The reaction mechanism of the Ga(III)Zn(II) derivative of uteroferrin and corresponding biomimetics

Biomimetics for purple acid phosphatases: A historical perspective

Biomimetics hold potential for varied applications in biotechnology and medicine but have also attracted particular interest as benchmarks for the functional study of their more complex biological counterparts, e.g. metalloenzymes. While many of the synthetic systems adequately mimic some structural and functional aspects of their biological counterparts the catalytic efficiencies displayed are mostly far inferior due to the smaller size and the associated lower complexity. Nonetheless they play an important role in bioinorganic chemistry. Numerous examples of biologically inspired and informed artificial catalysts have been reported, designed to mimic a plethora of chemical transformations, and relevant examples are highlighted in reviews and scientific reports. Herein, we discuss biomimetics of the metallohydrolase purple acid phosphatase (PAP), examples of which have been used to showcase synergistic research advances for both the biological and synthetic systems. In particular, we focus on the seminal contribution of our colleague Prof. Ademir Neves, and his group, pioneers in the design and optimization of suitable ligands that mimic the active site of PAP.

Rational Design of Potent Inhibitors of a Metallohydrolase Using a Fragment-Based Approach

Metallohydrolases form a large group of enzymes that have fundamental importance in a broad range of biological functions. Among them, the purple acid phosphatases (PAPs) have gained attention due to their crucial role in the acquisition and use of phosphate by plants and also as a promising target for novel treatments of bone-related disorders and cancer. To date, no crystal structure of a mammalian PAP with drug-like molecules bound near the active site is available. Herein, we used a fragment-based design approach using structures of a mammalian PAP in complex with the Maybridge^TM fragment CC063346, the amino acid L-glutamine and the buffer molecule HEPES, as well as various solvent molecules to guide the design of highly potent and efficient mammalian PAP inhibitors. These inhibitors have improved aqueous solubility when compared to the clinically most promising PAP inhibitors available to date. Furthermore, drug-like fragments bound in newly discovered binding sites mapped out additional scaffolds for further inhibitor discovery, as well as scaffolds for the design of inhibitors with novel modes of action.

New AlIIIZnII and AlIIICuII dinuclear complexes: Phosphatase-like activity and cytotoxicity

Herein, we report the synthesis and characterization of the first two Al^III(μ-OH)M^II (M = Zn (1) and Cu (2)) complexes with the unsymmetrical ligand H₂L{2-[[(2-hydroxybenzyl)(2-pyridylmethyl)]aminomethyl]-6-bis(pyridylmethyl)aminomethyl}-4-methylphenol. The complexes were characterized through elemental analysis, X-ray crystallography, IR spectroscopy, mass spectrometry and potentiometric titration. In addition, complex 2 was characterized by electronic spectroscopy. Kinetics studies on the hydrolysis of the model substrate bis(2,4-dinitrophenyl)phosphate by 1 and 2 show Michaelis-Menten behavior, with 1 being slightly more active (8.31%) than 2 (at pH 7.0). The antimicrobial effect of the compounds was studied using four bacterial strains (Staphylococcus aureus, Pseudomonas aeuruginosa, Shigella sonnei and Shigella dysenteriae) and for both complexes the inhibition of bacterial growth was superior to that caused by sulfapyridine, but inferior to that of tetracycline. The dark cytotoxicity and photocytotoxicity (under UV-A light) of the complexes in a chronic myelogenous leukemia cell line were investigated. Complexes 1 and 2 exhibited significant cytotoxic activity against K562 cells, which undergoes a 2-fold increase on applying 5 min of irradiation with UV-A light. Complex 2 was more effective and a good correlation between cytotoxicity and intracellular concentration was observed, the intracellular copper concentration required to inhibit 50% of cell growth being 3.5 × 10^-15 mol cell^-1.

Mechanistic Studies of Homo- and Heterodinuclear Zinc Phosphoesterase Mimics: What Has Been Learned?

