High-Affinity Copolymers Inhibit Digestive Enzymes by Surface Recognition

Synthetic Polymer Nanoparticles as an Abiotic Artificial Inhibitor of Tyrosinase

An innovative methodology is presented for synthesizing synthetic polymer nanoparticles (TINPs) as potent tyrosinase inhibitors. This inhibition strategy combines the integration of two distinct functionalities, phenol, and phenylboronic acid, within the TINPs structure. The phenyl group mimics the natural monophenol substrate, forming a strong coordination with the catalytic copper ion, significantly inhibiting tyrosinase activity. Additionally, phenylboronic acid interacts with catechol, another tyrosinase substrate, further reducing enzyme efficiency. The shared benzene ring in phenyl and phenylboronic acid enhances binding to tyrosinase's hydrophobic pocket near its copper active site, contributing to potent inhibition. TINPs exhibit exceptional performance, boasting an impressive IC50 value of 3.5×10-8 m and an inhibition constant of 9.8×10-9 m. Validation of the approach is unequivocally demonstrated through the successful inhibition of tyrosinase activity and melanin production, substantiated in both in vitro and in vivo scenarios. The mechanism of TINP inhibition is elucidated through circular dichroism and Fourier transform infrared spectroscopy. This study introduces a versatile design approach for developing abiotic polymer-based enzyme inhibitors, expanding possibilities in enzyme inhibition research.

Bioactive Synthetic Polymers

Synthetic polymers are omnipresent in society as textiles and packaging materials, in construction and medicine, among many other important applications. Alternatively, natural polymers play a crucial role in sustaining life and allowing organisms to adapt to their environments by performing key biological functions such as molecular recognition and transmission of genetic information. In general, the synthetic and natural polymer worlds are completely separated due to the inability for synthetic polymers to perform specific biological functions; in some cases, synthetic polymers cause uncontrolled and unwanted biological responses. However, owing to the advancement of synthetic polymerization techniques in recent years, new synthetic polymers have emerged that provide specific biological functions such as targeted molecular recognition of peptides, or present antiviral, anticancer, and antimicrobial activities. In this review, the emergence of this generation of bioactive synthetic polymers and their bioapplications are summarized. Finally, the future opportunities in this area are discussed.

A Biomimetic of Endogenous Tissue Inhibitors of Metalloproteinases: Inhibition Mechanism and Contribution of Composition, Polymer Size, and Shape to the Inhibitory Effect

A biomimetic of endogenous tissue inhibitors of metalloproteinases (TIMPs) was engineered by introducing three binding elements to a synthetic tetrapolymer. We evaluated the contribution of composition, size, and shape of the TIMP-mimicking polymers to the inhibition of BaP1, a P-I class snake venom metalloproteinase (SVMP). Inhibition was achieved when the size of the linear polymer (LP) was comparable to or greater than that of the enzyme, indicating the efficacy requires binding to a significant portion of the enzyme surface in the vicinity of the active site. The efficacy of a low cross-linked polymer hydrogel nanoparticle (NP) of substantially greater molecular weight was comparable to that of the LPs despite differences in size and shape, an important finding for in vivo applications. The abiotic TIMP was effective against two classes of SVMPs in whole snake venom. The results can serve as a design principle for biomimetic polymer inhibitors of enzymes.

Design of Functional Nanoparticles for Intractable Disease Therapy

Protein affinity reagents are widely used for basic research, diagnostics, and disease therapy. Antibodies and their fragments are known as the most common protein affinity reagents. They specifically and strongly bind to target molecules and inhibit their functions. Thus, antibody drugs have increased in the recent two decades for disease therapy, such as cancer. These strong protein-protein interactions are composed of a nexus of multiple weak interactions. Synthetic polymers that bind to target molecules have been developed by the imitation of protein-protein interactions. These polymers show nanomolar affinity for the target and neutralize their functions; thus, they are of significant interest as a cost-effective protein affinity reagent. We have been developing synthetic polymer nanoparticles (NPs) that bind to target peptides and proteins by the inclusion of several functional monomers, such as charged and hydrophobic monomers. In this review, the focus is on the design of synthetic polymer NPs that bind to target molecules for disease therapy. We succeeded in neutralization of toxic peptides and signaling proteins both in vitro and in vivo. Additionally, linear polymers were modified on a lipid nanoparticle surface to improve polymer biodistribution. Our recent findings should provide useful information for the development of abiotic protein affinity reagents.

