Phosphate ester cleavage promoted by a tetrameric iron(III) complex

Synthesis, characterization and computational investigation of the phosphatase activity of a dinuclear Zinc(II) complex containing a new heptadentate asymmetric ligand

We report the synthesis of a new asymmetric heptadentate ligand based on the 1,3-diaminopropan-2-ol backbone. The ligand 3-[[3-(bis-pyridin-2-ylmethyl-amino)-2-hydroxy-propyl]-(2-carbamoyl-ethyl)-amino]-propionamide (HL1) contains two amide and two pyridine groups attached to the 1,3-diaminopropan-2-ol core. Reaction between HL1 and Zn(ClO₄)₂.6H₂O resulted in the formation of the dinuclear [Zn₂(L1)(μ-OAc)](ClO₄)₂ complex, characterized by single crystal X-ray diffraction, ¹H, ¹³C and ¹⁵N NMR, ESI-(+)-MS, CHN elemental analysis as well as infrared spectroscopy. The phosphatase activity of the complex was studied in the pH range 6-11 employing pyridinium bis(2,4-dinitrophenyl)phosphate (py(BDNPP)) as substrate. The complex exhibited activity dependent on the pH, presenting an asymmetric bell shape profile with the highest activity at pH 9; at high pH ligand exchange is rate-limiting. The hydrolysis of BDNPP^- at pH 9 displayed behavior characteristic of Michaelis-Menten kinetics, with k_cat = 5.06 × 10^-3 min^-1 and K_m = 5.7 ± 1.0 mM. DFT calculations map out plausible reaction pathways and identify a terminal, Zn(II)-bound hydroxide as likely nucleophile.

Dihydroxy‐Acid Dehydratases From Pathogenic Bacteria: Emerging Drug Targets to Combat Antibiotic Resistance

There is an urgent global need for the development of novel therapeutics to combat the rise of various antibiotic‐resistant superbugs. Enzymes of the branched‐chain amino acid (BCAA) biosynthesis pathway are an attractive target for novel anti‐microbial drug development. Dihydroxy‐acid dehydratase (DHAD) is the third enzyme in the BCAA biosynthesis pathway. It relies on an Fe−S cluster for catalytic activity and has recently also gained attention as a catalyst in cell‐free enzyme cascades. Two types of Fe−S clusters have been identified in DHADs, i.e. [2Fe−2S] and [4Fe−4S], with the latter being more prone to degradation in the presence of oxygen. Here, we characterise two DHADs from bacterial human pathogens, Staphylococcus aureus and Campylobacter jejuni (SaDHAD and CjDHAD). Purified SaDHAD and CjDHAD are virtually inactive, but activity could be reversibly reconstituted in vitro (up to ∼19,000‐fold increase with k_cat as high as ∼6.7 s⁻¹). Inductively‐coupled plasma‐optical emission spectroscopy (ICP‐OES) measurements are consistent with the presence of [4Fe−4S] clusters in both enzymes. N‐isopropyloxalyl hydroxamate (IpOHA) and aspterric acid are both potent inhibitors for both SaDHAD (K_i=7.8 and 51.6 μM, respectively) and CjDHAD (K_i=32.9 and 35.1 μM, respectively). These compounds thus present suitable starting points for the development of novel anti‐microbial chemotherapeutics.

LAM-1 from Lysobacter antibioticus: A potent zinc-dependent activity that inactivates β-lactam antibiotics

Resistance to β-lactam antibiotics, including the "last-resort" carbapenems, has emerged as a major threat to global health. A major resistance mechanism employed by pathogens involves the use of metallo-β-lactamases (MBLs), zinc-dependent enzymes that inactivate most of the β-lactam antibiotics used to treat infections. Variants of MBLs are frequently discovered in clinical environments. However, an increasing number of such enzymes have been identified in microorganisms that are less impacted by human activities. Here, an MBL from Lysobacter antibioticus, isolated from the rhizosphere, has been shown to be highly active toward numerous β-lactam antibiotics. Its activity is higher than that of some of the most effective MBLs linked to hospital-acquired antibiotic resistance and thus poses an interesting system to investigate evolutionary pressures that drive the emergence of such biocatalysts.

