Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis

How cyanophage S-2L rejects adenine and incorporates 2-aminoadenine to saturate hydrogen bonding in its DNA

Bacteriophages have long been known to use modified bases in their DNA to prevent cleavage by the host's restriction endonucleases. Among them, cyanophage S-2L is unique because its genome has all its adenines (A) systematically replaced by 2-aminoadenines (Z). Here, we identify a member of the PrimPol family as the sole possible polymerase of S-2L and we find it can incorporate both A and Z in front of a T. Its crystal structure at 1.5 Å resolution confirms that there is no structural element in the active site that could lead to the rejection of A in front of T. To resolve this contradiction, we show that a nearby gene is a triphosphohydolase specific of dATP (DatZ), that leaves intact all other dNTPs, including dZTP. This explains the absence of A in S-2L genome. Crystal structures of DatZ with various ligands, including one at sub-angstrom resolution, allow to describe its mechanism as a typical two-metal-ion mechanism and to set the stage for its engineering.

A method for the transient inhibition of toxicity of secretory recombinant proteins, exemplified by bacterial alkaline phosphatase. Novel protocol for problematic DNA termini dephosphorylation

Genes encoding proteins 'toxic' to recombinant host are difficult for cloning/expression and recombinant clones are unstable. Even tightly controlled inducible T7-lac, PBAD, PL, PR promoters are not totally silent in an uninduced state and thus not adequate for highly toxic proteins. An innovative approach to engineering and expression of the gene, encoding bacterial alkaline phosphatase (BAP) is proposed. The native precursor enzyme contains a signal peptide at the N-terminus and is secreted to the Escherichia coli (E. coli) periplasm. The signal peptide is then removed that allows oxidation and formation of active dimers. To decrease toxicity of the bap gene, its secretion leader coding section was replaced with a N-terminal His6-tag. The gene was expressed in E. coli in a PBAD vector, resulting in the accumulation of soluble His6-BAP in the cytoplasm. The His6-BAP was neutral to the cells, as no maturation was possible in the reducing cytoplasm. The purified homogenous protein was further reactivated in a redox buffer containing the protein structure stabilizing cofactors. The His6-BAP exhibited high activity. A dephosphorylation protocol for all types of DNA termini was developed.The method appears well suited for the industrial production of BAP and can be applied to other problematic proteins.• Efficient toxic gene expression • Novel approach to toxic gene cloning, engineering, expression, purification and reactivation of the transiently inactivated enzyme • Scaled-up production of ultrapure BAP • Improved protocol for all types of DNA termini dephosphorylation.

Dynamic cross correlation analysis of Thermus thermophilus alkaline phosphatase and determinants of thermostability

BACKGROUND

Understanding the determinants of protein thermostability is very important both from the theoretical and applied perspective. One emerging view in thermostable enzymes seems to indicate that a salt bridge/charged residue network plays a fundamental role in their thermostability.

METHODS

The structure of alkaline phosphatase (AP) from Thermus thermophilus HB8 was solved by X-ray crystallography at 2.1 Å resolution. The obtained structure was further analyzed by molecular dynamics studies at different temperatures (303 K, 333 K and 363 K) and compared to homologous proteins from the cold-adapted organisms Shewanella sp. and Vibrio strain G15-21. To analyze differences in measures of dynamic variation, several data reduction techniques like principal component analysis (PCA), residue interaction network (RIN) analysis and rotamer analysis were used. Using hierarchical clustering, the obtained results were combined to determine residues showing high degree dynamical variations due to temperature jumps. Furthermore, dynamic cross correlation (DCC) analysis was carried out to characterize networks of charged residues.

RESULTS

Top clustered residues showed a higher propensity for thermostabilizing mutations, indicating evolutionary pressure acting on thermophilic organisms. The description of rotamer distributions by Gini coefficients and Kullback-Leibler (KL) divergence both revealed significant correlations with temperature. DCC analysis revealed a significant trend to de-correlation of the movement of charged residues at higher temperatures.

SIGNIFICANCE

The de-correlation of charged residues detected in Thermus thermophilus AP, highlights the importance of dynamic electrostatic network interactions for the thermostability of this enzyme.

Alkaline Phosphatases: in Silico Study on the Catalytic Effect of Conserved Active Site Residues Using Human Placental Alkaline Phosphatase (PLAP) As a Model Protein

The metalloenzymes from the alkaline phosphatase (AP) superfamily catalyze the hydrolysis and transphosphorylation of phosphate monoesters. The role of several amino acids highly conserved in the active site of this family of enzymes was examined, using human placental AP (PLAP) as a model protein. By employing an active-site model based on the X-ray crystal structure of PLAP, mutations of several key residues were modeled by quantum mechanical methods in order to determine their impact on the catalytic activity. Kinetic and thermodynamic estimations were achieved for each reaction step of the catalytic mechanism by characterization of the intermediates and transition states on the reaction pathway, and the effects of mutations on the activation barriers were analyzed. A good accordance was observed between the present computational results and experimental measurements reported in the literature.

In vitro and in silico evaluation of the inhibitory effect of a curcumin-based oxovanadium (IV) complex on alkaline phosphatase activity and bacterial biofilm formation

The scientific interest in the development of novel metal-based compounds as inhibitors of bacterial biofilm-related infections and alkaline phosphatase (ALP) deregulating effects is continuous and rising. In the current study, a novel crystallographically defined heteroleptic V(IV)-curcumin-bipyridine (V-Cur) complex with proven bio-activity was studied as a potential inhibitor of ALP activity and bacterial biofilm. The inhibitory effect of V-Cur was evaluated on bovine ALP, with two different substrates: para-nitrophenyl phosphate (pNPP) and adenosine triphosphate (ATP). The obtained results suggested that V-Cur inhibited the ALP activity in a dose-dependent manner (IC₅₀ = 26.91 ± 1.61 μM for ATP, IC₅₀ = 2.42 ± 0.12 μM for pNPP) exhibiting a mixed/competitive type of inhibition with both substrates tested. The evaluation of the potential V-Cur inhibitory effect on bacterial biofilm formation was performed on Gram (+) bacteria Staphylococcus aureus (S. aureus) and Gram (-) Escherichia coli (E. coli) cultures, and it positively correlated with inhibition of bacterial ALP activity. In silico study proved the binding of V-Cur at eukaryotic and bacterial ALP, and its interaction with crucial amino acids of the active sites, verifying complex's inhibitory potential. The findings suggested a specific anti-biofilm activity of V-Cur, offering a further dimension in the importance of metal complexes, with naturally derived products as biological ligands, as therapeutic agents against bacterial infections and ALP-associated diseases. KEY POINTS: • V-Cur inhibits bovine and bacterial alkaline phosphatases and bacterial biofilm formation. • Alkaline phosphatase activity correlates with biofilm formation. • In silico studies prove binding of the complex on alkaline phosphatase.