Regulation of Thrombin Activity with Ultrasmall Nanoparticles: Effects of Surface Chemistry

Nanomaterials displaying well-tailored sizes and surface chemistries can provide novel ways with which to modulate the structure and function of enzymes. Recently, we showed that gold nanoparticles (AuNPs) in the ultrasmall size regime could perform as allosteric effectors inducing partial inhibition of thrombin activity. We now find that the nature of the AuNP surface chemistry controls the interactions to the anion-binding exosites 1 and 2 on the surface of thrombin, the allosterically induced changes to the active-site conformation, and, by extension, the enzymatic activity. Ultrasmall AuNPs passivated with p-mercaptobenzoic acid ligands (AuMBA) and a peptide-based (Ac-ECYN) biomimetic coat (AuECYN) were utilized in our investigations. Remarkably, we found that while AuMBA binds to exosites 1 and 2, AuECYN interacts primarily with exosite 2. It was further established that AuMBA behaves as a "mild denaturant" of thrombin leading to catalytic dysfunction over time. Conversely, AuECYN resembles a proper allosteric effector leading to partial and reversible inhibition of the activity. Collectively, our findings reveal how the distinct binding modes of different AuNP types may uniquely influence thrombin structure and catalysis. The present study further contributes to our understanding of how synthetic nanomaterials could be exploited in the allosteric regulation of enzymes.

Bayesian Data Integration Questions Classic Study on Protease Self-Digest Kinetics

We combine Bayesian data integration with kinetic modeling to rigorously identify reaction mechanisms. This approach forces models to be consistent not only with kinetic measurements but with all available information. We revisit a classic study on trypsin self-digest acceleration by colloidal silica. Bayesian data integration reveals that the mechanism suggested in that study is inconsistent with its presented data. We propose an improved hypothesis. However, the detailed mechanism of the surface reaction cannot be inferred from the available data.

Abiotic Mimic of Endogenous Tissue Inhibitors of Metalloproteinases: Engineering Synthetic Polymer Nanoparticles for Use as a Broad-Spectrum Metalloproteinase Inhibitor

We describe a process for engineering a synthetic polymer nanoparticle (NP) that functions as an effective, broad-spectrum metalloproteinase inhibitor. Inhibition is achieved by incorporating three functional elements in the NP: a group that interacts with the catalytic zinc ion, functionality that enhances affinity to the substrate-binding pocket, and fine-tuning of the chemical composition of the polymer to strengthen NP affinity for the enzyme surface. The approach is validated by synthesis of a NP that sequesters and inhibits the proteolytic activity of snake venom metalloproteinases from five clinically relevant species of snakes. The mechanism of action of the NP mimics that of endogenous tissue inhibitors of metalloproteinases. The strategy provides a general design principle for synthesizing abiotic polymer inhibitors of enzymes.

Accelerated trypsin autolysis by affinity polymer templates

Affinity copolymers specifically recognize the trypsin surface and act as templates for multiple protease molecules, leading to drastically accelerated autolysis – an unusual way for highly efficient enzyme inhibition at physiological conditions.

Affinity purification of multifunctional oligomeric ligands synthesizedviacontrolled radical polymerization

Abiotic oligomeric ligands with a strong affinity for a target peptide sequence were isolated by affinity purification from a pool of 30-mer acrylic random ter-oligomers that were synthesizedviaa controlled radical polymerization process.

Phenylboronic Acid-polymers for Biomedical Applications

Background:

Phenylboronic acid-polymers (PBA-polymers) have attracted tremendous attention as potential stimuli-responsive materials with applications in drug-delivery depots, scaffolds for tissue engineering, HIV barriers, and biomolecule-detecting/sensing platforms. The unique aspect of PBA-polymers is their interactions with diols, which result in reversible, covalent bond formation. This very nature of reversible bonding between boronic acids and diols has been fundamental to their applications in the biomedical area.

