodies where their behavior and function are regulated by interactions with their natural environment called the stem cell niche. To increase our understanding about the interplay between stem cells and their niche, 2D materials have been developed as tools to study how specific signals can affect stem cell behaviors. This article aims to review recent developments on fabricating cell-instructive interfaces to control cell adhesion processes towards directing stem cell behavior.

Win, Lose, or Tie: Mathematical Modeling of Ligand Competition at the Cell-Extracellular Matrix Interface

Integrin transmembrane proteins conduct mechanotransduction at the cell–extracellular matrix (ECM) interface. This process is central to cellular homeostasis and therefore is particularly important when designing instructive biomaterials and organoid culture systems. Previous studies suggest that fine-tuning the ECM composition and mechanical properties can improve organoid development. Toward the bigger goal of fully functional organoid development, we hypothesize that resolving the dynamics of ECM–integrin interactions will be highly instructive. To this end, we developed a mathematical model that enabled us to simulate three main interactions, namely integrin activation, ligand binding, and integrin clustering. Different from previously published computational models, we account for the binding of more than one type of ligand to the integrin. This competition between ligands defines the fate of the system. We have demonstrated that an increase in the initial concentration of ligands does not ensure an increase in the steady state concentration of ligand-bound integrins. The ligand with higher binding rate occupies more integrins at the steady state than does the competing ligand. With cell type specific, quantitative input on integrin-ligand binding rates, this model can be used to develop instructive cell culture systems.

Phenothiazine-Biaryl-Containing Fluorescent RGD Peptides

Cyclic RGD peptides are well-known ligands of integrins. The integrins αV β3 and α5 β1 are involved in angiogenesis, and integrin αV β3 is abundantly present on cancer cells, thus representing a therapeutic target. Hence, synthetic and biophysical studies continuously are being directed towards the understanding of ligand-integrin interaction. In this context, the development of versatile synthetic strategies to obtain fluorescent building blocks that can add molecular diversity and modular spectral characteristics while not compromising binding affinity or selectivity is a relevant task. An on-resin intramolecular Suzuki-Miyaura cross-coupling (SMC) between l- or d-7-bromotryptophan (7BrTrp) and a phenothiazine (Ptz) boronic acid affords fluorescent cyclic RGD pseudopeptides, c(RGD(W/w)Ptz). Ring closure by SMC establishes a phenothiazine-indole moiety with axial chirality. An array of eight novel compounds has been synthesized, among them one fluorescent compound with good affinity to integrin αV β3 . The fluorescence properties of the analogues can be efficiently tuned depending on the substituents in Ptz moiety even for fluorescence emission in the visible (red) spectral range.

Multivalency in Heteroternary Complexes on Cucurbit[8]uril-Functionalized Surfaces: Self-assembly, Patterning, and Exchange Processes

The spatial confinement of multivalent azopyridine guest molecules mediated by cucurbit[8]urils is described. Fluorescent dye-labelled multivalent azopyridine molecules were attached to preformed methyl viologen/cucurbit[8]uril inclusion complexes in solution and at surfaces. The formation of the resulting heteroternary host-guest complexes was verified in solution and on gold substrates. Surface binding constants of the multivalent ligands were two orders of magnitude higher than that of the monovalent one. Poly-l-lysine grafted with oligo(ethylene glycol) and maleimide moieties was deposited on cyclic olefin polymer surfaces and further modified with thiolated methyl viologen and cucurbit[8]uril. Defined micrometer-sized patterns were created by soft lithographic techniques. Supramolecular exchange experiments were performed on these surface-bound heterocomplexes, which allowed the creation of cross-patterns by taking advantage of the molecular valency, which led to the substitution of the monovalent guest by the multivalent guests but not vice versa.

ExonSkipDB: functional annotation of exon skipping event in human

Exon skipping (ES) is reported to be the most common alternative splicing event due to loss of functional domains/sites or shifting of the open reading frame (ORF), leading to a variety of human diseases and considered therapeutic targets. To date, systematic and intensive annotations of ES events based on the skipped exon units in cancer and normal tissues are not available. Here, we built ExonSkipDB, the ES annotation database available at https://ccsm.uth.edu/ExonSkipDB/, aiming to provide a resource and reference for functional annotation of ES events in multiple cancer and tissues to identify therapeutically targetable genes in individual exon units. We collected 14 272 genes that have 90 616 and 89 845 ES events across 33 cancer types and 31 normal tissues from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx). For the ES events, we performed multiple functional annotations. These include ORF assignment of exon skipped transcript, studies of lost protein functional features due to ES events, and studies of exon skipping events associated with mutations and methylations based on multi-omics evidence. ExonSkipDB will be a unique resource for cancer and drug research communities to identify therapeutically targetable exon skipping events.