Boosting toxic protein biosynthesis: transient in vivo inactivation of engineered bacterial alkaline phosphatase

BACKGROUND

The biotechnology production of enzymes is often troubled by the toxicity of the recombinant products of cloned and expressed genes, which interferes with the recombinant hosts' metabolism. Various approaches have been taken to overcome these limitations, exemplified by tight control of recombinant genes or secretion of recombinant proteins. An industrial approach to protein production demands maximum possible yields of biosynthesized proteins, balanced with the recombinant host's viability. Bacterial alkaline phosphatase (BAP) from Escherichia coli (E. coli) is a key enzyme used in protein/antibody detection and molecular cloning. As it removes terminal phosphate from DNA, RNA and deoxyribonucleoside triphosphates, it is used to lower self-ligated vectors' background. The precursor enzyme contains a signal peptide at the N-terminus and is secreted to the E. coli periplasm. Then, the leader is clipped off and dimers are formed upon oxidation.

RESULTS

We present a novel approach to phoA gene cloning, engineering, expression, purification and reactivation of the transiently inactivated enzyme. The recombinant bap gene was modified by replacing a secretion leader coding section with a N-terminal His6-tag, cloned and expressed in E. coli in a P_BAD promoter expression vector. The gene expression was robust, resulting in accumulation of His6-BAP in the cytoplasm, exceeding 50% of total cellular proteins. The His6-BAP protein was harmless to the cells, as its natural toxicity was inhibited by the reducing environment within the E. coli cytoplasm, preventing formation of the active enzyme. A simple protocol based on precipitation and immobilized metal affinity chromatography (IMAC) purification yielded homogeneous protein, which was reactivated by dialysis into a redox buffer containing reduced and oxidized sulfhydryl group compounds, as well as the protein structure stabilizing cofactors Zn²⁺, Mg²⁺ and phosphate. The reconstituted His6-BAP exhibited high activity and was used to develop an efficient protocol for all types of DNA termini, including problematic ones (blunt, 3'-protruding).

CONCLUSIONS

The developed method appears well suited for the industrial production of ultrapure BAP. Further, the method of transient inactivation of secreted toxic enzymes by conducting their biosynthesis in an inactive state in the cytoplasm, followed by in vitro reactivation, can be generally applied to other problematic proteins.

Applications of fluorescent materials in the detection of alkaline phosphatase activity

Alkaline phosphatase (ALP) is important in the diagnosis of many diseases. Because ALP is used to detect biomarkers for many diseases, many researchers conduct investigations to develop ALP detection strategies. The use of fluorescent material has attracted attention because of the technique's high sensitivity and the low sample volume required. Herein, we review and discuss the working mechanisms and advantages of four main categories:DNA fluorescent probes, molecular fluorescent probes, chemical coordination-based probes, and nanoparticle probes. Development prospects and trends are also discussed.

Executing a Series of Zinc(II) Complexes of Homologous Schiff Base Ligands for a Comparative Analysis on Hydrolytic, Antioxidant, and Antibacterial Activities

Six zinc(II) complexes, namely, [Zn(HL¹H)Cl₂] (1), [Zn(HL¹H)Br₂] (2), [Zn₂(HL¹H)₂(OH)I₂]·I (3), [Zn(HL²)Cl] (4), [Zn₂(HL²)Br₃] (5), and [Zn(HL²)I] (6) have been manufactured by using two homologous Schiff base ligands H₂L¹ and H₂L² for the purpose of perlustrating their phosphatase-like activity, antioxidant activity, and antibacterial activity. Complexes 1, 2, 4, and 5 have been reported earlier by us, whereas complexes 3 and 6 have been synthesized and structurally characterized by regular physicochemical methods The hydrolytic property of the six complexes has been evaluated by checking the hydrolysis of the P-O bond of a widely used substrate, namely, disodium salt of (para-nitrophenyl)phosphate (PNPP) in 97.5% (v/v) mixture of N,N-dimethylformamide and water (DMF-water). Complexes 2-5 have profound efficiency toward hydrolysis of phosphate ester bonds, and complexes 1 and 6 were noted to be inactive toward hydrolysis. Complex 3 displayed the highest efficacy among the six complexes. Additionally, antioxidant and antibacterial activities of the complexes were studied thoroughly. A detailed study of their antioxidant property revealed that complex 3 manifested superior radical scavenging activity, thus exhibiting the highest antioxidant property. The antibacterial activity was tested using four investigating bacteria, specifically Listeria monocytogenes ATCC19111, Staphylococcus aureus ATCC 700699, Salmonella typhimurium ATCC 23564, and Escherichia coli ATCC 25922 by determining minimum inhibitory concentration (MIC) values using the microdilution method. Here as well, complex 3 exhibited the highest activity to both Gram positive and Gram negative bacteria. The chemistry behind these experimental findings has been manifested by shedding light upon the structural features of the complexes. The suitable choice of ligand H₂L¹ where one methylene group is less than its homologous ligand and metal precursor (ZnI₂) imparts a unique hydroxo-bridged molecular geometry and 2D hydrogen bonding network which in turn probably enhances the hydrolytic and biological activities of complex 3.

