Interplay between structural parameters and reactivity of Zr6-based MOFs as artificial proteases

From Nanozymes to Multi-Purpose Nanomaterials: The Potential of Metal-Organic Frameworks for Proteomics Applications

Metal-organic frameworks (MOFs) have the potential to revolutionize the biotechnological and medical landscapes due to their easily tunable crystalline porous structure. Herein, the study presents MOFs' potential impact on proteomics, unveiling the diverse roles MOFs can play to boost it. Although MOFs are excellent catalysts in other scientific disciplines, their role as catalysts in proteomics applications remains largely underexplored, despite protein cleavage being of crucial importance in proteomics protocols. Additionally, the study discusses evolving MOF materials that are tailored for proteomics, showcasing their structural diversity and functional advantages compared to other types of materials used for similar applications. MOFs can be developed to seamlessly integrate into proteomics workflows due to their tunable features, contributing to protein separation, peptide enrichment, and ionization for mass spectrometry. This review is meant as a guide to help bridge the gap between material scientists, engineers, and MOF chemists and on the other side researchers in biology or bioinformatics working in proteomics.

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.

Molecular Insights into Sequence-Specific Protein Hydrolysis by a Soluble Zirconium-Oxo Cluster Catalyst

The development of catalysts for controlled fragmentation of proteins is a critical undertaking in modern proteomics and biotechnology. {Zr6O8}-based metal-organic frameworks (MOFs) have emerged as promising candidates for catalysis of peptide bond hydrolysis due to their high reactivity, stability, and recyclability. However, emerging evidence suggests that protein hydrolysis mainly occurs on the MOF surface, thereby questioning the need for their highly porous 3D nature. In this work, we show that the discrete and water-soluble [Zr6O4(OH)4(CH3CO2)8(H2O)2Cl3]+ (Zr6) metal-oxo cluster (MOC), which is based on the same hexamer motif found in various {Zr6O8}-based MOFs, shows excellent activity toward selective hydrolysis of equine skeletal muscle myoglobin. Compared to related Zr-MOFs, Zr6 exhibits superior reactivity, with near-complete protein hydrolysis after 24 h of incubation at 60 °C, producing seven selective fragments with a molecular weight in the range of 3-15 kDa, which are of ideal size for middle-down proteomics. The high solubility and molecular nature of Zr6 allow detailed solution-based mechanistic/interaction studies, which revealed that cluster-induced protein unfolding is a key step that facilitates hydrolysis. A combination of multinuclear nuclear magnetic resonance spectroscopy and pair distribution function analysis provided insight into the speciation of Zr6 and the ligand exchange processes occurring on the surface of the cluster, which results in the dimerization of two Zr6 clusters via bridging oxygen atoms. Considering the relevance of discrete Zr-oxo clusters as building blocks of MOFs, the molecular-level understanding reported in this work contributes to the further development of novel catalysts based on Zr-MOFs.

Pertechnetate/perrhenate-capped Zr/Hf-Dihydroxide Dimers: Elucidating Zr-TcO4 Co-Mobility in the Nuclear Fuel Cycle

Spent nuclear fuel contains heavy element fission products that must be separated for effective reprocessing for a safe and sustainable nuclear fuel cycle. 93 Zr and 99 Tc are high-yield fission products that co-transport in liquid-liquid extraction processes. Here we seek atomic-level information of this co-extraction process, as well as fundamental knowledge about ZrIV (and HfIV ) aqueous speciation in the presence of topology-directing ligands such as pertechnetate (TcO4 - ) and non-radioactive surrogate perrhenate (ReO4 - ). In this context, we show that the flat tetrameric oxyhydroxyl-cluster [MIV 4 (OH)8 (H2 O)16 ]8+ (and related polymers) is dissociated by perrhenate/pertechnetate to yield isostructural dimers, M2 (OH)2 (XO4 - )6 (H2 O)6  ⋅ 3H2 O (M=Zr/HfIV ; X=Re/TcVII ), elucidated by single-crystal X-ray diffraction. We used these model compounds to understand the pervasive 93 Zr-99 Tc coextraction with further speciation studies in water, nitric acid, and tetrabutylphosphate (TBP) -kerosene; where the latter two media are relevant to nuclear fuel reprocessing. SAXS (small angle X-ray scattering), compositional evaluation, and where experimentally feasible, ESI-MS (electrospray ionization mass spectrometry) showed that perrhenate/pertechnetate influence Zr/HfIV -speciation in water. In Zr-XO4 solvent extraction studies to simulate fuel reprocessing, we provide evidence that TcO4 - enhances extraction of ZrIV , and compositional analysis of the extracted metal-complexes (Zr-ReO4 study) is consistent with the crystallized ZrIV 2 (OH)2 (ReVII O4 - )6 (H2 O)6 ⋅dimer.

