Alcohol dehydrogenase and its simple inorganic models

Potential roles of the rhizospheric bacterial community in assisting Miscanthus floridulus in remediating multi-metal(loid)s contaminated soils

Phytoremediation technology is an important approach applied to heavy metal remediation, and how to improve its remediation efficiency is the key. In this study, we compared the rhizospheric bacterial communities and metals contents in Miscanthus floridulus (M. floridulus) of four towns, including Huayuan Town (HY), Longtan Town (LT), Maoer Village (ME), and Minle Town (ML) around the lead-zinc mining area in Huayuan County, China. The roles of rhizospheric bacterial communities in assisting the phytoremediation of M. floridulus were explored. It was found that the compositions of the rhizospheric bacterial community of M. floridulus differed in four regions, but majority of them were heavy metal-resistant bacteria that could promote plant growth. Results of bioconcentration factors showed the enrichment of Cu, Zn, and Pb by M. floridulus in these four regions were significantly different. The Zn enrichment capacity of ML was the strongest for Cu and stronger than LT and ME for Pb. The enrichment capacity of LT and ML was stronger than HY and ME. These bacteria may influence the different heavy metals uptake of M. floridulus by altering the soil physiochemical properties (e.g., soil peroxidase, pH and moisture content). In addition, co-occurrence network analysis also showed that LT and ML had higher network stability and complexity than HY and ME. Functional prediction analysis of the rhizospheric bacterial community showed that genes related to protein synthesis (e.g., zinc-binding alcohol dehydrogenase/oxidoreductase, Dtx R family transcriptional regulators and ACC deaminase) also contributed to phytoremediation in various ways. This study provides theoretical guidance for selecting suitable microorganisms to assist in the phytoremediation of heavy metals.

The discovery and characterization of AeHGO in the branching route from shikonin biosynthesis to shikonofuran in Arnebia euchroma

Shikonin derivatives are natural naphthoquinone compounds and the main bioactive components produced by several boraginaceous plants, such as Lithospermum erythrorhizon and Arnebia euchroma. Phytochemical studies utilizing both L. erythrorhizon and A. euchroma cultured cells indicate the existence of a competing route branching out from the shikonin biosynthetic pathway to shikonofuran. A previous study has shown that the branch point is the transformation from (Z)-3''-hydroxy-geranylhydroquinone to an aldehyde intermediate (E)-3''-oxo-geranylhydroquinone. However, the gene encoding the oxidoreductase that catalyzes the branch reaction remains unidentified. In this study, we discovered a candidate gene belonging to the cinnamyl alcohol dehydrogenase family, AeHGO, through coexpression analysis of transcriptome data sets of shikonin-proficient and shikonin-deficient cell lines of A. euchroma. In biochemical assays, purified AeHGO protein reversibly oxidized (Z)-3''-hydroxy-geranylhydroquinone to produce (E)-3''-oxo-geranylhydroquinone followed by reversibly reducing (E)-3''-oxo-geranylhydroquinone to (E)-3''-hydroxy-geranylhydroquinone, resulting in an equilibrium mixture of the three compounds. Time course analysis and kinetic parameters showed that the reduction of (E)-3''-oxo-geranylhydroquinone was stereoselective and efficient in presence of NADPH, which determined that the overall reaction proceeded from (Z)-3''-hydroxy-geranylhydroquinone to (E)-3''-hydroxy-geranylhydroquinone. Considering that there is a competition between the accumulation of shikonin and shikonofuran derivatives in cultured plant cells, AeHGO is supposed to play an important role in the metabolic regulation of the shikonin biosynthetic pathway. Characterization of AeHGO should help expedite the development of metabolic engineering and synthetic biology toward production of shikonin derivatives.

Deep Learning-Based Label-Free Surface-Enhanced Raman Scattering Screening and Recognition of Small-Molecule Binding Sites in Proteins

Identification of small-molecule binding sites in proteins is of great significance in analysis of protein function and drug design. Modified sites can be recognized via proteolytic cleavage followed by liquid chromatography-mass spectrometry (LC-MS); however, this has always been impeded by the complexity of peptide mixtures and the elaborate synthetic design for tags. Here, we demonstrate a novel technique for identifying protein binding sites using a deep learning-based label-free surface-enhanced Raman scattering (SERS) screening (DLSS) strategy. In DLSS, the deep learning model that was trained with large SERS signals could detect signal features of small molecules with high accuracy (>99%). Without any secondary tag, the small molecules are directly complexed with proteins. After proteolysis and LC, SERS signals of all LC fractions are collected and input into the model, whereby the fractions containing the small-molecule-modified peptides can be recognized by the model and sent to MS/MS to identify the binding site(s). By using an automated DLSS system, we successfully identified the modification sites of fomepizole in alcohol dehydrogenase, which is coordinated with zinc along with three peptides. We also showed that the DLSS strategy works for identification of amino-acid residues that covalently bond with ibrutinib in Bruton tyrosine kinase. These results suggest that the DLSS strategy, which provides high molecular recognition capability to LC-MS analysis, has potential in drug discovery, proteomics, and metabolomics.