Binuclear and tetranuclear Zn(ii) complexes with thiosemicarbazones: synthesis, X-ray crystal structures, ATP-sensing, DNA-binding, phosphatase activity and theoretical calculations

Two Zinc(ii) complexes [Zn₄(L¹)₄]·2H₂O (1) and [Zn₂(L²)₂]·2H₂O (2) of pyruvaldehydethiosemicarbazone ligands are reported. The complexes were characterized by elemental analysis, IR, NMR, UV-vis spectroscopy and by single-crystal X-ray crystallography. X-ray crystal structure determinations of the complexes show that though Zn : ligand stoichiometry is 1 : 1 in both the complexes, the molecular unit is tetranuclear for 1 and binuclear for 2. Both the complexes show selective sensing of ATP at pH 7.4 (0.01 M HEPES) in CH₃CN–H₂O (9 : 1) medium in the presence of other anions like AcO⁻, NO₃⁻, F⁻, Cl⁻, H₂PO₄⁻, HPO₄²⁻ and P₂O₇²⁻. The UV-titration experiments of complexes 1 and 2 with ATP results in binding constants of 2.0(±0.07) × 10⁴ M⁻¹ and 7.1(±0.05) × 10³ M⁻¹ respectively. The calculated detection limits of 6.7 μM and 1.7 μM for 1 and 2 respectively suggest that the complexes are sensitive detectors of ATP. High selectivity of the complexes is confirmed by the addition of ATP in presence of an excess of other anions. DFT studies confirm that the ATP complexes are more favorable than those with the other inorganic phosphate anions, in agreement with the experimental results. Phosphatase like activity of both complexes is investigated spectrophotometrically using 4-nitrophenylphosphate (NPP) as a substrate, indicating the complexes possess significant phosphate ester hydrolytic efficiency. The kinetics for the hydrolysis of the substrate NPP was studied by the initial rate method at 25 °C. Michaelis–Menten derived kinetic parameters indicate that rate of hydrolysis of the P–O bond by complex 1 is much greater than that of complex 2, the k_cat values being 212(±5) and 38(±2) h⁻¹ respectively. The DNA binding studies of the complexes were investigated using electronic absorption spectroscopy and fluorescence quenching. The absorption spectral titrations of the complexes with DNA indicate that the CT-DNA binding affinity (K_b) of complex 1 (2.10(±0.07) × 10⁶ M⁻¹) is slightly greater than that of 2 (1.11(±0.04) × 10⁶ M⁻¹). From fluorescence spectra the apparent binding constant (K_app) values were calculated and they are found to be 5.41(±0.01) × 10⁵ M⁻¹ for 1 and 3.93(±0.02) × 10⁵ M⁻¹ for 2. The molecular dynamics simulation demonstrates that the Zn(ii) complex 1 is a good intercalator of DNA.

A binuclear and a tetranuclear zinc(ii) of pyruvaldehyde thiosemicarbazone show selective sensing of ATP at pH 7.4 (0.01 M HEPES) in CH₃CN–H₂O (9 : 1) medium. The DNA binding and phosphatase activities of the complexes are also reported.

Zinc(ii) and copper(ii) complexes as tools to monitor/inhibit protein phosphorylation events

A perspective on the advance of copper(ii) and zinc(ii) complexes of varied ligand architectures as binders of phosphorylated peptides/proteins and as sensors of phosphorylation reactions is presented.

Resistance to the “last resort” antibiotic colistin: a single-zinc mechanism for phosphointermediate formation in MCR enzymes

Simulations show the mono-zinc form of MCR to be stable and competent for covalent phospho(ethanolamine) intermediate formation.

A novel phospho-modulatory mechanism contributes to the calcium-dependent regulation of T-type Ca2+ channels

Ca_v3 / T-type Ca²⁺ channels are dynamically regulated by intracellular Ca²⁺ ions, which inhibit Ca_v3 availability. Here, we demonstrate that this inhibition becomes irreversible in the presence of non-hydrolysable ATP analogs, resulting in a strong hyperpolarizing shift in the steady-state inactivation of the residual Ca_v3 current. Importantly, the effect of these ATP analogs was prevented in the presence of intracellular BAPTA. Additional findings obtained using intracellular dialysis of inorganic phosphate and alkaline phosphatase or NaN₃ treatment further support the involvement of a phosphorylation mechanism. Contrasting with Ca_v1 and Ca_v2 Ca²⁺ channels, the Ca²⁺-dependent modulation of Ca_v3 channels appears to be independent of calmodulin, calcineurin and endocytic pathways. Similar findings were obtained for the native T-type Ca²⁺ current recorded in rat thalamic neurons of the central medial nucleus. Overall, our data reveal a new Ca²⁺ sensitive phosphorylation-dependent mechanism regulating Ca_v3 channels, with potentially important physiological implications for the multiple cell functions controlled by T-type Ca²⁺ channels.

Transcriptome profiling analysis of the intoxication response in midgut tissue of Agrotis ipsilon larvae to Bacillus thuringiensis Vip3Aa protoxin

Vip insecticidal proteins are produced by Bacillus thuringiensis (Bt) during its vegetative growth phase. In the present study, Vip3Aa11 and Vip3Aa39 proteins were investigated. These two proteins present 39 amino acid differential sites and they shared 95.06% amino acid sequence similarity. They are effective against some Lepidoptera insect larvae. In a previous study, using artificial diet bioassays, we estimated the LC₅₀ of Vip3Aa11 and Vip3Aa39 strains against Agrotis ipsilon larvae were 73.41 μg/mL (with 95% confidence interval of 2.34-11.19) and 5.43 μg/mL (with 95% confidence interval of 43.20-115.03), respectively. To investigate the response of Agrotis ipsilon transcriptome in defending against Vip3Aa11 and Vip3Aa39 toxins, we performed high-throughput RNA-sequencing on cDNA generated from the midguts of Agrotis ipsilon larvae that consumed a control diet (CK-M-A), Vip3Aa11 (Vip3Aa11-M-A) and Vip3Aa39 (Vip3Aa39-M-A) proteins. We generated about 98.87 Gb bases in total on BGISEQ-500 sequencing platform. After assembling all samples together and filtering the abundance, we got 51,887 unigenes, the total length, average length, N50 and GC content of unigenes are 64,523,651 bp, 1243 bp, 2330 bp and 41.81% respectively. We revealed 558 midgut genes differential expressed in Vip3Aa11-M-A and 65 midgut genes differentially expressed in Vip3Aa39-M-A. The differentially expressed genes were enriched for serine proteases and potential Bt Vip toxin midgut receptor genes. Eleven serine proteases related genes and 13 Bt toxin potential receptor genes with differential expression were found. Based on transcriptome profiling, we focused on validation the sensitivity of these two Vip3Aa proteins to trypsin and their binding properties to Agrotis ipsilon midgut BBMV (Brush Border Membrane Vesicles). The results show that the sensitivity of the two proteins to trypsin is similar. Binding experiments revealed that both proteins can bind to Agrotis ipsilon midgut BBMV, and there is a competitive binding between them. This transcriptome dataset provided a comprehensive sequence resource of Agrotis ipsilon and provides a foundation for comparative studies with other species of insects.

