Chiral Carbon Dots Mimicking Topoisomerase I To Mediate the Topological Rearrangement of Supercoiled DNA Enantioselectively

Nanomaterials with enzyme-mimetic activities are possible alternatives to natural enzymes. Mimicking enzymatic enantioselectivity remains a great challenge. Herein, we report that cysteine-derived chiral carbon dots (CDs) can mimic topoisomerase I to mediate topological rearrangement of supercoiled DNA enantioselectively. d -CDs can more effectively catalyze the topological transition of plasmid DNA from supercoiled to nicked open-circular configuration than l -CDs. Experiments suggest the underlying mechanism: d -CDs intercalatively bind with DNA double helix more strongly than l -CDs; the intercalative CDs can catalyze the production of hydroxyl radicals to cleave phosphate backbone in one strand of the double helix, leading to topological rearrangement of supercoiled DNA. Molecular dynamics (MD) simulation show that the stronger affinity for hydrogen-bond formation and hydrophobic interaction between d -cysteine and DNA than that of l -cysteine is the origin of enantioselectivity.     

Highly Fluorescent Chiral N‐S‐Doped Carbon Dots from Cysteine: Affecting Cellular Energy Metabolism

Cysteine‐based chiral optically active carbon dots (CDs) and their effects on cellular energy metabolism, which is vital for essential cellular functions, have been barely reported. A green and effective synthesis strategy for chiral N‐S‐doped CDs (fluorescence quantum yield ca. 41.26 %) based on hydrothermal treatment of l ‐ or d ‐cysteine at as low as 60 °C has been developed. This suggested that cysteine was instable in aqueous solutions and acts as a warning for high‐temperature synthesis of nanomaterials using cysteine as stabilizer. Human bladder cancer T24 cells treated with l ‐CDs showed up‐regulated glycolysis, while d ‐CDs had no similar effects. In contrast, no disturbance to the basal mitochondrial aerobic respiration of T24 cells was caused by either chiral CD.     

Enantiomeric and Diastereomeric Self‐Assembled Multivalent Nanostructures: Understanding the Effects of Chirality on Binding to Polyanionic Heparin and DNA

A family of four self‐assembling lipopeptides containing Ala‐Lys peptides attached to a C₁₆ aliphatic chain were synthesised. These compounds form two enantiomeric pairs that bear a diastereomeric relationship to one another (C₁₆‐l ‐Ala‐l ‐Lys/C₁₆‐d ‐Ala‐d ‐Lys) and (C₁₆‐d ‐Ala‐l ‐Lys/C₁₆‐l ‐Ala‐d ‐Lys). These diastereomeric pairs have very different critical micelle concentrations (CMCs). The self‐assembled multivalent (SAMul) systems bind biological polyanions as a result of the cationic lysine groups on their surfaces. For heparin binding, there was no significant enantioselectivity, but there was a binding preference for the diastereomeric assemblies with lower CMCs. Conversely, for DNA binding, there was significant enantioselectivity for systems displaying d ‐lysine ligands, with a further slight preference for attachment to l ‐alanine, with the CMC being irrelevant.     

Non‐Hydrolytic β‐Lactam Antibiotic Fragmentation by l,d‐Transpeptidases and Serine β‐Lactamase Cysteine Variants

Enzymes often use nucleophilic serine, threonine, and cysteine residues to achieve the same type of reaction; the underlying reasons for this are not understood. While bacterial d,d ‐transpeptidases (penicillin‐binding proteins) employ a nucleophilic serine, l,d ‐transpeptidases use a nucleophilic cysteine. The covalent complexes formed by l,d ‐transpeptidases with some β‐lactam antibiotics undergo non‐hydrolytic fragmentation. This is not usually observed for penicillin‐binding proteins, or for the related serine β‐lactamases. Replacement of the nucleophilic serine of serine β‐lactamases with cysteine yields enzymes which fragment β‐lactams via a similar mechanism as the l,d ‐transpeptidases, implying the different reaction outcomes are principally due to the formation of thioester versus ester intermediates. The results highlight fundamental differences in the reactivity of nucleophilic serine and cysteine enzymes, and imply new possibilities for the inhibition of nucleophilic enzymes.     