A host-guest semibiological photosynthesis system coupling artificial and natural enzymes for solar alcohol splitting

Development of a versatile, sustainable and efficient photosynthesis system that integrates intricate catalytic networks and energy modules at the same location is of considerable future value to energy transformation. In the present study, we develop a coenzyme-mediated supramolecular host-guest semibiological system that combines artificial and enzymatic catalysis for photocatalytic hydrogen evolution from alcohol dehydrogenation. This approach involves modification of the microenvironment of a dithiolene-embedded metal-organic cage to trap an organic dye and NADH molecule simultaneously, serving as a hydrogenase analogue to induce effective proton reduction inside the artificial host. This abiotic photocatalytic system is further embedded into the pocket of the alcohol dehydrogenase to couple enzymatic alcohol dehydrogenation. This host-guest approach allows in situ regeneration of NAD⁺/NADH couple to transfer protons and electrons between the two catalytic cycles, thereby paving a unique avenue for a synergic combination of abiotic and biotic synthetic sequences for photocatalytic fuel and chemical transformation.

Abiotic–biotic hybrid systems are promising to trap light for fuel and chemical transformation with high efficacy and selectivity. This study reports a coenzyme-mediated supramolecular host-guest semibiological system combining supramolecular catalyst and enzymes for solar alcohol splitting.

Controlled Regulation of the Nitrile Activation of a Peroxocobalt(III) Complex with Redox-Inactive Lewis Acidic Metals

Redox-inactive metal ions play vital roles in biological O₂ activation and oxidation reactions of various substrates. Recently, we showed a distinct reactivity of a peroxocobalt(III) complex bearing a tetradentate macrocyclic ligand, [Co^III(TBDAP)(O₂)]⁺ (1) (TBDAP = N,N'-di-tert-butyl-2,11-diaza[3.3](2,6)pyridinophane), toward nitriles that afforded a series of hydroximatocobalt(III) complexes, [Co^III(TBDAP)(R-C(═NO)O)]⁺ (R = Me (3), Et, and Ph). In this study, we report the effects of redox-inactive metal ions on nitrile activation of 1. In the presence of redox-inactive metal ions such as Zn²⁺, La³⁺, Lu³⁺, and Y³⁺, the reaction does not form the hydroximatocobalt(III) complex but instead gives peroxyimidatocobalt(III) complexes, [Co^III(TBDAP)(R-C(═NH)O₂)]²⁺ (R = Me (2) and Ph (2^Ph)). These new intermediates were characterized by various physicochemical methods including X-ray diffraction analysis. The rates of the formation of 2 are found to correlate with the Lewis acidity of the additive metal ions. Moreover, complex 2 was readily converted to 3 by the addition of a base. In the presence of Al³⁺, Sc³⁺, or H⁺, 1 is converted to [Co^III(TBDAP)(O₂H)(MeCN)]²⁺ (4), and further reaction with nitriles did not occur. These results reveal that the reactivity of the peroxocobalt(III) complex 1 in nitrile activation can be regulated by the redox-inactive metal ions and their Lewis acidity. DFT calculations show that the redox-inactive metal ions stabilize the peroxo character of end-on Co-η¹-O₂ intermediate through the charge reorganization from a Co^II-superoxo to a Co^III-peroxo intermediate. A complete mechanistic model explaining the role of the Lewis acid is presented.