Mechanism of catalysis and inhibition of Mycobacterium tuberculosis SapM, implications for the development of novel antivirulence drugs

Mycobacterium tuberculosis (Mtb) SapM is a secreted virulence factor critical for intracellular survival of the pathogen. The role of SapM in phagosome maturation arrest in host macrophages suggests its potential as a drug target to assist in the clearance of tuberculosis infection. However, the mechanism of action of SapM at the molecular level remains unknown. In this study, we provide new insights into the mechanism of catalysis, substrate specificity and inhibition of SapM, and we identify the critical residues for catalysis and substrate binding. Our findings demonstrate that SapM is an atypical monoester alkaline phosphatase, with a serine-based mechanism of catalysis probably metal-dependent. Particularly relevant to SapM function and pathogenesis, is its activity towards PI(4,5)P₂ and PI3P, two phosphoinositides that function at the early stages of microbial phagocytosis and phagosome formation. This suggests that SapM may have a pleiotropic role with a wider importance on Mtb infection than initially thought. Finally, we have identified two inhibitors of SapM, L-ascorbic acid and 2-phospho-L-ascorbic, which define two different mechanisms by which the catalytic activity of this phosphatase could be regulated. Critically, we demonstrate that 2-phospho-L-ascorbic reduces mycobacterial survival in macrophage infections, hence confirming the potential of SapM as a therapeutic drug target.

Catalytic Hydrolysis of Phosphate Monoester by Supramolecular Complexes Formed by the Self-Assembly of a Hydrophobic Bis(Zn2+-cyclen) Complex, Copper, and Barbital Units That Are Functionalized with Amino Acids in a Two-Phase Solvent System

We previously reported on the preparation of supramolecular complexes by the 2:2:2 assembly of a dinuclear Zn²⁺-cyclen (cyclen = 1,4,7,10-tetraazacyclododecane) complex having a 2,2′-bipyridyl linker equipped with 0~2 long alkyl chains (Zn₂L¹~Zn₂L³), 5,5-diethylbarbituric acid (Bar) derivatives, and a copper(II) ion (Cu²⁺) in aqueous solution and two-phase solvent systems and their phosphatase activities for the hydrolysis of mono(4-nitrophenyl) phosphate (MNP). These supermolecules contain Cu₂(μ-OH)₂ core that mimics the active site of alkaline phosphatase (AP), and one of the ethyl groups of the barbital moiety is located in close proximity to the Cu₂(μ-OH)₂ core. The generally accepted knowledge that the amino acids around the metal center in the active site of AP play important roles in its hydrolytic activity inspired us to modify the side chain of Bar with various functional groups in an attempt to mimic the active site of AP in the artificial system, especially in two-phase solvent system. In this paper, we report on the design and synthesis of new supramolecular complexes that are prepared by the combined use of bis(Zn²⁺-cyclen) complexes (Zn₂L¹, Zn₂L², and Zn₂L³), Cu²⁺, and Bar derivatives containing amino acid residues. We present successful formation of these artificial AP mimics with respect to the kinetics of the MNP hydrolysis obeying Michaelis–Menten scheme in aqueous solution and a two-phase solvent system and to the mode of the product inhibition by inorganic phosphate.

Fluorometric and Colorimetric Dual-Readout Immunoassay Based on an Alkaline Phosphatase-Triggered Reaction

Alkaline phosphatase (ALP) usually acts as a signal transmitter in enzyme-linked immunosorbent assay (ELISA); therefore, developing an attractive ALP activity assay, especially using a preferable substrate, would help improve the efficiency and convenience of ELISA in practical applications. Herein we have first prepared an original and creative substrate, named m-hydroxyphenyl phosphate sodium salt ( m-HPP), with a desirable dephosphorylation site for ALP. On the basis of the ALP-catalyzed hydrolysis of m-HPP to resorcinol and its subsequent specific nucleophilic reaction with dopamine, we have exploited a fluorometric and colorimetric dual-readout ALP activity assay and ALP-based ELISA system. Under the employed experimental conditions, highly sensitive and specific assay of ALP and cardiac troponin I (cTnI) has been accomplished in a straightforward way. Furthermore, the commendable sensing performance of our proposed ELISA in the determination of the cTnI level in diluted human serum unambiguously illustrates great potential in the early diagnosis of acute myocardial infarction.

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.

Probing the high potency of pyrazolyl pyrimidinetriones and thioxopyrimidinediones as selective and efficient non-nucleotide inhibitors of recombinant human ectonucleotidases

With the aim to discover novel, efficient and selective inhibitors of human alkaline phosphatase and nucleotide pyrophosphatase enzymes, two new series of pyrazolyl pyrimidinetriones (PPTs) (6a-g) and thioxopyrimidinediones (PTPs) (6h-n) were synthesized in good chemical yields using Knoevenagel condensation reaction between pyrazole carbaldehydes (4a-g) and pharmacologically active N-alkylated pyrimidinetrione (5a) and thioxopyrimidinedione (5b). The inhibition potential of the synthesized hybrid compounds was evaluated against human alkaline phosphatase (h-TNAP and h-IAP) and ectonucleotidase (h-NPP1 and h-NPP3) enzymes. Most of the tested analogs were highly potent with a variable degree of inhibition depending on the functionalized hybrid structure. The detailed structure-activity relationship (SAR) of PPT and PTP derivatives suggested that the compound with unsubstituted phenyl ring from PPT series led to selective and potent inhibition (6a; IC₅₀ = 0.33 ± 0.02 µM) of h-TNAP, whereas compound 6c selectively inhibited h-IAP isozyme with IC₅₀ value of 0.86 ± 0.04 µM. Similarly, compounds 6b and 6h were identified as the lead scaffolds against h-NPP1 and h-NPP3, respectively. The probable binding modes for the most potent inhibitors were elucidated through molecular docking analysis. Structure-activity relationships, mechanism of action, cytotoxic effects and druglikeness properties are also discussed.