Zigzag‐Helix Transformation of Expanded Polyvaline Induced by Racemization

Biological macromolecules are essentially homochiral. For example, proteins mostly consist of l ‐amino acids. What happens when a chiral molecule meets itself in a mirror? For expanded polyvaline, zigzag‐helix transformation occurs. In this study, expanded polyvalines containing bis(pyridine)silver(I) moieties were synthesized and isolated as single crystals. The molecular structures were determined by X‐ray analysis, which revealed that chiral expanded poly(l ‐valine) and poly(d ‐valine) form zigzag chains. However, racemic mixture of these molecules form left‐ and right‐handed 4₁ helices that retain the original sequences. These secondary structures can be transformed by only flipping the C‐terminal amide plane for each unit, which is reminiscent of the relationship between an α‐helix and a β‐strand. Such expanded polypeptides can be built up into expanded protein, forming a tailor‐made three‐dimensional structure, which will lead to new functions.     

l‐Cysteinium semioxalate

The title salt, C₃H₈NO₂⁺·C₂HO₄⁻, formed between l ‐cysteine and oxalic acid, was studied as part of a comparison of the structures and properties of pure amino acids and their cocrystals. The structure of the title salt is very different from that formed by oxalic acid and equivalent amounts of d ‐ and l ‐cysteine molecules. The asymmetric unit contains an l ‐cysteinium cation and a semioxalate anion. The oxalate anion is only singly deprotonated, in contrast with the double deprotonation in the crystal structure of bis(dl ‐cysteinium) oxalate. The oxalate anion is not planar. The conformation of the l ‐cysteinium cation differs from that of the neutral cysteine zwitterion in the monoclinic and orthorhombic polymorphs of l ‐cysteine, but is similar to that of the cysteinium cation in bis(dl ‐cysteinium) oxalate. The structure of the title salt can be described as a three‐dimensional framework formed by ions linked by strong O—H...O and N—H...O and weak S—H...O hydrogen bonds, with channels running along the crystallographic a axis containing the bulky –CH₂SH side chains of the cysteinium cations. The cations are only linked through hydrogen bonds via semioxalate anions. There are no direct cation–cation interactions via N—H...O hydrogen bonds between the ammonium and carboxylate groups, or via weaker S—H...S or S—H...O hydrogen bonds.     

Cyclic lipoundecapeptide tensin from Pseudomonas fluorescens strain 96.578

The crystal structure of the non‐ribosomal lipoundecapeptide tensin from Pseudomonas fluorescens has been solved as an ethyl acetate/bis‐water solvate (tensin ethyl acetate dihydrate, C₆₇H₁₁₅N₁₂O₂₀·C₄H₈O₂·2H₂O) to a resolution of 0.8 Å. The primary structure of tensin is β‐hydroxydecanoyl‐d ‐Leu‐d ‐Asp‐d ‐allo‐Thr‐d ‐Leu‐d ‐Leu‐d ‐Ser‐l ‐Leu‐d ‐Gln‐l ‐Leu‐l ‐Ile‐l ‐Glu. The peptide is a lactone linking the Thr3 O_γ atom to the C‐terminal C atom. The stereochemistry of the β‐hydroxy acid has been shown to be S. The peptide shows structural resemblance to the non‐ribosomal cyclic lipopeptide fengycin from Bacillus subtilis. The structure of tensin is essentially helical (3₁₀‐helix), with the cyclic peptide wrapping around a hydrogen‐bonded water molecule. The lipopeptide is amphipathic in good agreement with its function as a biosurfactant.     