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.

Hydrolytic nanozymes: Preparation, properties, and applications

Hydrolytic nanozymes, as promising alternatives to hydrolytic enzymes, can efficiently catalyze the hydrolysis reactions and overcome the operating window limitations of natural enzymes. Moreover, they exhibit several merits such as relatively low cost, easier recovery and reuse, improved operating stability, and adjustable catalytic properties. Consequently, they have found relevance in practical applications such as organic synthesis, chemical weapon degradation, and biosensing. In this review, we highlight recent works addressing the broad topic of the development of hydrolytic nanozymes. We review the preparation, properties, and applications of six types of hydrolytic nanozymes, including AuNP-based nanozymes, polymeric nanozymes, surfactant assemblies, peptide assemblies, metal and metal oxide nanoparticles, and MOFs. Last, we discuss the remaining challenges and future directions. This review will stimulate the development and application of hydrolytic nanozymes.

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.

Green, Safe, and Reliable Synthesis of Bimetallic MOF-808 Nanozymes With Enhanced Aqueous Stability and Reactivity for Biological Applications

Bimetallic metal-organic frameworks (MOFs) are promising nanomaterials whose reactivity towards biomolecules remains challenging due to issues related to synthesis, stability, control over metal oxidation state, phase purity, and atomic level characterization. Here, these shortcomings are rationally addressed through development of a synthesis of mixed metal Zr/Ce-MOFs in aqueous environment, overcoming significant hurdles in the development of MOF nanozymes, sufficiently stable on biologically relevant conditions. Specifically, a green and safe synthesis of Zr/Ce-MOF-808 is reported in water/acetic acid mixture which affords remarkably water-stable materials with reliable nanozymatic reactivity, including MOFs with a high Ce content previously reported to be unstable in water. The new materials outperform analogous bimetallic MOF nanozymes, showcasing that rational synthesis modifications could impart outstanding improvements. Further, atomic-level characterization by X-ray Absorption Fine Structure (XAFS) and X-ray Diffraction (XRD) confirmed superior nanozymes arise from differences in the synthetic method, which results in aqueous stable materials, and Ce incorporation, which perturbs the ligand exchange dynamics of the material, and could ultimately be used to fine tune the intrinsic MOF reactivity. Similar rational strategies which leverage metals in a synergistic manner should enable other water-stable bimetallic MOF nanozymes able to surpass existing ones, laying the path for varied biotechnological applications.

Antioxidant and Prooxidant Nanozymes: From Cellular Redox Regulation to Next-Generation Therapeutics

Nanozymes, nanomaterials with enzyme-mimicking activity, have attracted tremendous interest in recent years owing to their ability to replace natural enzymes in various biomedical applications, such as biosensing, therapeutics, drug delivery, and bioimaging. In particular, the nanozymes capable of regulating the cellular redox status by mimicking the antioxidant enzymes in mammalian cells are of great therapeutic significance in oxidative-stress-mediated disorders. As the distinction of physiological oxidative stress (oxidative eustress) and pathological oxidative stress (oxidative distress) occurs at a fine borderline, it is a great challenge to design nanozymes that can differentially sense the two extremes in cells, tissues and organs and mediate appropriate redox chemical reactions. In this Review, we summarize the advances in the development of redox-active nanozymes and their biomedical applications. We primarily highlight the therapeutic significance of the antioxidant and prooxidant nanozymes in various disease model systems, such as cancer, neurodegeneration, and cardiovascular diseases. The future perspectives of this emerging area of research and the challenges associated with the biomedical applications of nanozymes are described.

