Hydrolysis of transferrin promoted by a cerium(IV)-Keggin polyoxometalate

Nanoproteases: Alternatives to Natural Protease for Biotechnological Applications

Some nanomaterials with intrinsic protease-like activity have the advantages of good stability, biosafety, low price, large-scale preparation and unique property of nanomaterials, which are promising alternatives for natural proteases in various applications. An especial term, "nanoprotease", has been coined to stress the intrinsic proteolytic property of these nanomaterials. As a new generation of artificial proteases, they have become a burgeoning field, attracting many researchers to design and synthesize high performance nanoproteases. In this review, we summarize recent progress on all types of nanoproteases with regard of their activity, mechanism and application and introduce a new and effective strategy for engineering high-performance nanoproteases. In addition, we discuss the challenges and opportunities of nanoprotease research in the future.

Selective Hydrolysis of Ovalbumin by Zr-Based Lacunary Polyoxotungstate in Surfactant Solutions

This study aims to design an artificial metalloprotease based on a Zr-containing polyoxometalate Na8[Zr(W5O18)2] [Zr(W5)2] for the hydrolysis of ovalbumin (OVA) in the presence of different surfactants, which can be used in many areas of the biological and medical sciences, particularly for targeted proteolytic drug design. For this reason, parameters, including the free energy of binding, the chemical nature of amino acid residues, secondary structures, and electrostatic potentials, of Zr(W5)2-OVA and Zr(W5)2-OVA-surfactant were analyzed by molecular docking simulations. The investigations showed that the presence of surfactants decreases the binding affinity of Zr(W5)2 for OVA amino acids, and hydrogen bonds and van der Waals interactions are formed between Zr(W5)2 and OVA amino acids. Additionally, GROMACS further illustrated the significance of SDS and CTAB surfactants in influencing the conformational changes of the OVA that lead to selective protein hydrolysis. In agreement with molecular dynamics simulation results, the experimental analysis showed more protein hydrolysis for the Zr(W5)2-OVA-surfactant systems. For instance, circular dichroism spectroscopy indicated that Zr(W5)2-OVA-CTAB and Zr(W5)2-OVA-TX-100 were more hydrolytically efficient due to the increased level of β-structures rather than α-chains, which showed that surfactants can facilitate the accessibility of Zr(W5)2 to the cleavage sites by inducing partial unfolding of the OVA structure.

Reactivity of metal-oxo clusters towards biomolecules: from discrete polyoxometalates to metal-organic frameworks

Metal-oxo clusters hold great potential in several fields such as catalysis, materials science, energy storage, medicine, and biotechnology. These nanoclusters of transition metals with oxygen-based ligands have also shown promising reactivity towards several classes of biomolecules, including proteins, nucleic acids, nucleotides, sugars, and lipids. This reactivity can be leveraged to address some of the most pressing challenges we face today, from fighting various diseases, such as cancer and viral infections, to the development of sustainable and environmentally friendly energy sources. For instance, metal-oxo clusters and related materials have been shown to be effective catalysts for biomass conversion into renewable fuels and platform chemicals. Furthermore, their reactivity towards biomolecules has also attracted interest in the development of inorganic drugs and bioanalytical tools. Additionally, the structural versatility of metal-oxo clusters allows for the efficiency and selectivity of the biomolecular reactions they promote to be readily tuned, thereby providing a pathway towards reaction optimization. The properties of the catalyst can also be improved through incorporation into solid supports or by linking metal-oxo clusters together to form Metal-Organic Frameworks (MOFs), which have been demonstrated to be powerful heterogeneous catalysts. Therefore, this review aims to provide a comprehensive and critical analysis of the state of the art on biomolecular transformations promoted by metal-oxo clusters and their applications, with a particular focus on structure-activity relationships.

Polyoxometalates as Potential Artificial Enzymes toward Biological Applications

Artificial enzymes, as alternatives to natural enzymes, have attracted enormous attention in the fields of catalysis, biosensing, diagnostics, and therapeutics because of their high stability and low cost. Polyoxometalates (POMs), a class of inorganic metal oxides, have recently shown great potential in mimicking enzyme activity due to their well-defined structure, tunable composition, high catalytic efficiency, and easy storage properties. This review focuses on the recent advances in POM-based artificial enzymes. Different types of POMs and their derivatives-based mimetic enzyme functions are covered, as well as the corresponding catalytic mechanisms (where available). An overview of the broad applications of representative POM-based artificial enzymes from biosensing to theragnostic is provided. Insight into the current challenges and the future directions for POMs-based artificial enzymes is discussed.