Topological solitons in an inhomogeneous DNA molecule

The dynamics of topological solitons describing the opening of the double helix of a DNA molecule is studied. The estimated actual values of the rigidity of the polynucleotide chains made it possible to develop a more precise DNA model and to show that four types of topological solitons can appear in the DNA double helix. Interactions between solitons are studied, as well as their interaction with the chain inhomogeneities and the stability of solitons with respect to thermal fluctuations. Thermal fluctuations promote propagation of solitons along an inhomogeneous base sequence.     

Introduction of d‐Amino Acids in Minimalistic Peptide Substrates by an S‐Adenosyl‐l‐Methionine Radical Epimerase

Post‐translational modifying enzymes from the S‐adenosyl‐l ‐methionine (AdoMet) radical superfamily garner attention due to their ability to accomplish challenging biochemical reactions. Among them, a family of AdoMet radical epimerases catalyze irreversible l ‐ to d ‐amino acid transformations of diverse residues, including 18 sites in the complex sponge‐derived polytheonamide toxins. Herein, the in vitro activity of the model epimerase OspD is reported and its catalytic mechanism and substrate flexibility is investigated. The wild‐type enzyme was capable of leader‐independent epimerization of not only the stand‐alone core peptide, but also truncated and cyclic core variants. Introduction of d ‐amino acids can drastically alter the stability, structure, and activity of peptides; thus, epimerases offer opportunities in peptide bioengineering.     

Impact of Cationic Charge Density and PEGylated Poly(Amino Acid) Tercopolymer Architecture on Their Use as Gene Delivery Vehicles. Part 2: DNA Protection,Stability, Cytotoxicity,and Transfection Efficiency

The impact of the molecular architecture on the transfection efficiency of PEGylated poly(amino acid) block copolymers was investigated for PEG‐b‐p(l ‐Lys)_x‐b‐p(l ‐Leu)_y, PEG‐b‐p(l ‐Leu)_x‐b‐p(l ‐Lys)_y, and PEG‐b‐p((l ‐Leu)_x‐co‐(l ‐Lys)_y). The block lengths of p(l ‐Lys) and p(l ‐Leu) were varied between 10, 20, and 40; and 10 and 20, respectively, to study the influence of the ionic/hydrophobic balance. The results show that ABC triblock copolymers form smaller and more stable polyplexes with plasmid DNA than AB diblock copolymers—as verified by long‐term aggregation and ethidium bromide exclusion studies—protect the DNA more effectively against nucleases, and provide better transfection efficiencies, as indicated by total protein as well as luciferase expression. More detailed studies revealed that triblock copolymers with p(l ‐Leu) forming the C‐block were most efficient in DNA complexation with a 2.3 times higher transfection rate. Furthermore, increasing the cationic character by increasing the p(l ‐Lys) chain length led to up to 25% higher transfection but at the same time induced some cytotoxicity. Diblock copolymers, where the amino acid–building blocks exist as a random copolymer, bind more loosely with DNA leading to less compact and less stable aggregates with lower transfection efficiencies.     

Cyclic lipoundecapeptide amphisin from Pseudomonas sp. strain DSS73

The crystal structure of the lipoundecapeptide amphisin, presented here as the tetrahydrate, C₆₆H₁₁₄N₁₂O₂₀·4H₂O, originating from non‐ribosomal biosynthesis by Pseudomonas sp. strain DSS73, has been solved to a resolution of 0.65 Å. The primary structure of amphisin is β‐hydroxy­decanoyl‐d ‐Leu‐d ‐Asp‐d ‐allo‐Thr‐d ‐Leu‐d ‐Leu‐d ‐Ser‐l ‐Leu‐d ‐Gln‐l ‐Leu‐l ‐Ile‐l ‐Asp (Leu is leucine, Asp is aspartic acid, Thr is threonine, Ser is serine, Gln is glut­amine and Ile is isoleucine). The peptide is a lactone, linking Thr4 O_γ to the C‐terminal. The stereochemistry of the β‐hydroxy acid is R. The peptide is a close analogue of the cyclic lipopeptides tensin and pholipeptin produced by Pseudomonas fluorescens. The structure of amphisin is mainly helical (3₁₀‐helix), with the cyclic peptide wrapping around a hydrogen‐bonded water mol­ecule. This lipopeptide is amphiphilic and has biosurfactant and antifungal properties.     