Nanomedicine in the Face of Parkinson's Disease: From Drug Delivery Systems to Nanozymes

The complexity and overall burden of Parkinson's disease (PD) require new pharmacological approaches to counteract the symptomatology while reducing the progressive neurodegeneration of affected dopaminergic neurons. Since the pathophysiological signature of PD is characterized by the loss of physiological levels of dopamine (DA) and the misfolding and aggregation of the alpha-synuclein (α-syn) protein, new proposals seek to restore the lost DA and inhibit the progressive damage derived from pathological α-syn and its impact in terms of oxidative stress. In this line, nanomedicine (the medical application of nanotechnology) has achieved significant advances in the development of nanocarriers capable of transporting and delivering basal state DA in a controlled manner in the tissues of interest, as well as highly selective catalytic nanostructures with enzyme-like properties for the elimination of reactive oxygen species (responsible for oxidative stress) and the proteolysis of misfolded proteins. Although some of these proposals remain in their early stages, the deepening of our knowledge concerning the pathological processes of PD and the advances in nanomedicine could endow for the development of potential treatments for this still incurable condition. Therefore, in this paper, we offer: (i) a brief summary of the most recent findings concerning the physiology of motor regulation and (ii) the molecular neuropathological processes associated with PD, together with (iii) a recapitulation of the current progress in controlled DA release by nanocarriers and (iv) the design of nanozymes, catalytic nanostructures with oxidoreductase-, chaperon, and protease-like properties. Finally, we conclude by describing the prospects and knowledge gaps to overcome and consider as research into nanotherapies for PD continues, especially when clinical translations take place.

Nanozyme-Based Artificial Organelles: An Emerging Direction for Artificial Organelles

Artificial organelles are compartmentalized nanoreactors, in which enzymes or enzyme-mimic catalysts exhibit cascade catalytic activities to mimic the functions of natural organelles. Importantly, research on artificial organelles paves the way for the bottom-up design of synthetic cells. Due to the separation effect of microcompartments, the catalytic reactions of enzymes are performed without the influence of the surrounding medium. The current techniques for synthesizing artificial organelles rely on the strategies of encapsulating enzymes into vesicle-structured materials or reconstituting enzymes onto the microcompartment materials. However, there are still some problems including limited functions, unregulated activities, and difficulty in targeting delivery that hamper the applications of artificial organelles. The emergence of nanozymes (nanomaterials with enzyme-like activities) provides novel ideas for the fabrication of artificial organelles. Compared with natural enzymes, nanozymes are featured with multiple enzymatic activities, higher stability, easier to synthesize, lower cost, and excellent recyclability. Herein, the most recent advances in nanozyme-based artificial organelles are summarized. Moreover, the benefits of compartmental structures for the applications of nanozymes, as well as the functional requirements of microcompartment materials are also introduced. Finally, the potential applications of nanozyme-based artificial organelles in biomedicine and the related challenges are discussed.

Nonaqueous Chemistry of Group 4 Oxo Clusters and Colloidal Metal Oxide Nanocrystals

We review the nonaqueous precursor chemistry of the group 4 metals to gain insight into the formation of their oxo clusters and colloidal oxide nanocrystals. We first describe the properties and structures of titanium, zirconium, and hafnium oxides. Second, we introduce the different precursors that are used in the synthesis of oxo clusters and oxide nanocrystals. We review the structures of group 4 metal halides and alkoxides and their reactivity toward alcohols, carboxylic acids, etc. Third, we discuss fully condensed and atomically precise metal oxo clusters that could serve as nanocrystal models. By comparing the reaction conditions and reagents, we provide insight into the relationship between the cluster structure and the nature of the carboxylate capping ligands. We also briefly discuss the use of oxo clusters. Finally, we review the nonaqueous synthesis of group 4 oxide nanocrystals, including both surfactant-free and surfactant-assisted syntheses. We focus on their precursor chemistry and surface chemistry. By putting these results together, we connect the dots and obtain more insight into the fascinating chemistry of the group 4 metals. At the same time, we also identify gaps in our knowledge and thus areas for future research.

A zirconium metal-organic framework with SOC topological net for catalytic peptide bond hydrolysis

The discovery of nanozymes for selective fragmentation of proteins would boost the emerging areas of modern proteomics, however, the development of efficient and reusable artificial catalysts for peptide bond hydrolysis is challenging. Here we report the catalytic properties of a zirconium metal-organic framework, MIP-201, in promoting peptide bond hydrolysis in a simple dipeptide, as well as in horse-heart myoglobin (Mb) protein that consists of 153 amino acids. We demonstrate that MIP-201 features excellent catalytic activity and selectivity, good tolerance toward reaction conditions covering a wide range of pH values, and importantly, exceptional recycling ability associated with easy regeneration process. Taking into account the catalytic performance of MIP-201 and its other advantages such as 6-connected Zr₆ cluster active sites, the green, scalable and cost-effective synthesis, and good chemical and architectural stability, our findings suggest that MIP-201 may be a promising and practical alternative to commercially available catalysts for peptide bond hydrolysis.