Regioselective protein oxidative cleavage enabled by enzyme-like recognition of an inorganic metal oxo cluster ligand

Oxidative modifications of proteins are key to many applications in biotechnology. Metal-catalyzed oxidation reactions efficiently oxidize proteins but with low selectivity, and are highly dependent on the protein surface residues to direct the reaction. Herein, we demonstrate that discrete inorganic ligands such as polyoxometalates enable an efficient and selective protein oxidative cleavage. In the presence of ascorbate (1 mM), the Cu-substituted polyoxometalate K₈[Cu²⁺(H₂O)(α₂-P₂W₁₇O₆₁)], (Cu^IIWD, 0.05 mM) selectively cleave hen egg white lysozyme under physiological conditions (pH =7.5, 37 °C) producing only four bands in the gel electropherogram (12.7, 11, 10, and 5 kDa). Liquid chromatography/mass spectrometry analysis reveals a regioselective cleavage in the vicinity of crystallographic Cu^IIWD/lysozyme interaction sites. Mechanistically, polyoxometalate is critical to position the Cu at the protein surface and limit the generation of oxidative species to the proximity of binding sites. Ultimately, this study outlines the potential of discrete, designable metal oxo clusters as catalysts for the selective modification of proteins through radical mechanisms under non-denaturing conditions.

Hydrolysis of Acetamide on Low-Index CeO2 Surfaces: Ceria as a Deamidation and General De-esterification Catalyst

Using DFT calculations and acetamide as the main example, we show that ceria is a potential catalyst for the hydrolysis of amide and similar bonds. The overall reaction is endergonic in the gas phase, yielding acetic acid and ammonia, but is slightly exergonic in the aqueous phase, which facilitates ionization of the products (CH₃COO^– and NH₄⁺). Neighboring Ce and O sites on the CeO₂(111), (110), and (100) facets are conducive to the formation of an activated metastable tetrahedral intermediate (TI) complex, followed by C–N bond scission. With van der Waals and solvation effects taken into account, the overall reaction energetics is found to be most favorable on the (111) facet as desorption of acetic acid is much more uphill energetically on (110) and (100). We further suggest that the Ce–O–Ce sites on ceria surfaces can activate X(=Y)–Z type bonds in amides, amidines, and carboxylate and phosphate esters, among many others that we term “generalized esters”. A Brønsted-Evans–Polanyi relationship is identified correlating the stability of the transition and final states of the X–Z generalized ester bond scission. A simple descriptor (ΣΔχ) based on the electronegativity of the atoms that constitute the bond (X, Y, Z) versus those of the catalytic site (O, Ce, Ce) captures the trend in the stability of the transition state of generalized ester bond scission and suggests a direction for modifying ceria for targeting specific organic substrates.

Expanding the reactivity of inorganic clusters towards proteins: the interplay between the redox and hydrolytic activity of Ce(iv)-substituted polyoxometalates as artificial proteases