Homodinuclear copper(II) and zinc(II) complexes of a carboxylate-rich ligand as synthetic mimics of phosphoester hydrolase in aqueous solutions

The synthesis, characterization and catalytic activities of two homodinuclear Cu(II) and Zn(II) complexes of a carboxylate-rich ligand, N,N'-Bis[2-carboxybenzomethyl]-N,N' -Bis[carboxymethyl]-1,3-diaminopropan-2-ol (H₅ccdp) ligand towards the hydrolysis of (p-nitrophenyl phosphate) (PNPP) and bis(p-nitrophenyl) phosphate (BNPP) substrates in aqueous systems are described. Kinetic investigations were carried out using UV-Vis spectrophotometric techniques at 25 °C and 37 °C and different pH (7-10) conditions. The kinetic studies revealed that the turnover rate (k_cat) values among the PNPP hydrolysis systems, the highest and the lowest k_cat values were displayed by [Cu₂(ccdp)(μ-OAc)]^2- at 2.34 × 10^-6 s^-1 (pH 8 and 37 °C) and 2.13 × 10^-8 s^-1 (pH 8 and 25 °C), respectively. However, similar comparisons among the BNPP hydrolysis revealed that highest and the lowest k_cat values were displayed by [Zn₂(ccdp)(μ-OAc)]^2- at 4.64 × 10^-8 s^-1 (pH 9 and 37 °C) and 2.38 × 10^-9 (pH 9 and 25 °C). Significantly enough, the catalyst-substrate adduct species containing a metal bound PNPP and BNPP have been detected by ESI-MS techniques. Additionally, a PNPP-bound copper complex has been isolated and crystalized using single crystal X-ray diffraction technique. Based on the structural and activity information obtained in this study, reaction mechanisms for the hydrolysis of PNPP have been proposed.

Recent Advances in Heterogeneous Catalytic Systems Containing Metal Ions for Phosphate Ester Hydrolysis

Organophosphates are a class of organic compounds that are important for living organisms, forming the building blocks for DNA, RNA, and some essential cofactors. Furthermore, non-natural organophosphates are widely used in industrial applications, including as pesticides; in laundry detergents; and, unfortunately, as chemical weapons agents. In some cases, the natural degradation of organophosphates can take thousands of years; this longevity creates problems associated with handling and the storage of waste generated by such phosphate esters, in particular. Efforts to develop new catalysts for the cleavage of phosphate esters have progressed in recent decades, mainly in the area of homogeneous catalysis. In contrast, the development of heterogeneous catalysts for the hydrolysis of organophosphates has not been as prominent. Herein, examples of heterogeneous systems are described and the importance of the development of heterogeneous catalysts applicable to organophosphate hydrolysis is highlighted, shedding light on recent advances related to different solid matrices that have been employed.

Polynuclear zinc(II) complexes of thiosemicarbazone: Synthesis, X-ray structure and biological evaluation

Two new dimeric Zn(II) ([{ZnL¹(DMSO₂)}₂]·DMSO (1), [{ZnL²Cl}₂] (2)) and a novel tetrameric Zn(II) complex ([(Zn₂L³)₂(μ-OAc)₂(μ₃-O)₂] (3)), where H₂L¹ = 4-(p-methoxyphenyl) thiosemicarbazone of o-hydroxynapthaldehyde, HL² = 4-(p-methoxyphenyl)thiosemicarbazone of benzoyl pyridine and H₂L³ = 4-(p-chlorophenyl)thiosemicarbazone of o-vanillin are reported. Ligands and their complexes were characterized by spectroscopic and single crystal X-ray diffraction techniques. In addition, the complexes exhibited good binding affinity towards HSA (10¹² M^-1), which is supported by their ability to quench the tryptophan fluorescence emission spectra of HSA. The complexes were also screened for their DNA binding propensity through UV-vis absorption titration, circular dichroism and fluorescence spectral studies. Results show that they effectively interact with CT-DNA through an intercalative mode of binding, with binding constants ranging from 10³ to 10⁴ M^-1. Among the three complexes 1 has the highest binding affinity towards CT-DNA. Further, the phosphatase activity was evaluated using bis(2,4-dinitrophenyl)phosphate (BDNPP) as substrate, however, the complexes did not yield any measurable catalytic activity. Nevertheless the complexes showed significant cytotoxic potential against HeLa and HT-29 cancer cell lines that was assessed through MTT assay and DAPI staining. Remarkably, complex 1 showed better activity than cisplatin against HT-29 cell line.