Phosphoesterases hydrolyze the phosphorus oxygen bond of phosphomono-, di- or triesters and are involved in various important biological processes. Carboxylate and/or hydroxido-bridged dizinc(II) sites are a widespread structural motif in this enzyme class. Much effort has been invested to unravel the mechanistic features that provide the enormous rate accelerations observed for enzymatic phosphate ester hydrolysis and much has been learned by using simple low-molecular-weight model systems for the biological dizinc(II) sites. This review summarizes the knowledge and mechanistic understanding of phosphoesterases that has been gained from biomimetic dizinc(II) complexes, showing the power as well as the limitations of model studies.

Synthesis and evaluation of novel purple acid phosphatase inhibitors

Transgenic studies in animals have demonstrated a direct association between the level of expression of purple acid phosphatase (PAP; also known as tartrate-resistant acid phosphatase) and the progression of osteoporosis. Consequently, PAP has emerged as a promising target for the development of novel therapeutic agents to treat this debilitating disorder. PAPs are binuclear hydrolases that catalyse the hydrolysis of phosphorylated substrates under acidic to neutral conditions. A series of phenyltriazole carboxylic acids, prepared by the reactions of azide derivatives with propiolic acid through copper(i)-catalysed azide-alkyne cycloaddition click reactions, has been assessed for their inhibitory effect on the catalytic activity of pig and red kidney bean PAPs. The binding mode of most of these compounds is purely uncompetitive with K _iuc values as low as ∼23 μM for the mammalian enzyme. Molecular modelling has been used to examine the binding modes of these triazole compounds in the presence of a substrate in the active site of the enzyme in order to rationalise their activities and to design more potent and specific derivatives.

Synthesis, Magnetic Properties, and Catalytic Properties of a Nickel(II)-Dependent Biomimetic of Metallohydrolases

A dinickel(II) complex of the ligand 1,3-bis(bis(pyridin-2-ylmethyl)amino)propan-2-ol (HL1) has been prepared and characterized to generate a functional model for nickel(II) phosphoesterase enzymes. The complex, [Ni2(L1)(μ-OAc)(H2O)2](ClO4)2·H2O, was characterized by microanalysis, X-ray crystallography, UV-visible, and IR absorption spectroscopy and solid state magnetic susceptibility measurements. Susceptibility studies show that the complex is antiferromagnetically coupled with the best fit parameters J = -27.4 cm-1, g = 2.29, D = 28.4 cm-1, comparable to corresponding values measured for the analogous dicobalt(II) complex [Co2(L1)(μ-OAc)](ClO4)2·0.5 H2O (J = -14.9 cm-1 and g = 2.16). Catalytic measurements with the diNi(II) complex using the substrate bis(2,4-dinitrophenyl)phosphate (BDNPP) demonstrated activity toward hydrolysis of the phosphoester substrate with K m ~10 mM, and k cat ~0.025 s-1. The combination of structural and catalytic studies suggests that the likely mechanism involves a nucleophilic attack on the substrate by a terminal nucleophilic hydroxido moiety.

Modeling the Active Site of the Purple Acid Phosphatase Enzyme with Hetero-Dinuclear Mixed Valence M(II)-Fe(III) [M = Zn, Ni, Co, and Cu] Complexes Supported over a [N6O] Unsymmetrical Ligand