Developing efficient and reusable artificial catalysts for peptide bond hydrolysis is challenging. This work presents the catalytic properties of a Zr-MOF, MIP-201, which features excellent catalytic activity and selectivity, good condition tolerance, and exceptional recycling ability.

Magnetic CuFe2O4 with intrinsic protease-like activity inhibited cancer cell proliferation and migration through mediating intracellular proteins

Protease has been widely used in biological and industrial fields. Developing efficient artificial enzyme mimics remains a major technical challenge due to the high stability of peptide bonds. Nanoenzymes with high stability, high activity and low cost, provided new opportunities to break through natural enzyme inherent limitations. However, compared with many nanomaterials with inherent peroxidase activity, the intrinsic mimic proteases properties of magnetic nanomaterials were seldom explored, let alone the interaction between magnetic nanomaterials and cellular proteins. Herein, we reported for the first time that magnetic CuFe₂O₄ possesses inherent protease activity to hydrolyze bovine serum albumin (BSA) and casein under physiological conditions, and the CuFe₂O₄ is more resistant to high temperature than the natural trypsin. It also exhibited significantly higher catalytic efficiency than other copper nanomaterials and can be recycled for many times. Protease participated in pathophysiological processes and all stages of tumor progression. Interesting, CuFe₂O₄ exhibited anti-proliferative effect on A549, SKOV3, HT-29, BABL-3T3 and HUVEC cells, as well as it was particularly sensitive against SKOV3 cells. CuFe₂O₄ was about 30 times more effective than conventional chemotherapy drugs oxaliplatin and artesunate against SKOV3 cells. In addition, CuFe₂O₄ also mediated the expression of intracellular proteins, such as MMP-2, MMP-9, F-actin, and NF-kB, which may be associated with global protein hydrolysis by CuFe₂O₄, leading to inhibition of cell migration. The merits of the high magnetic properties, good protease-mimic and antitumor activities make CuFe₂O₄ nanoparticles very prospective candidates for many applications such as proteomics and biotechnology.

Enhancing the Catalytic Activity of MOF-808 Towards Peptide Bond Hydrolysis through Synthetic Modulations

The performance of MOFs in catalysis is largely derived from structural features, and much work has focused on introducing structural changes such as defects or ligand functionalisation to boost the reactivity of the MOF. However, the effects of different parameters chosen for the synthesis on the catalytic reactivity of the resulting MOF remains poorly understood. Here, we evaluate the role of metal precursor on the reactivity of Zr-based MOF-808 towards hydrolysis of the peptide bond in the glycylglycine model substrate. In addition, the effect of synthesis temperature and duration has been investigated. Surprisingly, the metal precursor was found to have a large influence on the reactivity of the MOF, surpassing the effect of particle size or number of defects. Additionally, we show that by careful selection of the Zr-salt precursor and temperature used in MOF syntheses, equally active MOF catalysts could be obtained after a 20 minute synthesis compared to 24 h synthesis.

Heterogeneous nanozymatic activity of Hf oxo-clusters embedded in a metal-organic framework towards peptide bond hydrolysis

Materials with enzyme-like activities and proteolytic potential are emerging as a robust and effective alternative to natural enzymes. Herein, a Hf₆O₈-based NU-1000 metal organic framework (Hf-MOF) is shown to act as a heterogeneous catalyst for the hydrolysis of peptide bonds under mild conditions. In the presence of Hf-MOF, a glycylglycine model dipeptide was hydrolysed with a rate constant of k_obs = 8.33 × 10^-7 s^-1 (half-life (t_1/2) of 231 h) at 60 °C and pD 7.4, which is significantly faster than the uncatalyzed reaction. Other Gly-X peptides (X = Ser, Asp, Ile, Ala, and His) were also smoothly hydrolysed under the same conditions with similar rates, except for the faster reactions observed for Gly-His and Gly-Ser. Moreover, the Hf₆O₈-based NU-1000 MOF also exhibits a high selectivity in the cleavage of a protein substrate, hen egg white lysozyme (HEWL). Our results suggest that embedding Hf₆O₈ oxo-clusters is an efficient strategy to conserve the hydrolytic activity while smoothing the strong substrate adsorption previously observed for a discrete Hf oxo-cluster that hindered further development of its proteolytic potential. Furthermore, comparison with isostructural Zr-NU-1000 shows that although the Hf variant afforded the same cleavage pattern towards HEWL but slightly slower reaction rates, it exhibited a larger stability window and a better recyclability profile. The results suggest that these differences originate from the intrinsic differences between Hf^IV and Zr^IV centers, and from the lower surface area of Hf-NU-1000 in comparison to Zr-NU-1000.

