En Route to a Heterogeneous Catalytic Direct Peptide Bond Formation by Zr-Based Metal–Organic Framework Catalysts

Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling

The formation of an amide bond is an essential step in the synthesis of materials and drugs, and in the assembly of amino acids to form peptides. The mechanism of this reaction has been studied extensively, in particular to understand how it can be catalyzed, but a representation capable of explaining all the experimental data is still lacking. Numerical simulation should provide the necessary molecular description, but the solvent involvement poses a number of challenges. Here, we combine the efficiency and accuracy of neural network potential-based reactive molecular dynamics with the extensive and unbiased exploration of reaction pathways provided by transition path sampling. Using microsecond-scale simulations at the density functional theory level, we show that this method reveals the presence of two competing distinct mechanisms for peptide bond formation between alanine esters in aqueous solution. We describe how both reaction pathways, via a general base catalysis mechanism and via direct cleavage of the tetrahedral intermediate respectively, change with pH. This result contrasts with the conventional mechanism involving a single pathway in which only the barrier heights are affected by pH. We show that this new proposal involving two competing mechanisms is consistent with the experimental data, and we discuss the implications for peptide bond formation under prebiotic conditions and in the ribosome. Our work shows that integrating deep potential molecular dynamics with path sampling provides a powerful approach for exploring complex chemical mechanisms.

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.

Highly defective ultra-small tetravalent MOF nanocrystals

The size and defects in crystalline inorganic materials are of importance in many applications, particularly catalysis, as it often results in enhanced/emerging properties. So far, applying the strategy of modulation chemistry has been unable to afford high-quality functional Metal-Organic Frameworks (MOFs) nanocrystals with minimized size while exhibiting maximized defects. We report here a general sustainable strategy for the design of highly defective and ultra-small tetravalent MOFs (Zr, Hf) crystals (ca. 35% missing linker, 4-6 nm). Advanced characterizations have been performed to shed light on the main factors governing the crystallization mechanism and to identify the nature of the defects. The ultra-small nanoMOFs showed exceptional performance in peptide hydrolysis reaction, including high reactivity, selectivity, diffusion, stability, and show emerging tailorable reactivity and selectivity towards peptide bond formation simply by changing the reaction solvent. Therefore, these highly defective ultra-small M(IV)-MOFs particles open new perspectives for the development of heterogeneous MOF catalysts with dual functions.

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.

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.

Trimethylaluminum-mediated one-pot peptide elongation

Efficient and straightforward peptide bond formation of N-, and C-terminal unprotected amino acids was successfully achieved by using trimethylaluminum. The coupling reaction was accomplished by pre-reaction of N-, and C-terminal unprotected amino acids and trimethylaluminum to form a five-membered ring that smoothly reacted with nucleophilic amino acid esters. This simple and highly efficient reaction system allows one-pot tripeptide synthesis without the need for expensive coupling reagents. Furthermore, peptide bond formation can be effectively achieved even for amino acids with bulky substituents at the side chain to afford the corresponding tripeptides in high yields in a one-pot manner. In addition, the reaction can be applied for further peptide elongation by the subsequent addition of amino acids and trimethylaluminum. We anticipate that this cost-effective, straightforward, and efficient protocol will be useful for the synthesis of a wide variety of peptides.

Concise Synthesis of 2,5-Diketopiperazines via Catalytic Hydroxy-Directed Peptide Bond Formations

2,5-Diketopiperazines (DKPs) with hydroxymethyl functional groups are essential structures found in many bioactive molecules and functional materials. We have established a simple protocol for the concise synthesis of this type of DKPs through diboronic acid anhydride-catalyzed hydroxy-directed peptide bond formations. The sequential reactions in this report, which consist of three steps, an intermolecular catalytic condensation reaction in which water is the only byproduct, a simple deprotection of the nitrogen-protecting group, and an intramolecular cyclization, enabled the synthesis of functionalized DKPs in high to excellent yields without any intermediate purification. The utility of this protocol has been demonstrated by synthesizing natural products, phomamide and Cyclo(Deala-l-Leu).

Exploring the Reactivity of Polyoxometalates toward Proteins: From Interactions to Mechanistic Insights

The latest advances in the study of the reactivity of metal-oxo clusters toward proteins showcase how fundamental insights obtained so far open new opportunities in biotechnology and medicine. In this Perspective, these studies are discussed through the lens of the reactivity of a family of soluble anionic metal-oxo nanoclusters known as polyoxometalates (POMs). POMs act as catalysts in a wide range of reactions with several different types of biomolecules and have promising therapeutic applications due to their antiviral, antibacterial, and antitumor activities. However, the lack of a detailed understanding of the mechanisms behind biochemically relevant reactions-particularly with complex biological systems such as proteins-still hinders further developments. Hence, in this Perspective, special attention is given to reactions of POMs with peptides and proteins showcasing a molecular-level understanding of the reaction mechanism. In doing so, we aim to highlight both existing limitations and promising directions of future research on the reactivity of metal-oxo clusters toward proteins and beyond.

