Enhancing Phosphate Diester Cleavage by a Zinc Complex through Controlling Nucleophile Coordination

Molecularly imprinted self-buffering double network hydrogel containing bi-amidoxime functional groups for the rapid hydrolysis of organophosphates

The development of high-performance catalyst materials with high catalytic activity for the hydrolysis of organophosphorus toxicants without additional pH buffer conditions has become an urgent need for practical application. Here, a multifunctional molecularly imprinted polymer double network hydrogel (MIP-DN) material has been prepared by integrating the first polymer network containing the functional group of bi-amidoxime as the catalytic active center and the cationic polymer polyethyleneimine (PEI) with pH buffer function as the main component of the second network. Advantageously, the resultant MIP-DN hydrogel showed excellent catalytic performance without additional pH buffer conditions, exhibiting a half-life of 25 min for the hydrolysis of paraoxon in pure water. Together with multi-functions of high catalytic activity, self-buffering function and excellent processability, the MIP-DN hydrogel prepared in this work provides a new strategy for the preparation of catalytic materials with practical application value toward toxic organophosphates.

Nuclease-like metalloscissors: Biomimetic candidates for cancer and bacterial and viral infections therapy

Despite the extensive and rapid discovery of modern drugs for treatment of cancer, microbial infections, and viral illnesses; these diseases are still among major global health concerns. To take inspiration from natural nucleases and also the therapeutic potential of metallopeptide antibiotics such as the bleomycin family, artificial metallonucleases with the ability of promoting DNA/RNA cleavage and eventually affecting cellular biological processes can be introduced as a new class of therapeutic candidates. Metal complexes can be considered as one of the main categories of artificial metalloscissors, which can prompt nucleic acid strand scission. Accordingly, biologists, inorganic chemists, and medicinal inorganic chemists worldwide have been designing, synthesizing and evaluating the biological properties of metal complexes as artificial metalloscissors. In this review, we try to highlight the recent studies conducted on the nuclease-like metalloscissors and their potential therapeutic applications. Under the light of the concurrent Covid-19 pandemic, the human need for new therapeutics was highlighted much more than ever before. The nuclease-like metalloscissors with the potential of RNA cleavage of invading viral pathogens hence deserve prime attention.

Ag(I) Pyridine-Amidoxime Complex as the Catalysis Activity Domain for the Rapid Hydrolysis of Organothiophosphate-Based Nerve Agents: Mechanistic Evaluation and Application

Two novel Ag(I) complexes containing synergistic pyridine and amidoxime ligands (Ag-DPAAO and Ag-PAAO) were first designed as complex monomers. Taking advantage of the molecular imprinting technique and solvothermal method, molecular imprinted porous cross-linked polymers (MIPCPs) were developed as a robust platform for the first time to incorporate Ag-PAAO into a polymer material as a recyclable catalyst. Advantageously, the observed pseudo first-order rate constant (k_obs) of MIPCP-Ag-PAAO-20% for ethyl-parathion (EP) hydrolysis is about 1.2 × 10⁴-fold higher than that of self-hydrolysis (30 °C, pH = 9). Furthermore, the reaction mechanism of the MIPCP-containing Ag-PAAO-catalyzed organothiophosphate was analyzed in detail using density functional theory and experimental spectra, indicating that the amidoxime can display dual roles for both the key coordination with the silver ion and nucleophilic attack to weaken the P-OAr bond in the catalytic active site.

Cleavage of an RNA Model Compound by an Arylmercury Complex

A water-soluble arylmercury complex has been synthesized, and its ability to catalyze the cleavage of the phosphodiester linkage of the RNA model compound adenylyl-3',5'-(2',3'-O-methyleneadenosine) has been assessed over a pH range of 3-8.5 and a catalyst concentration range of 0-7 mM. In the presence of 1 mM catalyst, the observed pH-rate profile featured a new pH-independent region between pH 6 and 7, the catalyzed reaction being as much as eight times faster than the background reaction. At pH 7, the acceleration increased linearly from three- to 17-fold upon increasing the catalyst concentration from 1 to 7 mM. The linear dependence indicates a relatively low affinity of the catalyst for the substrate and, hence, the potential for considerable improvement on tethering to an appropriate targeting group, such as an oligonucleotide.