The ability of soluble metal-oxo clusters to specifically interact with protein surfaces makes them attractive as potential inorganic drugs and as artificial enzymes. In particular, metal-substituted polyoxometalates (MS-POMs) are remarkably selective in hydrolyzing a range of different proteins. However, the influence of MS-POMs' redox chemistry on their proteolytic activity remains virtually unexplored. Herein we report a highly site-selective hydrolysis of hemoglobin (Hb), a large tetrameric globular protein, by a Ce(iv)-substituted Keggin polyoxometalate (CeIVK), and evaluate the effect of CeIVK's redox chemistry on its reactivity and selectivity as an artificial protease. At pH 5.0, incubation of Hb with CeIVK resulted in strictly selective protein hydrolysis at six Asp-X bonds, two of which were located in the α-chain (α(Asp75-Leu76) and α(Asp94-Pro95)) and five at the β-chain (β(Asp51-Ala52), β(Asp68-Ser69), β(Asp78-Asp79), β(Asp98-Pro99) and β(Asp128-Phe129)). However, increasing the pH of the reaction mixture to 7.4 decreased the CeIVK hydrolytic reactivity towards Hb, resulting in the cleavage of only one peptide bond (β(Asp128-Phe129)). Combination of UV-Vis, circular dichroism and Trp fluorescence spectroscopy indicated similar interactions between Hb and CeIVK at both pH conditions; however, 31P NMR spectroscopy showed faster reduction of CeIVK into the hydrolytically inactive CeIIIK form in the presence of protein at pH 7.4. In agreement with these results, careful mapping of all hydrolyzed Asp-X bonds on the protein structure revealed that the lower reactivity toward the α-chain was consistent with the presence of more redox-active amino acids (Tyr and His) in this subunit in comparison with the β-chain. This points towards a link between the presence of the redox-active sites on the protein surface and efficiency and selectivity of redox-active MS-POMs as artificial proteases. More importantly, the study provides a way to tune the redox and hydrolytic reactivity of MS-POMs towards proteins through adjustment of reaction parameters like temperature and pH.

The Dawn of Metal-Oxo Clusters as Artificial Proteases: From Discovery to the Present and Beyond

The selective cleavage of peptide bonds in proteins is of paramount importance in many areas of the biological and medical sciences, playing a key role in protein structure/function/folding analysis, protein engineering, and targeted proteolytic drug design. Current applications that depend on selective protein hydrolysis largely rely on costly proteases such as trypsin, which are sensitive to the pH, ionic strength, and temperature conditions. Moreover, >95% of peptides deposited in databases are generated from trypsin digests, restricting the information within the analyzed proteomes. On the other hand, harsh and toxic chemical reagents such as BrCN are very active but cause permanent modifications of certain amino acid residues. Consequently, transition-metal complexes have emerged as smooth and selective artificial proteases owing to their ability to provide larger fragments and complementary structural information. In the past decade, our group has discovered the unique protease activity of diverse metal-oxo clusters (MOC) and pioneered a distinctive approach to the development of selective artificial proteases. In contrast to classical coordination complexes which often depend on amino acid side chains to control the regioselectivity, the selectivity profile of MOCs is determined by a complex combination of structural factors, such as the protein surface charge, metal coordination to specific side chains, and hydrogen bonding between the protein surface and the MOC scaffold.In this Account, we present a critical overview of our detailed kinetic, spectroscopic, and crystallographic studies in MOC-assisted peptide bond hydrolysis, from its origins to the current rational and detailed mechanistic understanding. To this end, reactivity trends related to the structure and properties of MOCs based on the hydrolysis of small model peptides and key structural aspects governing the selectivity of protein hydrolysis are presented. Finally, our endeavors in seeking the next generation of heterogeneous MOC-based proteases are briefly discussed by embedding MOCs in metal-organic frameworks or using them as discrete nanoclusters in the development of artificial protease-like materials (i.e., nanozymes). The deep and comprehensive understanding sought experimentally and theoretically over the years in aqueous systems with intrinsic polar and charged substrates provides a unique view of the reactivity between inorganic moieties and biomolecules, thereby broadly impacting several different fields (e.g., catalysis in biochemistry, inorganic chemistry, and organic chemistry).

Hydrolysis of Peptide Bonds in Protein Micelles Promoted by a Zirconium(IV)-Substituted Polyoxometalate as an Artificial Protease