Anastrozole Aromatase Inhibitor Plasma Drug Concentration Genome-Wide Association Study: Functional Epistatic Interaction Between SLC38A7 and ALPPL2

Anastrozole is a widely prescribed aromatase inhibitor for the therapy of estrogen receptor positive (ER+) breast cancer. We performed a genome‐wide association study (GWAS) for plasma anastrozole concentrations in 687 postmenopausal women with ER+ breast cancer. The top single‐nucleotide polymorphism (SNP) signal mapped across SLC38A7 (rs11648166, P = 2.3E‐08), which we showed to encode an anastrozole influx transporter. The second most significant signal (rs28845026, P = 5.4E‐08) mapped near ALPPL2 and displayed epistasis with the SLC38A7 signal. Both of these SNPs were cis expression quantitative trait loci (eQTL)s for these genes, and patients homozygous for variant genotypes for both SNPs had the highest drug concentrations, the highest SLC38A7 expression, and the lowest ALPPL2 expression. In summary, our GWAS identified a novel gene encoding an anastrozole transporter, SLC38A7, as well as epistatic interaction between SNPs in that gene and SNPs near ALPPL2 that influenced both the expression of the transporter and anastrozole plasma concentrations.

Transition-State Interactions in a Promiscuous Enzyme: Sulfate and Phosphate Monoester Hydrolysis by Pseudomonas aeruginosa Arylsulfatase

Pseudomonas aeruginosa arylsulfatase (PAS) hydrolyzes sulfate and, promiscuously, phosphate monoesters. Enzyme-catalyzed sulfate transfer is crucial to a wide variety of biological processes, but detailed studies of the mechanistic contributions to its catalysis are lacking. We present linear free energy relationships (LFERs) and kinetic isotope effects (KIEs) of PAS and analyses of active site mutants that suggest a key role for leaving group (LG) stabilization. In LFERs PASWT has a much less negative Brønsted coefficient (βleaving groupobs-Enz = -0.33) than the uncatalyzed reaction (βleaving groupobs = -1.81). This situation is diminished when cationic active site groups are exchanged for alanine. The considerable degree of bond breaking during the transition state (TS) is evidenced by an 18Obridge KIE of 1.0088. LFER and KIE data for several active site mutants point to leaving group stabilization by active site K375, in cooperation with H211. 15N KIEs and the increased sensitivity to leaving group ability of the sulfatase activity in neat D2O (Δβleaving groupH-D = +0.06) suggest that the mechanism for S-Obridge bond fission shifts, with decreasing leaving group ability, from charge compensation via Lewis acid interactions toward direct proton donation. 18Ononbridge KIEs indicate that the TS for PAS-catalyzed sulfate monoester hydrolysis has a significantly more associative character compared to the uncatalyzed reaction, while PAS-catalyzed phosphate monoester hydrolysis does not show this shift. This difference in enzyme-catalyzed TSs appears to be the major factor favoring specificity toward sulfate over phosphate esters by this promiscuous hydrolase, since other features are either too similar (uncatalyzed TS) or inherently favor phosphate (charge).

Mechanism of Intramolecular Nucleophilic Substitution in the Catalytic Hydrolysis of Bis(4-Nitrophenyl) Phosphate Ester in a Metallomicelle

A macrocyclic Schiff base ligand and the corresponding Cu(II) and Ni(II) complexes were synthesized and characterized. The catalytic ability of metallomicelles, made from these complexes and micelles, as mimic hydrolytic metalloenzymes, was investigated in the catalytic hydrolysis of bis(p-nitrophenyl) phosphate (BNPP). The rate of the BNPP catalytic reaction in the metallomicelles is ca 2.0 × 106-fold faster than that of the spontaneous hydrolysis of BNPP in aqueous solution under the same conditions. The analysis of absorption spectra of the hydrolytic reaction systems indicates that key intermediates, comprising BNPP and the Ni(II) or Cu(II) complexes, have been formed and the catalytic hydrolysis of BNPP is an intramolecular nucleophilic substitution reaction. Based on the analysis of the absorption spectrum, a mechanism for the catalytic hydrolysis of BNPP has been proposed and a kinetic mathematical model has been established.

Comparative studies on the interaction between biogenic polyamines and bovine intestinal alkaline phosphatases: spectroscopic and theoretical approaches

In this work, the effect of two organic polyamines (spermine and spermidine) on the fluorescence intensity and activity of bovine intestinal alkaline phosphatase (BIALP) are investigated. The interaction of BIALP with spermine and spermidine was studied in a diethanolamine buffer with 0.5 mM magnesium chloride (pH 9.8) and at two temperatures by using the fluorescence quenching method. Furthermore, the activity of enzyme was studied using UV-Vis spectrophotometry in a diethanolamine buffer with 0.5 mM magnesium chloride, at 37 °C, in the absence and presence of different concentrations of each polyamine (0-5 mM). It was demonstrated that both polyamines quenched the intrinsic fluorescence of BIALP by the static quenching process. Based on these results, the values of the binding site for both polyamines were close to each other and decreased by increasing the temperature. The calculated thermodynamic parameters (ΔH° < 0 and ΔS° < 0) also showed that the acting forces in the formation of the complex between BIALP and polyamines were hydrogen bonds and van der Waals forces with an overall favorable Gibbs free energy change (∆G° < 0). In addition, kinetic studies revealed that these polyamines enhanced the enzyme activity of BIALP in a concentration-dependent manner. This result also indicated that spermine had more of an effect on BIALP activity in the same condition. Also, molecular docking as well as thermodynamic parameters showed that hydrogen bonds and van der Waals forces played an important role in the stabilization of BIALP-polyamine complexes.