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.

Reaction mechanism of the metallohydrolase CpsB from Streptococcus pneumoniae, a promising target for novel antimicrobial agents

CpsB is a metal ion-dependent hydrolase involved in the biosynthesis of capsular polysaccharides in bacterial organisms. The enzyme has been proposed as a promising target for novel chemotherapeutics to combat antibiotic resistance. The crystal structure of CpsB indicated the presence of as many as three closely spaced metal ions, modelled as Mn²⁺, in the active site. While the preferred metal ion composition in vivo is obscure Mn²⁺ and Co²⁺ have been demonstrated to be most effective in reconstituting activity. Using isothermal titration calorimetry (ITC) we have demonstrated that, in contrast to the crystal structure, only two Mn²⁺ or Co²⁺ ions bind to a monomer of CpsB. This observation is in agreement with magnetic circular dichroism (MCD) and electron paramagnetic resonance (EPR) data that indicate the presence of two weakly ferromagnetically coupled Co²⁺ ions in the active site of catalytically active CpsB. While CpsB is known to be a phosphoesterase we have also been able to demonstrate that this enzyme is efficient in hydrolyzing the β-lactam substrate nitrocefin. Steady-state and stopped-flow kinetics measurements further indicated that phosphoesters and nitrocefin undergo catalysis in a conserved manner with a metal ion-bridging hydroxide acting as a nucleophile. Thus, the combined physicochemical studies demonstrate that CpsB is a novel member of the dinuclear metallohydrolase family.

Dinuclear metal(ii)-acetato complexes based on bicompartmental 4-chlorophenolate: syntheses, structures, magnetic properties, DNA interactions and phosphodiester hydrolysis

A series of dinuclear metal(ii)-acetato complexes: [Ni2(μ-L(Cl)O)(μ2-OAc)2](PF6)·3H2O (1), [Ni2(μ-L(Cl)O)(μ2-OAc)2](ClO4)·CH3COCH3 (2), [Cu2(μ-L(Cl)O)(μ2-OAc)(ClO4)](ClO4) (3), [Cu2(μ-L(Cl)O)(OAc)2](PF6)·H2O (4), [Zn2(μ-L(Cl)O)(μ2-OAc)2](PF6) (5) and [Mn2(L(Cl)-O)(μ2-OAc)2](ClO4)·H2O (6), where L(Cl)O(-) = 2,6-bis[bis(2-pyridylmethyl)aminomethyl]-4-chlorophenolate, were synthesized. The complexes were structurally characterized by spectroscopic techniques and single crystal X-ray crystallography. Six-coordinate geometries with doubly bridged acetato ligands were found in Ni(ii), Zn(ii) and Mn(ii) complexes 1, 2, 5 and 6, whereas with Cu(ii) complexes a five-coordinate species was obtained with 4, and mixed five- and six-coordinate geometries with a doubly bridged dimetal core were observed in 3. The magnetic properties of complexes 1-4 and 6 were studied at variable temperatures and revealed weak to very weak antiferromagnetic interactions in 1, 2, 4 and 6 (J = -0.55 to -9.4 cm(-1)) and ferromagnetic coupling in 3 (J = 15.4 cm(-1)). These results are consistent with DFT calculations performed at the B3LYP/def2-TZVP(-f) level of theory. Under physiological conditions, the interaction of the dinculear complexes 1-5 with supercoiled plasmid ds-DNA did not show any pronounced nuclease activity, but Ni(ii) complexes 1 and 2 revealed a strong ability to unwind the supercoiled conformation of ds-DNA. The mechanistic studies performed on the interaction of the Ni(ii) complexes with DNA demonstrated the important impact of the nickel(ii) ion in the unwinding process. In combination with the DNA study, the phosphatase activity of complexes 1, 3, and 5 was examined by the phosphodiester hydrolysis of bis(2,4-dinitrophenol)phosphate (BDNPP) in the pH range of 5.5-10.5 at 25 °C. The Michaelis-Menten kinetics performed at pH 7 and 10.7 showed that catalytic efficiencies kcat/KM (kcat = catalytic rate constant, KM = substrate binding constant) decrease in the order: Ni(ii), 1 > Zn(ii), 5 > Cu(ii), 3. A similar trend was also observed with the turnover numbers at pH = 7. The results are discussed in relation to the coordination geometry and nature of the metal center as well as the steric environment imposed by the compartmental phenoxido ligand.