Mechanistic study of carboxylic acid and phosphate ester cleavage by oximate metal complexes surpassing the limiting reactivity of highly basic free oximate anions

Two tridentate and one tetradentate new ligands containing the terminal oxime group separated from secondary amino and pyridine groups as additional binding sites by two or three methylene groups have been prepared. Their acid-base properties, as well as the composition and stability of their complexes with Zn(ii) and Cd(ii) ions, were determined by potentiometric and spectrophotometric titrations. The X-ray structure of a Cd(ii) complex of a related tridentate oxime ligand previously studied in solution was determined. All oximate complexes show high reactivity in the cleavage of aryl acetates, paraoxon, parathion and 4-nitrophenyl diphenyl phosphate, with rate constants significantly surpassing the limiting rate constants observed for highly basic free oximate anions. The second-order rate constants for individual oximate complexes in solution are assigned to each ligand, metal cation and substrate. The results of the cleavage of 4-substituted phenyl acetates were analyzed in terms of Brønsted correlations with the leaving group pKa, which demonstrated a change in the rate determining step from the nucleophilic attack to the leaving group departure upon an increase in the leaving group basicity. The zero slope of the Brønsted correlation for the nucleophilic attack indicates transition state stabilization through electrophilic assistance by the metal ion. This interpretation is supported by metal selectivity in the relative efficiency of the cleavage of paraoxon and parathion. The existence of the alpha-effect in ester cleavage by coordinated oximates is confirmed by an analysis of the Brønsted correlations with the nucleophile basicity for metal bound oximate and alkoxo or hydroxo nucleophiles. The very high reactivity of the oximate complexes of the new ligands is attributed to transition state stabilization and to the removal of the solvational imbalance of oximate anions that impedes the expected increase in the reactivity of highly basic free anions.

Unraveling mechanisms of the uncoordinated nucleophiles: theoretical elucidations of the cleavage of bis(p-nitrophenyl) phosphate mediated by zinc-complexes with apical nucleophiles

A theoretical approach was used to investigate the hydrolytic cleavage mechanisms of the bis(p-nitrophenyl) phosphate (BNPP⁻) catalyzed by Zn(ii)-complexes featuring uncoordinated nucleophiles. Ligand-based and alternative solvent-based nucleophilic attack reaction models are proposed. The pK_a values of the Zn(ii)-bound water molecules or ligands in the [Zn(LⁿH)(η-H₂O)(H₂O)]²⁺ (n = 1, 2 and 3) complexes, as well as the dimerization tendency of the mononuclear Zn(ii)-complexes, were found to significantly influence the reaction mechanisms. The Zn(ii)-L³ complexes were found to be more favorable for the hydrolytic cleavage of the BNPP⁻via a ligand-based nucleophilic attack pathway. This was due to the lower pK_a value for the deprotonation of the oxime ligand, the hard dimerization of the mononuclear Zn(ii)-L³ species, and the presence of an uncoordinated nucleophile. The origins of the uncoordinated reactions were systematically elucidated. The theoretical results reported here are in good agreement with experimental observations and more importantly, help to elucidate the factors that influence intermolecular nucleophilic attack reactions with coordinated/uncoordinated nucleophiles.

A theoretical approach was used to investigate the hydrolytic cleavage mechanisms of the bis(p-nitrophenyl) phosphate (BNPP⁻) catalyzed by Zn(ii)-complexes featuring uncoordinated nucleophiles.