Methods:

We have searched peer-reviewed articles including reviews from Scopus, PubMed, and Google Scholar with a focus on the 1) chemistry of PBA, 2) synthesis of PBA-polymers, and 3) their biomedical applications.

Results:

We have summarized approximately 179 papers in this review. Most of the applications described in this review are focused on the unique ability of PBA molecules to interact with diol molecules and the dynamic nature of the resulting boronate esters. The strong sensitivity of boronate ester groups towards the surrounding pH also makes these molecules stimuli-responsive. In addition, we also discuss how the re-arrangement of the dynamic boronate ester bonds renders PBA-based materials with other unique features such as self-healing and shear thinning.

Conclusion:

The presence of PBA in the polymer chain can render it with diverse functions/ relativities without changing their intrinsic properties. In this review, we discuss the development of PBA polymers with diverse functions and their biomedical applications with a specific focus on the dynamic nature of boronate ester groups.

Design of Synthetic Polymer Nanoparticles Specifically Capturing Indole, a Small Toxic Molecule

Synthetic polymers are of interest as stable and cost-effective biomolecule-affinity reagents, since these polymers interact with target biomolecules both in vitro and in the bloodstream. However, little has been reported about orally administered polymers capable of capturing a target molecule and inhibiting its intestinal absorption. Here, we describe the design of synthetic polymer nanoparticles (NPs) specifically capturing indole, a major factor exacerbating chronic kidney disease, in the intestine. N-isopropylacrylamide-based NPs were prepared with various hydrophobic monomers. The amounts of indole captured by NPs depended on the structures and feed ratios of the hydrophobic monomers and the polymer density but not on the particle size. The combination of hydrophobic and quadrupole interaction was effective to enhance the affinity and specificity of NPs for indole. The optimized NPs specifically inhibited intestinal absorption of orally administered indole in mice. These results showed the potential of synthetic polymer NPs for inhibiting the intestinal absorption of a target molecule.

Locating Large, Flexible Ligands on Proteins

Many biologically important ligands of proteins are large, flexible, and in many cases charged molecules that bind to extended regions on the protein surface. It is infeasible or expensive to locate such ligands on proteins with standard methods such as docking or molecular dynamics (MD) simulation. The alternative approach proposed here is scanning of a spatial and angular grid around the protein with smaller fragments of the large ligand. Energy values for complete grids can be computed efficiently with a well-known fast Fourier transform-accelerated algorithm and a physically meaningful interaction model. We show that the approach can readily incorporate flexibility of the protein and ligand. The energy grids (EGs) resulting from the ligand fragment scans can be transformed into probability distributions and then directly compared to probability distributions estimated from MD simulations and experimental structural data. We test the approach on a diverse set of complexes between proteins and large, flexible ligands, including a complex of sonic hedgehog protein and heparin, three heparin sulfate substrates or nonsubstrates of an epimerase, a multibranched supramolecular ligand that stabilizes a protein-peptide complex, a flexible zwitterionic ligand that binds to a surface basin of a Kringle domain, and binding of ATP to a flexible site of an ion channel. In all cases, the EG approach gives results that are in good agreement with experimental data or MD simulations.

Effect of Terminal-Group Functionality on the Ability of Dendrimers to Bind Proteins

It is known that dendrimers can bind proteins with good selectively. This selectivity comes about from an optimization based on matching the size of the dendrimer with the size of the protein's interfacial binding area. In this paper, we report how this selectivity can be moderated by the functionality on the surface of the dendrimer. Specifically, we describe the synthesis of amino acid functionalized dendrimers and the effect of functionality on the dendrimer's ability to bind and inhibit the enzymatic protein, chymotrypsin. The results show how dendrimer binding can be increased or decreased depending on the terminal functionality. These results will allow new ligands to be designed and synthesized, possessing increased and selective protein-binding abilities.