Structure-based mechanisms: On the way to apply alcohol dehydrogenases/reductases to organic-aqueous systems

Alcohol dehydrogenases/reductases catalyze enantioselective syntheses of versatile chiral compounds relying on direct hydride transfer from cofactor to substrates, or to an intermediate and then to substrates. Since most of the substrates catalyzed by alcohol dehydrogenases/reductases are insoluble in aqueous solutions, increasing interest has been turning to organic-aqueous systems. However, alcohol dehydrogenases/reductases are normally instable in organic solvents, leading to the unsatisfied enantioselective synthesis efficiency. The behaviors of these enzymes in organic solvents at an atomic level are unclear, thus it is of great importance to understand its structure-based mechanisms in organic-aqueous systems to improve their relative stability. Here, we summarized the accessible structures of alcohol dehydrogenases/reductases in Protein Data Bank crystallized in organic-aqueous systems, and compared the structures of alcohol dehydrogenases/reductases which have different tolerance towards organic solvents. By understanding the catalytic behaviors and mechanisms of these enzymes in organic-aqueous systems, the efficient enantioselective syntheses mediated by alcohol dehydrogenases/reductases and further challenges are also discussed through solvent engineering and enzyme-immobilization in the last decade.

Ligand Conjugation Directs the Formation of a 1,3-Dihydropyridinate Regioisomer

The selective formation of the 1,4-dihydropyridine isomer of NAD(P)H is mirrored by the selective formation of 1,4-dihydropyridinate ligand-metal complexes in synthetic systems. Here we demonstrate that ligand conjugation can be used to promote selective 1,3-dihydropyridinate formation. This represents an advance toward controlling and tuning the selectivity in dihydropyridinate formation chemistry. The reaction of (I₂P^2-)Al(THF)Cl [1; I₂P = bis(imino)pyridine; THF = tetrahydrofuran] with the one-electron oxidant (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) afforded (I₂P^-)Al(TEMPO)Cl (2), which can be reduced with sodium to the twice-reduced ligand complex (I₂P^2-)Al(TEMPO) (3). Compounds 2 and 3 serve as precursors for high-yielding and selective routes to an aluminum-supported 1,3-dihydropyridinate complex via the reaction of 2 with 3 equiv of potassium metal or the reaction of 3 with KH.

Immobilization of alcohol dehydrogenase from Saccharomyces cerevisiae onto carboxymethyl dextran-coated magnetic nanoparticles: a novel route for biocatalyst improvement via epoxy activation

A novel method is described for the immobilization of alcohol dehydrogenase (ADH) from Saccharomyces cerevisiae onto carboxymethyl dextran (CMD) coated magnetic nanoparticles (CMD-MNPs) activated with epoxy groups, using epichlorohydrin (EClH). EClH was used as an activating agent to bind ADH molecules on the surface of CMD-MNPs. Optimal immobilization conditions (activating agent concentration, temperature, rotation speed, medium pH, immobilization time and enzyme concentration) were set to obtain the highest expressed activity of the immobilized enzyme. ADH that was immobilized onto epoxy-activated CMD-MNPs (ADH-CMD-MNPs) maintained 90% of the expressed activity. Thermal stability of ADH-CMD-MNPS after 24 h at 20 °C and 40 °C yielded 79% and 80% of initial activity, respectively, while soluble enzyme activity was only 19% at 20 °C and the enzyme was non-active at 40 °C. Expressed activity of ADH-CMD-MNPs after 21 days of storage at 4 °C was 75%. Kinetic parameters (K_M, v_max) of soluble and immobilized ADH were determined, resulting in 125 mM and 1.2 µmol/min for soluble ADH, and in 73 mM and 4.7 µmol/min for immobilized ADH.

A host-guest approach to combining enzymatic and artificial catalysis for catalyzing biomimetic monooxygenation

Direct transfer of protons and electrons between two tandem reactions is still a great challenge, because overall reaction kinetics is seriously affected by diffusion rate of the proton and electron carriers. We herein report a host–guest supramolecular strategy based on the incorporation of NADH mimics onto the surface of a metal-organic capsule to encapsulate flavin analogues for catalytic biomimetic monooxygenations in conjunction with enzymes. Coupling an artificial catalysis and a natural enzymatic catalysis in the pocket of an enzyme, this host–guest catalyst–enzyme system allows direct proton and electron transport between two catalytic processes via NADH mimics for the monooxygenation of both cyclobutanones and thioethers. This host–guest approach, which involves the direct coupling of abiotic and biotic catalysts via a NADH-containing host, is quite promising compared to normal catalyst–enzyme systems, as it offers the key advantages of supramolecular catalysis in integrated chemical and biological synthetic sequences.

Combining artificial and natural enzymes is a strategy to mimic biocatalytic processes with high efficiency and selectivity. This study reports a dual catalytic system composed of flavin adenine dinucleotide model and NADH mimics to catalyze the monooxygenation of cyclobutanones and thioethers.