The Zn(II)-1,4,7-Trimethyl-1,4,7-Triazacyclononane Complex: A Monometallic Catalyst Active in Two Protonation States

In this paper, the unusual reactivity of the complex Zn(II)-1,4,7-trimethyl-1, 4,7-triazacyclononane (2) in the transesterification of the RNA-model substrate, HPNP (3), is reported. The dependence of the reactivity (k₂) with pH does not follow the characteristic bell-shape profile typical of complexes with penta-coordinated metal centers. By the contrary, two reactive species, featuring different deprotonation states, are present, with the tri-aqua complex being more reactive than the mono-hydroxy-diaqua one. Apparently, such a difference arises from the total complex charge which plays an important role in the stability of the transition state/s of the reactions. Relevant insight on the reaction mechanism were hence obtained.

Catalytic Hydrolysis of Phosphate Monoester by Supramolecular Phosphatases Formed from a Monoalkylated Dizinc(II) Complex, Cyclic Diimide Units, and Copper(II) in Two-Phase Solvent System

Design and synthesis of enzyme mimic with programmed molecular interaction among several building blocks including metal complexes and metal chelators is of intellectual and practical significance. The preparation of artificial enzymes that mimic the natural enzymes such as hydrolases, phosphatases, etc. remains a great challenge in the field of supramolecular chemistry. Herein we report on the design and synthesis of asymmetric (nonsymmetric) supermolecules by the 2:2:2 self-assembly of an amphiphilic zinc(II)-cyclen complex containing a 2,2'-bipyridyl linker and one long alkyl chain (Zn₂L³), barbital analogues, and Cu²⁺ as model compounds of an enzyme alkaline phosphatase that catalyzes the hydrolysis of phosphate monoesters such as mono(4-nitrophenyl)phosphate at neutral pH in two-phase solvent system (H₂O/CHCl₃) in pH 7.4 and 37 °C. Hydrolytic activity of these complexes was found to be catalytic, and their catalytic turnover numbers are 3-4. The mechanistic studies based on the UV/vis and emission spectra of the H₂O and CHCl₃ phases of the reaction mixtures suggest that the hydrophilicity/hydrophobicity balance of the supramolecular catalysts is an important factor for catalytic activity.

Quantum Mechanical/Molecular Mechanical Analysis of the Catalytic Mechanism of Phosphoserine Phosphatase

Phosphoserine phosphatase (PSP), a member of the haloacid dehalogenase (HAD) superfamily that comprises the vast majority of phosphotransferases, is likely a steady-state regulator of the level of d-serine in the brain. The proposed catalytic cycle of PSP consists of a two-step mechanism: formation of a phospho-enzyme intermediate by phosphate transfer to Asp11 and its subsequent hydrolysis. Our combined quantum mechanical/molecular mechanical (QM/MM) calculations of the reaction pathways favour a dissociative mechanism of nucleophilic substitution via a trigonal-planar metaphosphate-like configuration for both steps, associated with proton transfer to the leaving group or from the nucleophile. This proton transfer is facilitated by active site residue Asp13 that acts as both a general base and a general acid. Free energy calculation on the reaction pathways further support the structural role of the enzymatic environment and the active site architecture. The choice of a proper reaction coordinate along which to bias the free energy calculations can be guided by a projection of the canonical reaction coordinate obtained from a chain-of-state optimisation onto important internal coordinates.

The 3rd degree of biomimetism: associating the cavity effect, ZnII coordination and internal base assistance for guest binding and activation

The synthesis and characterization of a resorcinarene-based tetra(imidazole) ligand is reported. The properties of the corresponding ZnII complex are studied in depth, notably by NMR spectroscopy. In MeCN, acid-base titration reveals that one out of the four imidazole arms is hemi-labile and can be selectively protonated, thereby opening a coordination site in the exo position. Quite remarkably, the 4th imidazole arm promotes binding of an acidic molecule (a carboxylic acid, a β-diketone or acetamide), by acting as an internal base, which allows guest binding as an anion to the metal center in the endo position. Most importantly, the presence of this labile imidazole arm makes the ZnII complex active for the catalyzed hydration of acetonitrile. It is proposed that it acts as a general base for activating a water molecule in the vicinity of the metal center during its nucleophilic attack to the endo-bound MeCN substrate. This system presents a unique degree of biomimetism when considering zinc enzymes: a pocket for guest binding, a similar first coordination sphere, a coordination site available for water activation in the cis position relative to the substrate and finally an internal imidazole residue that plays the role of a general base.