The active site of the purple acid phosphatase enzyme has been successfully modeled by a series of hetero-dinuclear M(II)-Fe(III) [M = Zn, Ni, Co, and Cu] type complexes of an unsymmetrical [N₆O] ligand that contained a bridging phenoxide moiety and one imidazoyl and three pyridyl moieties as the terminal N-binding sites. In particular, the hetero-dinuclear complexes, {L[M^II(μ-OAc)₂Fe^III]}(ClO₄)₂ [M = Zn (3a), Ni (3b), Co (4a), and Cu (4b)], were obtained directly from the phenoxy-bridged ligand (HL), namely 2-{[bis(2-methylpyridyl)amino]methyl}-6-{[((1-methylimidazol-2-yl)methyl)(2-pyridylmethyl)amino]methyl}-4-t-butylphenol (2), upon sequential addition of Fe(ClO₄)₃·XH₂O and M(ClO₄)₂·6H₂O (M = Zn and Ni) or M(OAc)₂·XH₂O (M = Co and Cu), in a low-to-moderate (ca. 32-53%) yield. The temperature-dependent magnetic susceptibility measurements indicated weak antiferromagnetic coupling interactions occurring between the two metal centers in their high-spin states. All of the 3(a-b) and 4(a-b) complexes successfully carried out the hydrolysis of the bis(2,4-dinitrophenyl)phosphate (2,4-BDNPP) substrate in a mixed CH₃CN/H₂O (v/v 1:1) medium in the pH range of 5.5-10.5 at room temperature, thereby mimicking the functional activity of the native enzyme. The spectrophotometric titration suggested a monoaquated and dihydroxo species of the type {L[(H₂O)M^II(μ-OH)Fe^III(OH)]}²⁺ to be the catalytically active species for the phosphodiester hydrolysis reaction within the pH range of ca. 5.80-7.15. Last, the kinetic studies on the hydrolysis of the model substrate, 2,4-BDNPP, divulge a Michaelis-Menten-type behavior for all complexes.

Metallohydrolase biomimetics with catalytic and structural flexibility

The phosphatase activity of zinc complexes containing six- and seven-dentate ligands was evaluated through kinetic and³¹P NMR studies.

The Evolution of New Catalytic Mechanisms for Xenobiotic Hydrolysis in Bacterial Metalloenzymes

An increasing number of bacterial metalloenzymes have been shown to catalyse the breakdown of xenobiotics in the environment, while others exhibit a variety of promiscuous xenobiotic-degrading activities. Several different evolutionary processes have allowed these enzymes to gain or enhance xenobiotic-degrading activity. In this review, we have surveyed the range of xenobiotic-degrading metalloenzymes, and discuss the molecular and catalytic basis for the development of new activities. We also highlight how our increased understanding of the natural evolution of xenobiotic-degrading metalloenzymes can be been applied to laboratory enzyme design.

β-Lactam antibiotic-degrading enzymes from non-pathogenic marine organisms: a potential threat to human health

Metallo-β-lactamases (MBLs) are a family of Zn(II)-dependent enzymes that inactivate most of the commonly used β-lactam antibiotics. They have emerged as a major threat to global healthcare. Recently, we identified two novel MBL-like proteins, Maynooth IMipenemase-1 (MIM-1) and Maynooth IMipenemase-2 (MIM-2), in the marine organisms Novosphingobium pentaromativorans and Simiduia agarivorans, respectively. Here, we demonstrate that MIM-1 and MIM-2 have catalytic activities comparable to those of known MBLs, but from the pH dependence of their catalytic parameters it is evident that both enzymes differ with respect to their mechanisms, with MIM-1 preferring alkaline and MIM-2 acidic conditions. Both enzymes require Zn(II) but activity can also be reconstituted with other metal ions including Co(II), Mn(II), Cu(II) and Ca(II). Importantly, the substrate preference of MIM-1 and MIM-2 appears to be influenced by their metal ion composition. Since neither N. pentaromativorans nor S. agarivorans are human pathogens, the precise biological role(s) of MIM-1 and MIM-2 remains to be established. However, due to the similarity of at least some of their in vitro functional properties to those of known MBLs, MIM-1 and MIM-2 may provide essential structural insight that may guide the design of as of yet elusive clinically useful MBL inhibitors.