An electrically and magnetically responsive nanocomposite of GdPO4·H2O/P3HT/PLGA with electrical stimulation for synergistically enhancing the proliferation and differentiation of pre-osteoblasts

The electric–magnetic responsive nanocomposite GdPO₄·H₂O/P3HT/PLGA could enhance MRI signals, and synergistically accelerate proliferation and osteogenic differentiation upon electrical stimulation.

Balancing Specificity and Promiscuity in Enzyme Evolution: Multidimensional Activity Transitions in the Alkaline Phosphatase Superfamily

Highly proficient, promiscuous enzymes can be springboards for functional evolution, able to avoid loss of function during adaptation by their capacity to promote multiple reactions. We employ a systematic comparative study of structure, sequence, and substrate specificity to track the evolution of specificity and reactivity between promiscuous members of clades of the alkaline phosphatase (AP) superfamily. Construction of a phylogenetic tree of protein sequences maps out the likely transition zone between arylsulfatases (ASs) and phosphonate monoester hydrolases (PMHs). Kinetic analysis shows that all enzymes characterized have four chemically distinct phospho- and sulfoesterase activities, with rate accelerations ranging from 10¹¹- to 10¹⁷-fold for their primary and 10⁹- to 10¹²-fold for their promiscuous reactions, suggesting that catalytic promiscuity is widespread in the AP-superfamily. This functional characterization and crystallography reveal a novel class of ASs that is so similar in sequence to known PMHs that it had not been recognized as having diverged in function. Based on analysis of snapshots of catalytic promiscuity "in transition", we develop possible models that would allow functional evolution and determine scenarios for trade-off between multiple activities. For the new ASs, we observe largely invariant substrate specificity that would facilitate the transition from ASs to PMHs via trade-off-free molecular exaptation, that is, evolution without initial loss of primary activity and specificity toward the original substrate. This ability to bypass low activity generalists provides a molecular solution to avoid adaptive conflict.

China's most typical nonferrous organic-metal facilities own specific microbial communities

The diversity and function of microorganisms have yet to be explored at non-ferrous metal mining facilities (NMMFs), which are the world’s largest and potentially most toxic sources of co-existing metal(loid)s and flotation reagents (FRs). The diversity and inferred functions of different bacterial communities inhabiting two types of sites (active and abandoned) in Guangxi province (China) were investigated for the first time. Here we show that the structure and diversity of bacteria correlated with the types of mine sites, metal(loid)s, and FRs concentrations; and best correlated with the combination of pH, Cu, Pb, and Mn. Combined microbial coenobium may play a pivotal role in NMMFs microbial life. Arenimonas, specific in active mine sites and an acidophilic bacterium, carries functions able to cope with the extreme conditions, whereas Latescibacteria specific in abandoned sites can degrade organics. Such a bacterial consortium provides new insights to develop cost-effective remediation strategies of co-contaminated sites that currently remain intractable for bioremediation.

Hydrolysis of Methionine- and Histidine-Containing Peptides Promoted by Dinuclear Platinum(II) Complexes with Benzodiazines as Bridging Ligands: Influence of Ligand Structure on the Catalytic Ability of Platinum(II) Complexes

Dinuclear platinum(II) complexes, [{Pt(en)Cl}₂(μ-qx)]Cl₂·2H₂O (1), [{Pt(en)Cl}₂(μ-qz)](ClO₄)₂ (2), and [{Pt(en)Cl}₂(μ-phtz)]Cl₂·4H₂O (3), were synthesized and characterized by different spectroscopic techniques. The crystal structure of 1 was determined by single-crystal X-ray diffraction analysis, while the DFT M06-2X method was applied in order to optimize the structures of 1-3. The chlorido Pt(II) complexes 1-3 were converted into the corresponding aqua species 1a-3a, and their reactions with an equimolar amount of Ac-L-Met-Gly and Ac-L-His-Gly dipeptides were studied by ¹H NMR spectroscopy in the pH range 2.0 < pH < 2.5 at 37°C. It was found that, in all investigated reactions with the Ac-L-Met-Gly dipeptide, the cleavage of the Met-Gly amide bond had occurred, but complexes 2a and 3a showed lower catalytic activity than 1a. However, in the reactions with Ac-L-His-Gly dipeptide, the hydrolysis of the amide bond involving the carboxylic group of histidine was observed only with complex 1a. The observed disparity in the catalytic activity of these complexes is thought to be due to different relative positioning of nitrogen atoms in the bridging qx, qz, and phtz ligands and consequent variation in the intramolecular separation of the two platinum(II) metal centers.

Intranasal melatonin nanoniosomes: pharmacokinetic, pharmacodynamics and toxicity studies

AIM

Intranasal melatonin encapsulated in nanosized niosomes was preclinically evaluated.

METHODOLOGY

A formula of melatonin niosomes (MN) was selected through physicochemical and cytotoxic data for pharmacokinetic, pharmacodynamics and toxicity studies in male Wistar rats.

RESULTS

Intranasal MN was bioequivalent to intravenous injection of melatonin, providing therapeutic level doses. Acute and subchronic toxicity screening showed no abnormal signs, symptoms or hematological effects in any animals. Transient nasal irritations with no inflammation were observed with intranasal MN, leading it to be categorized as relatively harmless.

CONCLUSION

The intranasal MN could deliver melatonin to the brain to induce sleep and provide delayed systemic circulation, relative to intravenous injection and also distribute to peripheral tissue.