A Cu/Zn heterometallic complex with solvent-binding cavity, catalytic activity for the oxidation of 1-phenylethanol and unusual magnetic properties

Mononuclear and polymeric complexes of zinc(ii) and copper(ii) have been synthesized using two isomers of the hemi-salen ligand with a different mutual orientation of donor atoms. The heterometallic Cu/Zn metallocycle features a catalytic niche filled with the molecule of water and molecules of methanol. This unusual compound exhibits both pronounced catalytic activity in the reaction of oxidation of a secondary alcohol to ketone and field induced slow magnetic relaxation, which is a very rare phenomenon among Cu(ii) complexes.

Understanding (R) Specific Carbonyl Reductase from Candida parapsilosis ATCC 7330 [CpCR]: Substrate Scope, Kinetic Studies and the Role of Zinc

CpCR, an (R) specific carbonyl reductase, so named because it gave (R)-alcohols on asymmetric reduction of ketones and ketoesters, is a recombinantly expressed enzyme from Candida parapsilosis ATCC 7330. It turns out to be a better aldehyde reductase and catalyses cofactor (NADPH) specific reduction of aliphatic and aromatic aldehydes. Kinetics studies against benzaldehyde and 2,4-dichlorobenzaldehyde show that the enzyme affinity and rate of reaction change significantly upon substitution on the benzene ring of benzaldehyde. CpCR, an MDR (medium chain reductase/dehydrogenase) containing both structural and catalytic Zn atoms, exists as a dimer, unlike the (S) specific reductase (SRED) from the same yeast which can exist in both dimeric and tetrameric forms. Divalent metal salts inhibit the enzyme even at nanomolar concentrations. EDTA chelation decreases CpCR activity. However, chelation done after the enzyme is pre-incubated with the NADPH retains most of the activity implying that Zn removal is largely prevented by the formation of the enzyme-cofactor complex.

Zinc Oxide-Catalyzed Dehydrogenation of Primary Alcohols into Carboxylic Acids

Zinc oxide has been developed as a catalyst for the dehydrogenation of primary alcohols into carboxylic acids and hydrogen gas. The reaction is performed in mesitylene solution in the presence of potassium hydroxide, followed by workup with hydrochloric acid. The transformation can be applied to both benzylic and aliphatic primary alcohols and the catalytically active species was shown to be a homogeneous compound by a hot filtration test. Dialkylzinc and strongly basic zinc salts also catalyze the dehydrogenation with similar results. The mechanism is believed to involve the formation of a zinc alkoxide which degrades into the aldehyde and a zinc hydride. The latter reacts with the alcohol to form hydrogen gas and regenerate the zinc alkoxide. The degradation of a zinc alkoxide into the aldehyde upon heating was confirmed experimentally. The aldehyde can then undergo a Cannizzaro reaction or a Tishchenko reaction, which in the presence of hydroxide leads to the carboxylic acid.

Silver complexes stabilized by large silanethiolate ligands - crystal structures and luminescence properties

Bulky silanethiolate and disiladithiolate ligands were applied to synthesize one mononuclear and three trinuclear silver complexes including two cyclic "microclusters" and a linear tri-nuclear silanethiolate complex. All obtained compounds are characterized by X-ray diffraction and FT-IR. NMR and emission spectroscopies were used where possible. The first trinuclear anionic silver thiolate is structurally characterized. The influence of the different charge of cyclic silver complexes as well as the overall ligand environment on the structural properties is demonstrated. The impact of the different synthetic routes on the final structures of the obtained clusters - cyclic or linear - is discussed.

Second sphere ligand modifications enable a recyclable catalyst for oxidant-free alcohol oxidation to carboxylates

Ruthenium–terpyridine complexes appended with secondary amines impart hydride stability and recyclability toward catalytic dehydrogenative alcohol oxidation to carboxylates.

A bio-inspired design and computational prediction of scorpion-like SCS nickel pincer complexes for lactate racemization

Computationally predicted scorpion-like SCS nickel pincer complexes are promising for the catalysis of lactate racemization under mild conditions.