Applications of Cucurbiturils in Medicinal Chemistry and Chemical Biology

The supramolecular chemistry of cucurbit[n]urils (CBn) has been rapidly developing to encompass diverse medicinal applications, including drug formulation and delivery, controlled drug release, and sensing for bioanalytical purposes. This is made possible by their unique recognition properties and very low cytotoxicity. In this review, we summarize the host-guest complexation of biologically important molecules with CBn, and highlight their implementation in medicinal chemistry and chemical biology.

Synthetic Host-Guest Assembly in Cells and Tissues: Fast, Stable, and Selective Bioorthogonal Imaging via Molecular Recognition

Bioorthogonal strategies are continuing to pave the way for new analytical tools in biology. Although a significant amount of progress has been made in developing covalent reaction based bioorthogonal strategies, balanced reactivity, and stability are often difficult to achieve from these systems. Alternatively, despite being kinetically beneficial, the development of noncovalent approaches that utilize fully synthetic and stable components remains challenging due to the lack of selectivity in conventional noncovalent interactions in the living cellular environment. Herein, we introduce a bioorthogonal assembly strategy based on a synthetic host-guest system featuring Cucurbit[7]uril (CB[7]) and adamantylamine (ADA). We demonstrate that highly selective and ultrastable host-guest interaction between CB[7] and ADA provides a noncovalent mechanism for assembling labeling agents, such as fluorophores and DNA, in cells and tissues for bioorthogonal imaging of molecular targets. Additionally, by combining with covalent reaction, we show that this CB[7]-ADA based noncovalent interaction enables simultaneous bioorthogonal labeling and multiplexed imaging in cells as well as tissue sections. Finally, we show that interaction between CB[7] and ADA fulfills the demands of specificity and stability that is required for assembling molecules in the complexities of a living cell. We demonstrate this by sensitive detection of metastatic cancer-associated cell surface protein marker as well as by showing the distribution and dynamics of F-actin in living cells.

Protecting Encapsulin Nanoparticles with Cysteine-Knot Miniproteins

A big hurdle for the use of protein-based drugs is that they are easily degraded by proteases in the human body. In an attempt to solve this problem, we show the possibility to functionalize TM encapsulin nanoparticles with an mEETI-II knottin miniprotein from the cysteine-stabilized knot class. The resulting particles did not show aggregation and retained part of their protease inhibitive function. This imposes a protection toward protease, in this case, trypsin, degradation of the protein cage. The used chemistry is easy to apply and thus suitable to protect other protein systems from degradation. In addition, this proof of principle opens up the use of other knottins or cysteine-stabilized knots, which can be attached to protein cages to create a heterofunctionalized protein nanocage. This allows specific targeting and tumor suppression among other types of functionalization. Overall, this is a promising strategy to protect a protein of interest which brings oral administration of protein-based drugs one step closer.

Directional Self-Sorting with Cucurbit[8]uril Controlled by Allosteric π-π and Metal-Metal Interactions

To maximize Coulombic interactions, cucurbit[8]uril (CB[8]) typically forms ternary complexes that distribute the positive charges of the pair of guests (if any) over both carbonylated portals of the macrocycle. We present here the first exception to this recognition pattern. Platinum(II) acetylides flanked by 4'-substituted terpyridyl ligands (tpy) form 2:1 complexes with CB[8] in an exclusively stacked head-to-head orientation in a water/acetonitrile mixture. The host encapsulates the pair of tpy substituents, and both positive Pt centers sit on top of each other at the same CB[8] rim, leaving the other rim free of any interaction with the guests. This dramatic charge imbalance between the CB[8] rims would be electrostatically penalizing, were it not for allosteric π-π interactions between the stacked tpy ligands, and possible metal-metal interactions between both Pt centers. When both tpy and acetylides are substituted with aryl units, the metal-ligand complexes form 2:2 assemblies with CB[8] in aqueous medium, and the directionality of the assembly (head-to-head or head-to-tail) can be controlled, both kinetically and thermodynamically.