Novel Anti‐Biofouling Soft Contact Lens: l‐Cysteine Conjugated Amphiphilic Conetworks via RAFT and Thiol–Ene Click Chemistry

A unique l ‐cysteine conjugated antifouling amphiphilic conetwork (APCN) is synthesized through end‐crosslinking of well‐defined triblock copolymers poly(allyl methacrylate)‐b‐poly(ethylene glycol)‐b‐poly(allyl methacrylate) via a combination of reversible addition‐fragmentation chain transfer (RAFT) polymerization and thiol–ene “click” chemistry. The synthesized poly(ethylene glycol) macro‐RAFT agent initiates the polymerization of allyl methacrylate in a controlled manner. The vinyl pendant groups of the precursor partially conjugate with l ‐cysteine and the rest fully crosslink with mercaptopropyl‐containing siloxane via thiol–ene click chemistry under UV irradiation into APCNs, which show distinguished properties, that is, excellent biocompatibility, more than 39.6% water content, 101 barrers oxygen permeability, optimized mechanical properties, and more than 93% visible light transmittance. What's more, the resultant APCNs exhibit eminent resistance to protein adsorption, where the bovine serum albumin and lysozyme adsorption are decreased to 12 and 21 µg cm⁻², respectively. The outstanding properties of APCNs depend on the RAFT controlled method, which precisely designs the hydrophilic/hydrophobic segments and eventually greatly improves the crosslinking efficiency and homogeneity. Meantime, the l ‐cysteine monolayer can effectively reduce the surface hydrophobicity and prevent protein adsorption, which exhibits the viability for antifouling surface over and under ophthalmic devices, suggesting a promising soft contact lens.

     

Methyl Benzoate Gallium(III) corrole complexes: DNA‐binding,Photocleavage Activity,Cytotoxicity on Tumor Cells

Two new gallium corrole complexes, 10‐(4‐Methoxycarbonylphenyl) ‐5, 15‐bis(pentafluorophenyl)corrolatogallium(III)( 1 ‐Ga) and 5,15‐bis(4‐Methoxycarbonylphenyl)‐10‐(pentafluorophenyl)corrolatogallium(III)( 2 ‐Ga), were synthesized and characterized. The interaction of these gallium corrole complexes with CT‐DNA was studied by fluorescence methods, UV–visible, viscosity measurements, molecular docking as well as agarose gel electrophoresis. The results revealed that both 1 ‐Ga and 2 ‐Ga interact with DNA via major groove binding and could cleavage the supercoiled plasmid DNA efficiently under irradiation. The inhibitor and singlet oxygen test indicated that singlet oxygen was the reactive oxygen species involved in the photocleavage DNA initiated by 1 ‐Ga or 2 ‐Ga. Cell viability experiments indicated that 1 ‐Ga and 2 ‐Ga show high photocytotoxicity and low dark toxicity towards tested QGY‐7701 and MHCC‐H/L tumor cell lines. Fluorescence probe tests showed the absorbed 1 ‐Ga and 2 ‐Ga in tumor cells are mainly localized in mitochondria, and the mitochondria membrane potential disruption was observed after irradiation.     

Homochiral MOF–Polymer Mixed Matrix Membranes for Efficient Separation of Chiral Molecules