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).

Broadening the Scope of Polyoxometalates as Artificial Proteases in Surfactant Solutions: Hydrolysis of Ovalbumin by Zr(IV)-Substituted Keggin Complex

Development of catalysts for the selective hydrolysis of proteins is challenging, yet important for many applications in biotechnology and proteomics. The hydrolysis of hydrophobic proteins is particularly challenging, as due to their poor solubility, the use of surfactants is often required. In this study, the proteolytic potential of catalyst systems based on the Zr(IV)-substituted Keggin polyoxometalate (Et2NH2)10[Zr(PW11O39)2] (Zr-K 1:2) and three different surfactants (ionic SDS (sodium dodecyl sulfate); zwitterionic Zw3-12 (n-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate); and CHAPS (3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate)), which differ in structure and polarity, has been investigated. Hydrolysis of ovalbumin (OVA) was examined in the presence of Zr-K 1:2 and surfactants by sodium dodecyl sulfate poly(acrylamide) gel electrophoresis (SDS-PAGE), which showed the appearance of new polypeptide fragments at lower molecular weight, indicating that selective hydrolysis of OVA took place for all three catalyst systems. The same fragmentation pattern was observed, showing that the selectivity was not affected by surfactants. However, the surfactants influenced the performance of the catalyst. Hence, the interactions of OVA with surfactants and Zr-K 1:2 were investigated using different techniques such as tryptophan fluorescence, Circular Dichroism, and Dynamic Light Scattering. The speciation of the catalyst in surfactant solutions was also followed by 31P Nuclear Magnetic Resonance spectroscopy providing insight into its stability under reaction conditions.

Metal-organic frameworks as advanced materials for sample preparation of bioactive peptides

Development of novel affinity materials and separation techniques is crucial for the progress of modern proteomics and peptidomics. Detection of peptides and proteins from complex matrices still remains a challenging task due to the highly complicated biological composition, low abundance of target molecules, and large dynamic range of proteins. As an emerging area of analytical science, metal-organic framework (MOF)-based separation of proteins and peptides is attracting growing interest. This minireview summarizes the recent advances in MOF-based affinity materials for the sample preparation of proteins and peptides. Some newly emerging MOF nanoreactors for the degradation of peptides and proteins are introduced. An update of MOF-based affinity materials for the isolation of glycopeptides, phosphopeptides and low-abundance endogenous peptides in the last two years is focused on. The separation mechanism is discussed along with the chemical structures of MOFs. Finally, the remaining challenges and future development of MOFs in analyzing peptides and proteins in complicated biological samples are discussed.

Mechanism of the highly effective peptide bond hydrolysis by MOF-808 catalyst under biologically relevant conditions

Efficient and selective hydrolysis of inert peptide bonds is of paramount importance. MOF-808, a metal-organic framework based on Zr₆ nodes, can hydrolyze peptide bonds efficiently under biologically relevant conditions. However, the details of the catalyst structure and of the underlying catalytic reaction mechanism are challenging to establish. By means of DFT calculations we first investigate the speciation of the Zr₆ nodes and identify the nature of ligands that bind to the Zr₆O₈H_4-x core in aqueous conditions. The core is predicted to strongly prefer a Zr₆O₈H₄ protonation state and to be predominantly decorated by bridging formate ligands, giving Zr₆(μ₃-O)₄(μ₃-OH)₄(BTC)₂(HCOO)₆ and Zr₆(μ₃-O)₄(μ₃-OH)₄(BTC)₂(HCOO)₅(OH)(H₂O) as the most favorable structures at physiological pH. The GlyGly peptide can bind MOF in several different ways, with the preferred structure involving coordination through the terminal carboxylate analogously to the binding mode of formate ligand. The pre-reactive binding mode in which the amide carbonyl oxygen coordinates the metal core lies 7 kcal higher in free energy. The preferred reaction pathway is predicted to have two close-lying transition states, either of which could be the rate-determining step: nucleophilic attack on the amide carbon atom and C-N bond breaking, with calculated relative free energies of 31 and 32 kcal mol^-1, respectively. Replacement of formate by water and hydroxide at the Zr₆ node is predicted to be possible, but does not appear to play a role in the hydrolysis mechanism.

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.