Catalytic mechanisms of metallohydrolases containing two metal ions

At least one-third of enzymes contain metal ions as cofactors necessary for a diverse range of catalytic activities. In the case of polymetallic enzymes (i.e., two or more metal ions involved in catalysis), the presence of two (or more) closely spaced metal ions gives an additional advantage in terms of (i) charge delocalisation, (ii) smaller activation barriers, (iii) the ability to bind larger substrates, (iv) enhanced electrostatic activation of substrates, and (v) decreased transition-state energies. Among this group of proteins, enzymes that catalyze the hydrolysis of ester and amide bonds form a very prominent family, the metallohydrolases. These enzymes are involved in a multitude of biological functions, and an increasing number of them gain attention for translational research in medicine and biotechnology. Their functional versatility and catalytic proficiency are largely due to the presence of metal ions in their active sites. In this chapter, we thus discuss and compare the reaction mechanisms of several closely related enzymes with a view to highlighting the functional diversity bestowed upon them by their metal ion cofactors.

Binuclear metallohydrolases: complex mechanistic strategies for a simple chemical reaction

Binuclear metallohydrolases are a large family of enzymes that require two closely spaced transition metal ions to carry out a plethora of hydrolytic reactions. Representatives include purple acid phosphatases (PAPs), enzymes that play a role in bone metabolism and are the only member of this family with a heterovalent binuclear center in the active form (Fe(3+)-M(2+), M = Fe, Zn, Mn). Other members of this family are urease, which contains a di-Ni(2+) center and catalyzes the breakdown of urea, arginase, which contains a di-Mn(2+) center and catalyzes the final step in the urea cycle, and the metallo-β-lactamases, which contain a di-Zn(2+) center and are virulence factors contributing to the spread of antibiotic-resistant pathogens. Binuclear metallohydrolases catalyze numerous vital reactions and are potential targets of drugs against a wide variety of human disorders including osteoporosis, various cancers, antibiotic resistance, and erectile dysfunctions. These enzymes also tend to catalyze more than one reaction. An example is an organophosphate (OP)-degrading enzyme from Enterobacter aerogenes (GpdQ). Although GpdQ is part of a pathway that is used by bacteria to degrade glycerolphosphoesters, it hydrolyzes a variety of other phosphodiesters and displays low levels of activity against phosphomono- and triesters. Such a promiscuous nature may have assisted the apparent recent evolution of some binuclear metallohydrolases to deal with situations created by human intervention such as OP pesticides in the environment. OP pesticides were first used approximately 70 years ago, and therefore the enzymes that bacteria use to degrade them must have evolved very quickly on the evolutionary time scale. The promiscuous nature of enzymes such as GpdQ makes them ideal candidates for the application of directed evolution to produce new enzymes that can be used in bioremediation and against chemical warfare. In this Account, we review the mechanisms employed by binuclear metallohydrolases and use PAP, the OP-degrading enzyme from Agrobacterium radiobacter (OPDA), and GpdQ as representative systems because they illustrate both the diversity and similarity of the reactions catalyzed by this family of enzymes. The majority of binuclear metallohydrolases utilize metal ion-activated water molecules as nucleophiles to initiate hydrolysis, while some, such as alkaline phosphatase, employ an intrinsic polar amino acid. Here we only focus on catalytic strategies applied by the former group.

Promiscuity comes at a price: catalytic versatility vs efficiency in different metal ion derivatives of the potential bioremediator GpdQ

The glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) is a highly promiscuous dinuclear metallohydrolase with respect to both substrate specificity and metal ion composition. While this promiscuity may adversely affect the enzyme's catalytic efficiency its ability to hydrolyse some organophosphates (OPs) and by-products of OP degradation have turned GpdQ into a promising candidate for bioremedial applications. Here, we investigated both metal ion binding and the effect of the metal ion composition on catalysis. The prevalent in vivo metal ion composition for GpdQ is proposed to be of the type Fe(II)Zn(II), a reflection of natural abundance rather than catalytic optimisation. The Fe(II) appears to have lower binding affinity than other divalent metal ions, and the catalytic efficiency of this mixed metal center is considerably smaller than that of Mn(II), Co(II) or Cd(II)-containing derivatives of GpdQ. Interestingly, metal ion replacements do not only affect catalytic efficiency but also the optimal pH range for the reaction, suggesting that different metal ion combinations may employ different mechanistic strategies. These metal ion-triggered modulations are likely to be mediated via an extensive hydrogen bond network that links the two metal ion binding sites via residues in the substrate binding pocket. The observed functional diversity may be the cause for the modest catalytic efficiency of wild-type GpdQ but may also be essential to enable the enzyme to evolve rapidly to alter substrate specificity and enhance k(cat) values, as has recently been demonstrated in a directed evolution experiment. This article is part of a Special Issue entitled: Chemistry and mechanism of phosphatases, diesterases and triesterases.