Homochiral metal–organic framework (MOF) membranes have been recently reported for chiral separations. However, only a few high‐quality homochiral polycrystalline MOF membranes have been fabricated due to the difficulty in crystallization of a chiral MOF layer without defects on porous substrates. Alternatively, mixed matrix membranes (MMMs), which combine potential advantages of MOFs and polymers, have been widely demonstrated for gas separation and water purification. Here we report novel homochiral MOF–polymer MMMs for efficient chiral separation. Homochirality was successfully incorporated into achiral MIL‐53‐NH₂ nanocrystals by post‐synthetic modification with amino acids, such as l ‐histidine (l ‐His) and l ‐glutamic acid (l ‐Glu). The MIL‐53‐NH‐l ‐His and MIL‐53‐NH‐l ‐Glu nanocrystals were then embedded into polyethersulfone (PES) matrix to form homochiral MMMs, which exhibited excellent enantioselectivity for racemic 1‐phenylethanol with the highest enantiomeric excess value up to 100 %. This work, as an example, demonstrates the feasibility of fabricating diverse large‐scale homochiral MOF‐based MMMs for chiral separation.     

Probing the mechanism of the interaction between l‐cysteine‐capped‐CdTe quantum dots and Hg2+ using capillary electrophoresis with ensemble techniques

A good understanding of the mechanism of interaction between quantum dots (QDs) and heavy metal ions is essential for the design of more effective sensor systems. In this work, CE was introduced to explore how l ‐cysteine‐capped‐CdTe QDs (l ‐cys‐CdTe QDs) interacts with Hg²⁺. The change in electrophoretic mobility can synchronously reflect the change in the composition and property of QDs. The effects of the free and capping ligands on the system are discussed in detail. ESI‐MS, dynamic light scattering (DLS), zeta potential, and fluorescence (FL) were also applied as cooperative tools to study the interaction mechanism. Furthermore, the interaction mechanism, which principally depended on the concentration of Hg²⁺, was proposed reasonably. At the low concentration of Hg²⁺, the formation of a static complex between Hg²⁺ and the carboxyl and amino groups of l ‐cys‐CdTe QDs surface was responsible for the FL quenching. With the increase of Hg²⁺ concentration, the capping l ‐cys was stripped from the surface of l ‐cys‐CdTe QDs due to the high affinity of Hg²⁺ to the thiol group of l ‐cys. Our study demonstrates that CE can reveal the mechanism of the interaction between QDs and heavy metal ions, such as FL quenching.     

Functional Genome Mining Reveals a Class V Lanthipeptide Containing a d‐Amino Acid Introduced by an F420H2‐Dependent Reductase

Lantibiotics are a type of ribosomally synthesized and post‐translationally modified peptides (termed lanthipeptides) with often potent antimicrobial activity. Herein, we report the discovery of a new lantibiotic, lexapeptide, using the library expression analysis system (LEXAS) approach. Lexapeptide has rare structural modifications, including N‐terminal (N,N)‐dimethyl phenylalanine, C‐terminal (2‐aminovinyl)‐3‐methyl‐cysteine, and d ‐Ala. The characteristic lanthionine moiety in lexapeptide is formed by three proteins (LxmK, LxmX, and LxmY), which are distinct from enzymes known to be involved in lanthipeptide biosynthesis. Furthermore, a novel F₄₂₀H₂‐dependent reductase (LxmJ) from the lexapeptide biosynthetic gene cluster (BGC) is identified to catalyze the reduction of dehydroalanine to install d ‐Ala. Our findings suggest that lexapeptide is the founding member of a new class of lanthipeptides that we designate as class V. We also identified further class V lanthipeptide BGCs in actinomycetes and cyanobacteria genomes, implying that other class V lantibiotics await discovery.     

Circularly Polarized Luminescence of Chiral Perylene Diimide Based Enantiomers Triggered by Supramolecular Self‐Assembly

Two perylene diimide (PDI) enantiomers ( d/l ‐PDI ) incorporating the d /l ‐alanine moiety have been designed and synthesized. d/l ‐PDI in chloroform displays bright‐yellow fluorescence that is redshifted to orange‐red when the solvent contains a methanol fraction of 99 vol %. No circular dichroism (CD) or circularly polarized luminescence (CPL) signals were observed for d/l ‐PDI enantiomers in CHCl₃. Interestingly, the d/l ‐PDI enantiomers exhibit clear mirror‐image Cotton effects and CPL emission in the aggregate state. The optical anisotropy factor (g_lum) is as high as 0.02 at f_m=99 %, which can be attributed to self‐assembly through intermolecular π–π interactions in the aggregate state.     