Distinctive inhibition of alkaline phosphatase isozymes by thiazol-2-ylidene-benzamide derivatives: Functional insights into their anticancer role

In the recent years, the role of alkaline phosphatase (AP) isozymes in the cause of neoplastic diseases such as breast, liver, renal, and bone cancer has been confirmed and, thus they represent a novel target for the discovery of anticancer drugs. In this study different derivatives of thiazol-2-ylidene-benzamide were evaluated for their potential to inhibit alkaline phosphatase (AP) isozymes. Their anticancer potential was assessed using human breast cancer (MCF-7), bone-marrow cancer (K-562), and cervical cancer (HeLa) cell lines in comparison to normal cells from baby hamster kidney BHK-21. The results suggested that in comparison to other derivatives, compounds 2i, 2e, and 2a showed more sensitivity towards human tissue non-specific alkaline phosphatase (h-TNAP). Among these, 2″-chloro-N-(3-(4'-fluorophenyl)-4-methylthiazol-2(3H)-ylidene) benzamide (2e) was found as the most potent and selective inhibitor for h-TNAP with an IC₅₀ value of 0.079 ± 0.002 μM. Moreover, a significant correlation was observed between the enzyme inhibition profile and cytotoxic data. The compounds exhibiting maximum anticancer potential also induced maximum apoptosis in the respective cell lines. Furthermore, the DNA interaction studies exhibited the non-covalent mode of interaction with the herring sperm-DNA. Molecular docking studies also supported the in vitro inhibitory activity of potent compounds. Our findings suggested that potent and selective inhibitors might be useful candidates for the treatment or prevention of those diseases associated with the higher level of AP. Moreover, the study can be useful for the researcher to explore more molecular mechanisms of such derivatives and their analogues with the exact findings.

Transcriptional patterns identify resource controls on the diazotroph Trichodesmium in the Atlantic and Pacific oceans

The N₂-fixing cyanobacterium Trichodesmium is intensely studied because of the control this organism exerts over the cycling of carbon and nitrogen in the low nutrient ocean gyres. Although iron (Fe) and phosphorus (P) bioavailability are thought to be major drivers of Trichodesmium distributions and activities, identifying resource controls on Trichodesmium is challenging, as Fe and P are often organically complexed and their bioavailability to a single species in a mixed community is difficult to constrain. Further, Fe and P geochemistries are linked through the activities of metalloenzymes, such as the alkaline phosphatases (APs) PhoX and PhoA, which are used by microbes to access dissolved organic P (DOP). Here we identified significant correlations between Trichodesmium-specific transcriptional patterns in the North Atlantic (NASG) and North Pacific Subtropical Gyres (NPSG) and patterns in Fe and P biogeochemistry, with the relative enrichment of Fe stress markers in the NPSG, and P stress markers in the NASG. We also observed the differential enrichment of Fe-requiring PhoX transcripts in the NASG and Fe-insensitive PhoA transcripts in the NPSG, suggesting that metalloenzyme switching may be used to mitigate Fe limitation of DOP metabolism in Trichodesmium. This trait may underpin Trichodesmium success across disparate ecosystems.

A Method for Selective Depletion of Zn(II) Ions from Complex Biological Media and Evaluation of Cellular Consequences of Zn(II) Deficiency

We describe the preparation, evaluation, and application of an S100A12 protein-conjugated solid support, hereafter the "A12-resin", that can remove 99% of Zn(II) from complex biological solutions without significantly perturbing the concentrations of other metal ions. The A12-resin can be applied to selectively deplete Zn(II) from diverse tissue culture media and from other biological fluids, including human serum. To further demonstrate the utility of this approach, we investigated metabolic, transcriptomic, and metallomic responses of HEK293 cells cultured in medium depleted of Zn(II) using S100A12. The resulting data provide insight into how cells respond to acute Zn(II) deficiency. We expect that the A12-resin will facilitate interrogation of disrupted Zn(II) homeostasis in biological settings, uncovering novel roles for Zn(II) in biology.

Coenzyme M biosynthesis in bacteria involves phosphate elimination by a functionally distinct member of the aspartase/fumarase superfamily

For nearly 30 years, coenzyme M (CoM) was assumed to be present solely in methanogenic archaea. In the late 1990s, CoM was reported to play a role in bacterial propene metabolism, but no biosynthetic pathway for CoM has yet been identified in bacteria. Here, using bioinformatics and proteomic approaches in the metabolically versatile bacterium Xanthobacter autotrophicus Py2, we identified four putative CoM biosynthetic enzymes encoded by the xcbB1, C1, D1, and E1 genes. Only XcbB1 was homologous to a known CoM biosynthetic enzyme (ComA), indicating that CoM biosynthesis in bacteria involves enzymes different from those in archaea. We verified that the ComA homolog produces phosphosulfolactate from phosphoenolpyruvate (PEP), demonstrating that bacterial CoM biosynthesis is initiated similarly as the phosphoenolpyruvate-dependent methanogenic archaeal pathway. The bioinformatics analysis revealed that XcbC1 and D1 are members of the aspartase/fumarase superfamily (AFS) and that XcbE1 is a pyridoxal 5'-phosphate-containing enzyme with homology to d-cysteine desulfhydrases. Known AFS members catalyze β-elimination reactions of succinyl-containing substrates, yielding fumarate as the common unsaturated elimination product. Unexpectedly, we found that XcbC1 catalyzes β-elimination on phosphosulfolactate, yielding inorganic phosphate and a novel metabolite, sulfoacrylic acid. Phosphate-releasing β-elimination reactions are unprecedented among the AFS, indicating that XcbC1 is an unusual phosphatase. Direct demonstration of phosphosulfolactate synthase activity for XcbB1 and phosphate β-elimination activity for XcbC1 strengthened their hypothetical assignment to a CoM biosynthetic pathway and suggested functions also for XcbD1 and E1. Our results represent a critical first step toward elucidating the CoM pathway in bacteria.

In Vitro and in Silico Evidence of Phosphatase Diversity in the Biomineralizing Bacterium Ramlibacter tataouinensis

Microbial phosphatase activity can trigger the precipitation of metal-phosphate minerals, a process called phosphatogenesis with global geochemical and environmental implications. An increasing diversity of phosphatases expressed by diverse microorganisms has been evidenced in various environments. However, it is challenging to link the functional properties of genomic repertoires of phosphatases with the phosphatogenesis capabilities of microorganisms. Here, we studied the betaproteobacterium Ramlibacter tataouinensis (Rta), known to biomineralize Ca-phosphates in the environment and the laboratory. We investigated the functional repertoire of this biomineralization process at the cell, genome and molecular level. Based on a mineralization assay, Rta is shown to hydrolyse the phosphoester bonds of a wide range of organic P molecules. Accordingly, its genome has an unusually high diversity of phosphatases: five genes belonging to two non-homologous families, phoD and phoX, were detected. These genes showed diverse predicted cis-regulatory elements. Moreover, they encoded proteins with diverse structural properties according to molecular models. Heterologously expressed PhoD and PhoX in Escherichia coli had different profiles of substrate hydrolysis. As evidenced for Rta cells, recombinant E. coli cells induced the precipitation of Ca-phosphate mineral phases, identified as poorly crystalline hydroxyapatite. The phosphatase genomic repertoire of Rta (containing phosphatases of both the PhoD and PhoX families) was previously evidenced as prevalent in marine oligotrophic environments. Interestingly, the Tataouine sand from which Rta was isolated showed similar P-depleted, but Ca-rich conditions. Overall, the diversity of phosphatases in Rta allows the hydrolysis of a broad range of organic P substrates and therefore the release of orthophosphates (inorganic phosphate) under diverse trophic conditions. Since the release of orthophosphates is key to the achievement of high saturation levels with respect to hydroxyapatite and the induction of phosphatogenesis, Rta appears as a particularly efficient driver of this process as shown experimentally.