Peptide-based drug discovery: Current status and recent advances

The progressive development of peptides from reaction vessels to life-saving drugs via rigorous preclinical and clinical assessments is fascinating. Peptide therapeutics have gained momentum with the evolution of techniques in peptide chemistry, such as microwave irradiation in solid- and solution-phase synthesis, ligation chemistry, recombinant synthesis, and amalgamation with synthetic tools, including metal catalysis. Diverse emerging technologies, such as DNA-encoded libraries (DELs) and display techniques, are changing the status quo in the discovery of peptide therapeutics. In this review, we analyzed US Food and Drug Administration (FDA)-approved peptide drugs and those in clinical trials, highlighting recent advances in peptide-based drug discovery.

Highly Active La(III)-Based Metal-Organic Framework as a Heterogeneous Lewis Acid Catalyst for Friedel-Crafts Alkylation

In this study, a novel La(III)-based two-dimensional (2D) metal-organic framework, [La_2/3 (qptca)_1/2 ] (referred to as SLX-2), from LaCl₃ and 1,1' : 4',1'' : 4'',1''' : 4''',1''''-quinquephenyl]-2,2'',2'''',5''-tetracarboxylic acid (H₄ qptca) was synthesized by conventional solvothermal method and thoroughly characterized by using X-ray single-crystal diffraction, powder X-ray diffraction, and thermogravimetric analyses. The 2D SLX-2 features a unique lanthanum center exposed to the skeleton and was used as an efficient Lewis acid catalyst for the Friedel-Crafts alkylation of indole and pyrrole with β-nitrostyrene along with a wide substrate scope, giving the desired products in good-to-high yields under the optimal reaction conditions. Furthermore, the catalyst was used for twenty cycles, with nearly no effect on its activity, and the reaction was heterogeneous in nature. Moreover, compared to the previous hydrogen-bond-donating MOF catalysts for such alkylation reactions, SLX-2 showed an excellent stability toward harsh acidic and basic environment, and gave comparable catalytic activities.

MOF nanoparticles as heterogeneous catalysts for direct amide bond formations

The influence of composition and textural characteristics of a family of ultra-small isoreticular UiO-type metal-organic frameworks (MOFs) with different functionalized and extended linkers on their catalytic performance is evaluated. Two direct amide bond formations across four different substrates (benzylamine + phenylacetic acid and aniline + formic acid) are employed as proof-of-concept reactions to test the activity of the Zr-MOF nanoparticles. The reaction rates of amide bond formation are evaluated against physico-chemical properties such as crystallinity, porosity, particle size or linker functionality, alongside the Lewis acid and hydrophobic properties of the MOFs, in order to gain insights into the catalytic mechanism and optimal properties for its enhancement.

Postsynthetic Defect Formation in Three-Dimensional Hofmann-Type Coordination Polymers and Its Impact on Catalytic Activity

We report a systematic investigation of postsynthetic defect formation in Hofmann-type coordination polymers M(pz)[M'(CN)₄] (M = Fe²⁺, Co²⁺, Ni²⁺; M' = Pd²⁺, Pt²⁺; pz = pyrazine). These compounds readily undergo selective ligand exchange at the pyrazine site when immersed in methanol (MeOH) at ambient temperature. The ligand exchange changes the chemical formula to M(pz)_1-x(MeOH)_2x[M'(CN)₄] (0 < x < 0.3), affording a defective coordination environment around the M ions. The defect concentration is highly dependent on the combination of the metal ions and solvent species, reaching the defect concentration of ca. 30% (x ∼ 0.3) at maximum. The magnetic state of one such coordination polymer gives an additional control of the defect formation, making the compound less susceptible to the ligand exchange at the low-spin state. Structures that form the defects at a high concentration function as catalysts and promote an acetalization reaction heterogeneously by providing Lewis acidic sites. The solvent-dependent character of the defect formation can be used to control the catalytic activity of the active compounds, demonstrating a facile defect engineering for functionalizing solid materials.

Zirconium oxo clusters as discrete molecular catalysts for the direct amide bond formation

A discrete dodecanuclear Zr oxo cluster catalyzed the direct formation of amide bonds without the need of water scavenging or dry reactions conditions showcasing the potential of these molecular clusters to become a new class of efficient catalysts.

Nanochannel-Based {BaZn}-Organic Framework for Catalytic Activity on Cycloaddition Reaction of Epoxides with CO2 and Deacetalization-Knoevenagel Condensation

Because of the integrated properties from chemically dissimilar metals, microporous heterometallic MOFs have wider potential applicability, which prompts us to explore the tendency collocation of different metal cations in the...

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.

A green and sustainable approach for the synthesis of 1,5-benzodiazepines and spirooxindoles in one-pot using a MIL-101(Cr) metal–organic framework as a reusable catalyst

Green and efficient protocols for the synthesis of 1,5-benzodiazepines and spirooxindoles were developed utilizing MIL-101(Cr) in SFRC and water as solvent respectively.