A Potentially Polymerizable Heterodinuclear FeIIIZnII Purple Acid Phosphatase Mimic. Synthesis, Characterization, and Phosphate Ester Hydrolysis Studies

An analogue of the purple acid phosphatase biomimetic 2-((bis(pyridin-2-ylmethyl)amino)methyl)-6-(((2-hydroxybenzyl)(pyridin-2-ylmethyl)amino)methyl)-4-methylphenol has been synthesized. The analogue, 2-((bis(pyridin-2-ylmethyl)amino)methyl)-6-(((2-hydroxy-4-(4-vinylbenzyloxy)benzyl)(pyridin-2-ylmethyl)amino)methyl)-4-methylphenol (H2BPBPMPV) possesses a pendant olefin suitable for copolymerization. Complexation with FeIII/ZnII resulted in the complex [FeIIIZnII(BPBPMPV)(CH3COO)2](ClO4), characterized with mass spectrometry, microanalysis, UV/vis, and IR spectrometry. The catalytic activity of the complex toward bis-(2,4-dinitrophenyl) phosphate was determined, resulting in Km of 4.1 ± 0.6 mM, with kcat 3.8 ± 0.2 × 10–3 s–1 and a bell-shaped pH–rate profile with pKa values of 4.31, 5.66, 8.96, the profile exhibiting residual activity above pH 9.5.

The divalent metal ion in the active site of uteroferrin modulates substrate binding and catalysis

The purple acid phosphatases (PAP) are binuclear metallohydrolases that catalyze the hydrolysis of a broad range of phosphomonoester substrates. The mode of substrate binding during catalysis and the identity of the nucleophile is subject to debate. Here, we used native Fe(3+)-Fe(2+) pig PAP (uteroferrin; Uf) and its Fe(3+)-Mn(2+) derivative to investigate the effect of metal ion substitution on the mechanism of catalysis. Replacement of the Fe(2+) by Mn(2+) lowers the reactivity of Uf. However, using stopped-flow measurements it could be shown that this replacement facilitates approximately a ten-fold faster reaction between both substrate and inorganic phosphate with the chromophoric Fe(3+) site. These data also indicate that in both metal forms of Uf, phenyl phosphate hydrolysis occurs faster than formation of a mu-1,3 phosphate complex. The slower rate of interaction between substrate and the Fe(3+) site relative to catalysis suggests that the substrate is hydrolyzed while coordinated only to the divalent metal ion. The likely nucleophile is a water molecule in the second coordination sphere, activated by a hydroxide terminally coordinated to Fe(3+). The faster rates of interaction with the Fe(3+) site in the Fe(3+)-Mn(2+) derivative than the native Fe(3+)-Fe(2+) form are likely mediated via a hydrogen bond network connecting the first and second coordination spheres, and illustrate how the selection of metal ions may be important in fine-tuning the function of this enzyme.

Substrate-promoted formation of a catalytically competent binuclear center and regulation of reactivity in a glycerophosphodiesterase from Enterobacter aerogenes

The glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes is a promiscuous binuclear metallohydrolase that catalyzes the hydrolysis of mono-, di-, and triester substrates, including some organophosphate pesticides and products of the degradation of nerve agents. GpdQ has attracted recent attention as a promising enzymatic bioremediator. Here, we have investigated the catalytic mechanism of this versatile enzyme using a range of techniques. An improved crystal structure (1.9 A resolution) illustrates the presence of (i) an extended hydrogen bond network in the active site, and (ii) two possible nucleophiles, i.e., water/hydroxide ligands, coordinated to one or both metal ions. While it is at present not possible to unambiguously distinguish between these two possibilities, a reaction mechanism is proposed whereby the terminally bound H2O/OH(-) acts as the nucleophile, activated via hydrogen bonding by the bridging water molecule. Furthermore, the presence of substrate promotes the formation of a catalytically competent binuclear center by significantly enhancing the binding affinity of one of the metal ions in the active site. Asn80 appears to display coordination flexibility that may modulate enzyme activity. Kinetic data suggest that the rate-limiting step occurs after hydrolysis, i.e., the release of the phosphate moiety and the concomitant dissociation of one of the metal ions and/or associated conformational changes. Thus, it is proposed that GpdQ employs an intricate regulatory mechanism for catalysis, where coordination flexibility in one of the two metal binding sites is essential for optimal activity.

Cadmium(II) complexes of the glycerophosphodiester-degrading enzyme GpdQ and a biomimetic N,O ligand

The glycerophosphodiester-degrading enzyme GpdQ from Enterobacter aerogenes is a promising bioremediator owing to its ability to degrade some organophosphate pesticides and diester products originating from the hydrolysis of nerve agents such as VX. Here, the cadmium derivative of GpdQ was prepared by reconstituting the apoenzyme. Catalytic measurements with (Cd(2+))(2)-GpdQ and the phosphodiester substrate bis(4-nitrophenyl)phosphate yield k(cat) = 15 s(-1). The pK(a) of 9.4, determined from the pH dependence of the catalytic activity, implicates a hydroxide ligand as the catalytic nucleophile. Also prepared was the cadmium-containing biomimetic [Cd(2)((HP)(2)B)(OAc)(2)(OH(2))](PF(6)) (where (HP)(2)B is [2,6-bis([(2-pyridylmethyl)(2-hydroxyethyl)amino]methyl)-4-methylphenol]), which mimics the asymmetry of the metal ion coordination in the active site of GpdQ. The phosphoesterase-like activity of [Cd(2)((HP)(2)B)(OAc)(2)(OH(2))](PF(6)) was studied using the substrate bis(2,4-dinitrophenyl)phosphate, yielding a kinetically relevant pK(a) of 8.9, with k(cat) = 0.004 s(-1). In summary, the model is both an adequate structural and a reasonable functional mimic of GpdQ.

Crystal structures of a purple acid phosphatase, representing different steps of this enzyme's catalytic cycle

BACKGROUND

Purple acid phosphatases belong to the family of binuclear metallohydrolases and are involved in a multitude of biological functions, ranging from bacterial killing and bone metabolism in animals to phosphate uptake in plants. Due to its role in bone resorption purple acid phosphatase has evolved into a promising target for the development of anti-osteoporotic chemotherapeutics. The design of specific and potent inhibitors for this enzyme is aided by detailed knowledge of its reaction mechanism. However, despite considerable effort in the last 10 years various aspects of the basic molecular mechanism of action are still not fully understood.

RESULTS

Red kidney bean purple acid phosphatase is a heterovalent enzyme with an Fe(III)Zn(II) center in the active site. Two new structures with bound sulfate (2.4 A) and fluoride (2.2 A) provide insight into the pre-catalytic phase of its reaction cycle and phosphorolysis. The sulfate-bound structure illustrates the significance of an extensive hydrogen bonding network in the second coordination sphere in initial substrate binding and orientation prior to hydrolysis. Importantly, both metal ions are five-coordinate in this structure, with only one nucleophilic mu-hydroxide present in the metal-bridging position. The fluoride-bound structure provides visual support for an activation mechanism for this mu-hydroxide whereby substrate binding induces a shift of this bridging ligand towards the divalent metal ion, thus increasing its nucleophilicity.

CONCLUSION

In combination with kinetic, crystallographic and spectroscopic data these structures of red kidney bean purple acid phosphatase facilitate the proposal of a comprehensive eight-step model for the catalytic mechanism of purple acid phosphatases in general.