Kinetics study on recombinant alkaline phosphatase and correlation with the generated fluorescent signal

Alkaline phosphatase (AP) (EC 3.1.3.1) is one of the most commonly used enzymes in immunoassays. In VIDAS® assays (bioMérieux, Marcy l'Etoile, France), AP catalyzes the hydrolysis of 4-methylumbelliferyl phosphate (4-MUP) in 4-methylumbelliferone (4-MU) producing a fluorescent signal. This work introduces an original method of characterization of the kinetic parameters K_m, V_max, and K_cat of AP embedded in VIDAS® assays. Assessment of such constants allows us to predict the fluorescent signal generated for given amounts of enzyme and its associated substrate; in the particular case of VIDAS®, it has been estimated that 0.06 nmol/L of AP produces 3144 Relative Fluorescent Values (RFV).

ABBREVIATIONS

4-MUP, 4-Methylumbelliferyl phosphate; 4-MU, 4-Methylumbelliferone; RFV, Relative Fluorescent Values; RFU, Relative Fluorescent Units; QDs, Quantum Dots; LoD, Limit of Detection.

Over-expression, characterization, and modification of highly active alkaline phosphatase from a Shewanella genus bacterium

We isolated a Shewanella sp. T3-3 bacterium that yielded highly active alkaline phosphatase (APase). We then cloned the APase gene from Shewanella sp. T3-3 (T3-3AP), and expressed and purified the enzyme from Escherichia coli. Recombinant T3-3AP showed high comparative reactivity on colorimetric (pNPP) and luminescent substrates (PPD and ASP-5). Subsequently, we improved the residual activity after maleimide activation by introducing amino acid substitutions of two Lys residues that were located near the active site. The double mutant enzyme (K161S + K184S) showed much higher residual specific activity after maleimide activation than the wild type enzyme, and had approximately twofold increased sensitivity on sandwich enzyme linked immunosorbent assays (ELISA) compared with calf intestinal APase (CIAP), which is routinely used as a labeling enzyme for ELISA.

Antibacterial effects of carbon dots in combination with other antimicrobial reagents

This study was designed to investigate the antimicrobial effects of CDots in combination with other antimicrobial reagents, including H2O2, Na2CO3, and AcOH (acetic acid). CDots were synthesized and passivated with 2,2'-(ethylenedioxy)bis(ethylamine) (EDA). The minimal inhibitory concentration (MIC) of CDots was 64 μg/mL on both Gram negative bacteria E.coli cells and Gram positive bacteria Bacillus subtilis cells. When CDots were combined with H2O2, antibacterial synergistic effects were observed based on the fractional inhibitory concentration (FIC) index, and further confirmed by an isobologram analysis and viable cell number counting methods. With the combination treatment of 10 μg/mL CDots with 8.82 mM H2O2, the viable E.coli cell numbers decreased 2.46 log, which was significant lower than the log reduction from 8.82 mM H2O2 (1.57 log) or 10 μg/mL CDots (0.14 log) treatment alone. However, the combination of CDots with Na2CO3 or AcOH did not show synergistic effects, instead, exhibiting indifference effects according to the FIC index. This study indicated that the combination of CDots with their synergistic antimicrobial reagents, such as H2O2, could reach the goal of inhibiting bacteria growth by using lower concentration of each individual chemical in the combination than using one chemical treatment alone, reduce the risks imposed on environmental health and the possibilities of the development of microbial resistances.

Hypophosphatasia: An overview For 2017

Hypophosphatasia (HPP) is the inborn-error-of-metabolism that features low serum alkaline phosphatase (ALP) activity (hypophosphatasemia) caused by loss-of-function mutation(s) of the gene that encodes the tissue-nonspecific isoenzyme of ALP (TNSALP). Autosomal recessive or autosomal dominant inheritance from among >300 TNSALP (ALPL) mutations largely explains HPP's remarkably broad-ranging severity. TNSALP is a cell-surface homodimeric phosphohydrolase richly expressed in the skeleton, liver, kidney, and developing teeth. In HPP, TNSALP substrates accumulate extracellularly. Among them is inorganic pyrophosphate (PPi), a potent inhibitor of mineralization. Superabundance of extracellular PPi explains the hard tissue complications of HPP that feature premature loss of deciduous teeth and often rickets or osteomalacia as well as calcific arthropathies in some affected adults. In infants with severe HPP, blocked entry of minerals into the skeleton can cause hypercalcemia, and insufficient hydrolysis of pyridoxal 5'-phosphate (PLP), the major circulating form of vitamin B₆, can cause pyridoxine-dependent seizures. Elevated circulating PLP is a sensitive and specific biochemical marker for HPP. Also, the TNSALP substrate phosphoethanolamine (PEA) is usually elevated in serum and urine in HPP, though less reliably for diagnosis. Pathognomonic radiographic changes occur in pediatric HPP when the skeletal disease is severe. TNSALP mutation analysis is essential for recurrence risk assessment for HPP in future pregnancies and for prenatal diagnosis. HPP was the final rickets/osteomalacia to have a medical treatment. Now, significant successes using asfotase alfa, a mineral-targeted recombinant TNSALP, are published concerning severely affected newborns, infants, and children. Asfotase alfa was approved by regulatory agencies multinationally in 2015 typically for pediatric-onset HPP.