Phosphodiester models for cleavage of nucleic acids

Nucleic acids that store and transfer biological information are polymeric diesters of phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases, is one of the underlying biological processes. The remarkable catalytic efficiency of nucleases, together with the ability of ribonucleic acids to serve sometimes as nucleases, has made the cleavage of phosphodiesters a subject of intensive mechanistic studies. In addition to studies of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on synergistic participation of several catalytic entities. Many nucleases are metalloenzymes and small molecular models offer an excellent tool to construct models for their catalytic centers. The present review tends to be an up to date summary of what has been achieved by mechanistic studies with small molecular phosphodiesters.

Enhanced activity of trinuclear Zn(ii) complexes towards phosphate ester bond cleavage by introducing three-metal cooperativity

The catalytic efficiency (DNA binding followed by phosphate ester bond cleavage) of Zn(ii) complexes has been tuned by variation in the nuclearity, flexibility and coordination environment to explore the structure activity correlation.

Substrate Specificity and Leaving Group Effect in Ester Cleavage by Metal Complexes of an Oximate Nucleophile

Deprotonated zinc(II) and cadmium(II) complexes of a tridentate oxime nucleophile (1, OxH) show a very high reactivity, breaking by 2-3 orders of magnitude the previously established limiting reactivity of oximate nucleophiles in the cleavage of substituted phenyl acetates and phosphate triesters, but are unreactive with p-nitrophenyl phosphate di- and monoesters. With reactive substrates, these complexes operate as true catalysts through an acylation-deacylation mechanism. Detailed speciation and kinetic studies in a wide pH interval allowed us to establish as catalytically active forms [Cd(Ox)]⁺, [Zn(Ox)(OH)], and [Zn(Ox)(OH)₂]^- complexes. The formation of an unusual and most reactive zinc(II) oximatodihydroxo complex was confirmed by electrospray ionization mass spectrometry data and supported by density functional theory calculations, which also supported the previously noticed fact that the coordinated water in [Zn(OxH)(H₂O)₂]²⁺ deprotonates before the oxime. Analysis of the leaving group effect on the cleavage of phenyl acetates shows that the rate-determining step in the reaction with the free oximate anion is the nucleophilic attack, while with both zinc(II) and cadmium(II) oximate complexes, it changes to the expulsion of the leaving phenolate anion. The major new features of these complexes are (1) a very high esterolytic activity surpassing that of enzyme hydrolysis of aryl acetate esters and (2) an increased reactivity of coordinated oxime compared to free oxime in phosphate triester cleavage, contrary to the previously observed inhibitory effect of oxime coordination with these substrates.

Hydrolytic Metallo-Nanozymes: From Micelles and Vesicles to Gold Nanoparticles

Although the term nanozymes was coined by us in 2004 to highlight the enzyme-like properties of gold nanoparticles passivated with a monolayer of Zn(II)-complexes in the cleavage of phosphate diesters, systems resembling those metallo-nanoparticles, like micelles and vesicles, have been the subject of investigation since the mid-eighties of the last century. This paper reviews what has been done in the field and compares the different nanosystems highlighting the source of catalysis and frequent misconceptions found in the literature.

Comparative structure activity relationship for heterogeneous phosphatase-like catalytic activities of one-dimensional Cu(ii) coordination polymers

A structure activity relationship for heterogeneous phosphatase-like activities of one-dimensional Cu(ii) coordination polymers, has been studied. Complex 1 exhibits maximum activity due to coordinated water molecules, shorter metal–metal distance and exposed metal centers.