Synthesis and characterization of mononuclear Zn(II), Co(II) and Ni(II) complexes containing a sterically demanding silanethiolate ligand derived from tris(2,6-diisopropylphenoxy)silanethiol

Four heteroleptic complexes of nickel(ii), cobalt(ii) and zinc(ii), containing a monodentate silanethiolate ligand derived from tris(2,6-diisopropylphenoxy)silanethiol (TDST), were prepared and characterized. Nickel(ii) and cobalt(ii) complexes of the formula M(NH3)2(TDST)2 (M = Ni(ii) complex , M = Co(ii) complex ) were obtained from the respective chlorides. Zinc complexes of the general formula Zn(acac)(TDST)(L), where L = EtOH (complex ) or H2O (complex ), were obtained from zinc acetylacetonate. A single-crystal X-ray structural analysis revealed that all crystalline products are solvent adducts. The geometries of ligands in the complexes are typical: distorted tetrahedral in zinc and cobalt(ii) complexes and square planar in nickel(ii) compounds. Magnetic studies performed for Ni(ii) and Co(ii) compounds confirmed the diamagnetic character of the first complex and high-spin paramagnetic configuration of the latter. Nickel(ii) and cobalt(ii) complexes were additionally characterized by UV-Vis and IR spectroscopy. IR bands for ligands in the complexes were assigned with the help of the DFT vibrational frequency calculations.

Purification and enzymatic characterization of alcohol dehydrogenase from Arabidopsis thaliana

Alcohol dehydrogenases (ADH) catalyze the interconversion between alcohols and aldehydes with the reduction of nicotinamide adenine dinucleotide (NAD(+)) to NADH. In this study, for the first time we report an over-expression and purification strategy for the Arabidosis thaliana ADH (AtADH), and characterize its enzymatic properties. AtADH was expressed in an Escherichia coli system, the polyhistidine-tag was removed after the recombinant AtADH protein was purified by metal chelating affinity chromatography. Activity assays demonstrated that AtADH has distinct enzymatic properties when compared with many well-known ADHs. It held peak activity at pH 10.5 and showed broad substrate selectivity for primary and secondary alcohols. The kinetic Km parameters for both ethanol and coenzyme were in the order of mM. This relative low affinity may reflect the need of the plant to maintain a supply of NAD(+) in nature. Different from yeast ADH, AtADH showed almost the same activity for short straight chain alcohols and reduced activity for secondary alcohols. This broad spectrum in alcohol selection and the observed higher catalytic activity (high Vmax (EtOH)) may result from the requirement of the single enzyme to accommodate many substrates.

(1H-Pyrazole-κN)bis-(tri-tert-but-oxy-silane-thiol-ato-κ(2) O,S)cadmium

The Cd(II) atom in the title complex, [Cd(C12H27O3SSi)2(C3H4N2)], is penta-coordinated by two O and two S atoms from the O,S-chelating silane-thiol-ate residue and one pyrazole N atom in a distorted geometry that is slightly closer to trigonal-bipyramidal than to square-based pyramidal. The pyrazole ligand is stabilized within the complex by an intra-molecular N-H⋯O hydrogen bond. One of the tert-butyl groups is disordered over two orientations with occupancy ratio of 0.534 (6):0.466 (6).

Hydrogen evolution from aliphatic alcohols and 1,4-selective hydrogenation of NAD+ catalyzed by a [C,N] and a [C,C] cyclometalated organoiridium complex at room temperature in water

A [C,N] cyclometalated Ir complex, [Ir(III)(Cp*)(4-(1H-pyrazol-1-yl-κN(2))benzoic acid-κC(3))(H(2)O)](2)SO(4) [1](2)·SO(4), was reduced by aliphatic alcohols to produce the corresponding hydride complex [Ir(III)(Cp*)(4-(1H-pyrazol-1-yl-κN(2))-benzoate-κC(3))H](-)4 at room temperature in a basic aqueous solution (pH 13.6). Formation of the hydride complex 4 was confirmed by (1)H and (13)C NMR, ESI MS, and UV-vis spectra. The [C,N] cyclometalated Ir-hydride complex 4 reacts with proton to generate a stoichiometric amount of hydrogen when the pH was decreased to pH 0.8 by the addition of diluted sulfuric acid. Photoirradiation (λ > 330 nm) of an aqueous solution of the [C,N] cyclometalated Ir-hydride complex 4 resulted in the quantitative conversion to a unique [C,C] cyclometalated Ir-hydride complex 5 with no byproduct. The complex 5 catalyzed hydrogen evolution from ethanol in a basic aqueous solution (pH 11.9) under ambient conditions. The 1,4-selective catalytic hydrogenation of β-nicotinamide adenine dinucleotide (NAD(+)) by ethanol was also made possible by the complex 1 to produce 1,4-dihydro-β-nicotinamide adenine dinucleotide (1,4-NADH) at room temperature. The overall catalytic mechanism of hydrogenation of NAD(+), accompanied by the oxidation of ethanol, was revealed on the basis of the kinetic analysis and detection of the reaction intermediates.