A Combined Effect of Thermal and Enzymatic Racemization for d‐Aspartic Acid to l‐Aspartic Acid by High‐Performance Liquid Chromatography Assay

The racemization of d ‐aspartic acid to l ‐aspartic acid has been successfully performed with a coupled enzyme system at 90 °C and a pH of about 4.0 by the assay of high‐performance liquid chromatography. This coupled enzymatic racemization is a successive two‐step reaction first induced by d ‐amino acid oxidase and a subsequent coupled reaction by an aminotransferase clonezyme with the help of coenzyme pyridoxal 5′‐phosphate and cosubstrate l ‐glutamate. Due to the very high temperature, part of the l ‐aspartic acid is produced by the thermal effect. In fact the thermal racemization for aspartic acid can proceed from either d ‐ or l ‐aspartic acid via an intermediate fumaric acid and leads to the formation of d ,l ‐malic acid. The formation of α‐oxalacetic acid formed irreversibly from d ‐aspartic acid with d ‐amino acid oxidase can induce a side reaction to l ‐alanine. The thermal effect may also be responsible for the production of d ‐, and l ‐alanine.     

Oligonucleotide Analogues with a Nucleobase‐Including Backbone,Part 7, Molecular Dynamics Simulation of a DNA Duplex Containing a 2′‐Deoxyadenosine 8‐(Hydroxymethyl)‐Derived Nucleotide

The structure and stability of a 14‐mer DNA duplex containing a nucleotide analog with a hydroxymethyl substituent at the C(8) of 2′‐deoxyadenosine has been investigated by molecular‐dynamics simulation. The DNA duplex studied has the sequence 5′‐d(CGTAAGCTCGATAG)‐3′⋅5′‐d(CTATCGA*GCTTACG)‐3′, where the O(3′) of the dG₆ nucleotide in the second strand is linked through a phosphinato group with the O(10) of the dA 2′‐deoxyadenosine‐derived nucleotide. Previous experimental results showed that the stability of this duplex in aqueous solution of 0.1M NaCl at pH 7 and room temperature is significantly lower than that of the corresponding unmodified DNA duplex. Comparison of molecular‐dynamics trajectories of the unmodified and modified B‐DNA duplexes in aqueous solution, at similar conditions than the experiment, shows that the substitution of the dA nucleotide by the dA* nucleotide in the second strand induces stretching of the double helix, which results in opening of the grooves and consequent exposure of the double‐helix core to the solvent.     

Rationale on the Abnormal Effect of Temperature on the Enantioselectivity in the Asymmetric Borane Reduction of Ketones Catalyzed by L‐Prolinol

The effect of temperature on the enantioselectivity of the oxazaborolidine‐catalyzed asymmetric borane reduction of ketones was investigated in the presence of (5S)‐3‐oxa‐1‐aza‐2‐borabicyclo[3.3.0]octane (=(3aS)‐tetrahydro‐1H,3H‐pyrolo[1,2‐c][1,3,2]oxazaborole; 1a ) and its 2‐methoxy derivative ( 1b ) as catalysts, which were synthesized from L ‐prolinol with borane and trimethyl borate, respectively. The results indicate that the two catalysts induce a different temperature‐dependent enantioselectivity. The enantioselectivity of the B‐unsubstituted (5S)‐3‐oxa‐1‐aza‐borabicyclo[3.3.0]octane ( 1a ) increases with increasing temperature, while its B‐methoxy‐substituted derivative 1b shows the highest enantioselectivity at ca. 50°. (5S)‐3‐Oxa‐1‐aza‐2‐borabicyclo[3.3.0]octane ( 1a ) is more likely to dimerize than its 2‐methoxy derivative 1b . The conversion rates of L ‐proline to L ‐prolinol in the presence of different amounts of borane were also determined in this study.