Remarkable reactivity of alkoxide/acetato-bridged binuclear copper(II) complex as artificial carboxylesterase

Bromo-containing binuclear Schiff base copper(II) complex, Cu₂L(OAc), with an alkoxo/acetato-bridged moiety was employed as a model of carboxylesterases to promote the hydrolytic cleavage of p-nitrophenyl picolinate (PNPP). Furthermore, the reactivity of a mononuclear complex (CuHL) was evaluated for comparing it with that of binuclear one. The results reveal that the as-prepared binuclear Cu₂L(OAc) efficiently accelerated the hydrolysis of PNPP, giving rise to excess four orders of magnitude rate enhancement in contrast to the un-catalyzed reaction. Cu₂L(OAc) represented an enzyme-like bell-shaped pH-responsive kinetic behavior. Moreover, the binuclear one is more reactive than its mononuclear analogue (CuHL) by two orders of magnitude. The total efficiency of Cu₂L(OAc) is about 61-fold than that of its mononuclear analogue, CuHL. In addition, a contrast experiment reveals that binuclear Cu₂L(OAc) displayed good activity in the hydrolysis of PNPP as well another active ester, i.e., S-2-benzothiazolyl 2-amino-alpha-(methoxyimino)-4-thiazolethiolacetate (AE-active ester). Noteworthyly, it was found that mononuclear one inspired more obvious rate enhancement in the hydrolysis of AE-active ester relative to PNPP hydrolysis. The estimated pK _a1 of bound water on the binuclear Cu₂L(OAc) using second derivative method (SDM) is relatively smaller than that for CuHL by a gap of about 0.8 pK unit, which facilitates the hydrolysis of PNPP. Four orders of magnitude rate enhancement was observed for the catalytic hydrolysis of p-nitrophenyl picolinate (PNPP) by one μ-alkoxide/acetato-bridged binuclear copper(II) complex under physiological conditions. Substrate specificity of the resulting binuclear complexes was observed for the hydrolysis of PNPP and AE-active ester.

Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community

Microorganisms in the permafrost contain a potent mechanism to inactivate antibiotics.

Product release is rate-limiting for catalytic processing by the Dengue virus protease

Dengue Virus (DENV) is the most prevalent global arbovirus, yet despite an increasing burden to health care there are currently no therapeutics available to treat infection. A potential target for antiviral drugs is the two-component viral protease NS2B-NS3pro, which is essential for viral replication. Interactions between the two components have been investigated here by probing the effect on the rate of enzyme catalysis of key mutations in a mobile loop within NS2B that is located at the interface of the two components. Steady-state kinetic assays indicated that the mutations greatly affect catalytic turnover. However, single turnover and fluorescence experiments have revealed that the mutations predominantly affect product release rather than substrate binding. Fluorescence analysis also indicated that the addition of substrate triggers a near-irreversible change in the enzyme conformation that activates the catalytic centre. Based on this mechanistic insight, we propose that residues within the mobile loop of NS2B control product release and present a new target for design of potent Dengue NS2B-NS3 protease inhibitors.

Metal Ions Play an Essential Catalytic Role in the Mechanism of Ketol-Acid Reductoisomerase

Ketol-acid reductoisomerase (KARI) is a Mg(2+) -dependent enzyme in the branched-chain amino acid biosynthesis pathway. It catalyses a complex two-part reaction: an alkyl migration followed by a NADPH-dependent reduction. Both reactions occur within the one active site, but in particular, the mechanism of the isomerisation step is poorly understood. Here, using a combination of kinetic, thermodynamic and spectroscopic techniques, the reaction mechanisms of both Escherichia coli and rice KARI have been investigated. We propose a conserved mechanism of catalysis, whereby a hydroxide, bridging the two Mg(2+) ions in the active site, initiates the reaction by abstracting a proton from the C2 alcohol group of the substrate. While the μ-hydroxide-bridged dimetallic centre is pre-assembled in the bacterial enzyme, in plant KARI substrate binding leads to a reduction of the metal-metal distance with the concomitant formation of a hydroxide bridge. Only Mg(2+) is capable of promoting the isomerisation reaction, likely to be due to non-competent substrate binding in the presence of other metal ions.

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.

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.