The development of artificial proteases is challenging, but important for many applications in modern proteomics and biotechnology. The hydrolysis of hydrophobic or unstructured proteins is particularly difficult due to their poor solubility, which often requires the presence of surfactants. Herein, it is shown that a zirconium(IV)-substituted Keggin polyoxometalate (POM), (Et₂ NH₂ )₁₀ [Zr(α-PW₁₁ O₃₉ )₂ ] (1), is able to selectively hydrolyze β-casein, which is an intrinsically unstructured protein at pH 7.4 and 60 °C. Four surfactants (sodium dodecyl sulfate (SDS), N-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (ZW3-12), 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS), and polyethylene glycol tert-octylphenyl ether (TX-100)), which differ in the nature of their polar groups, were investigated for their role in influencing the selectivity and efficiency of protein hydrolysis. Under experimental conditions, β-casein forms micellar structures in which the hydrophilic part of the protein is water accessible and able to interact with 1. Identical fragmentation patterns of β-casein in the presence of 1 were observed through SDS poly(acrylamide) gel electrophoresis both in the presence and absence of surfactants, but the rate of hydrolysis varied, depending on the nature of surfactant. Whereas TX-100 surfactant, which has a neutral polar head, caused only a slight decrease in the hydrolysis rate, stronger inhibition was observed in the presence surfactants with charges in their polar heads (CHAPS, ZW3-12, SDS). These results were consistent with those of tryptophan fluorescencequenching studies, which showed that the binding between β-casein and 1 decreased with increasing repulsion between the POM and the polar heads of the surfactants. In all cases, the micellar structure of β-casein was not significantly affected by the presence of POM or surfactants, as indicated by circular dichroism spectroscopy.

Selective Hydrolysis of Transferrin Promoted by Zr-Substituted Polyoxometalates

The hydrolysis of the iron-binding blood plasma glycoprotein transferrin (Tf) has been examined at pH = 7.4 in the presence of a series of Zr-substituted polyoxometalates (Zr-POMs) including Keggin (Et2NH2)10[Zr(PW11O39)2]∙7H2O (Zr-K 1:2), (Et2NH2)8[{α-PW11O39Zr-(μ-OH) (H2O)}2]∙7H2O (Zr-K 2:2), Wells-Dawson K15H[Zr(α2-P2W17O61)2]·25H2O (Zr-WD 1:2), Na14[Zr4(α-P2W16O59)2(μ3-O)2(μ-OH)2(H2O)4]·57H2O (Zr-WD 4:2) and Lindqvist (Me4N)2[ZrW5O18(H2O)3] (Zr-L 1:1), (nBu4N)6[(ZrW5O18(μ-OH))2]∙2H2O (Zr-L 2:2)) type POMs. Incubation of transferrin with Zr-POMs resulted in formation of 13 polypeptide fragments that were observed on sodium dodecyl sulfate poly(acrylamide) gel electrophoresis (SDS-PAGE), but the hydrolysis efficiency varied depending on the nature of Zr-POMs. Molecular interactions between Zr-POMs and transferrin were investigated by using a range of complementary techniques such as tryptophan fluorescence, circular dichroism (CD), 31P-NMR spectroscopy, in order to gain better understanding of different efficiency of investigated Zr-POMs. A tryptophan fluorescence quenching study revealed that the most reactive Zr-WD species show the strongest interaction toward transferrin. The CD results demonstrated that interaction of Zr-POMs and transferrin in buffer solution result in significant secondary structure changes. The speciation of Zr-POMs has been followed by 31P-NMR spectroscopy in the presence and absence of transferrin, providing insight into stability of the catalysts under reaction condition.

Molecular docking of polyoxometalates as potential α-glucosidase inhibitors

α-Glucosidase is an important target enzyme for the treatment of type 2 diabetes in humans. In our previous studies, it was found that polyoxometalates exhibited an effective inhibitory effect on the activity of α-glucosidase, while polyoxometalates have the characteristics of structural diversity and unique properties. Herein, we investigated the inhibition of two different series of polyoxometalates on α-glucosidases by enzyme kinetics and molecular docking. The results demonstrated that all of the studied compounds had a significant inhibitory ability on α-glucosidase as compared with the positive control acarbose. H₈[P₂Mo₁₇Cr(OH₂)O₆₁] reversibly inhibited α-glucosidase in a competitive manner with IC₅₀ of 115.50 ± 1.64 μM and K_I value of 44.31 μM. All other compounds reversibly inhibited enzymatic activity in a mixed manner. H₆PMo₉V₃O₄₀ and H₈[P₂Mo₁₇Cu(OH₂)O₆₁] were the best inhibitors in the Keggin and Dawson series, respectively, with IC₅₀ of 9.63 ± 0.43 and 40.13 ± 0.61 μM, respectively. We conducted molecular docking study and found that the compound and α-glucosidase were mainly non-covalently interacting with hydrogen bonds and van der Waals forces. This result further confirmed the inhibition mechanism of enzyme kinetic experiments.