Intramolecular general base catalyzed ester hydrolysis. The hydrolysis of 2-aminobenzoate esters

Malonyl-based Chemosensors: Selective Detection of Fe3+ Ion in Aqueous Medium

Two novel malonyl-based chemosensors, N,N'-bis(ethyl-4'-benzoate)-1,3-propanediamide (1) and N,N'-bis(ethyl-3'-benzoate)-1,3-propanediamide (2), have been synthesized and screened towards various biologically important metal ions such as Na⁺, Mg²⁺, K⁺, Ca²⁺, Al³⁺, Cr³⁺, Mn²⁺, Fe²⁺, Fe³⁺, Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺, Ag⁺, Cd²⁺, Hg²⁺, Ti³⁺, and Pb²⁺. The emission spectral studies of both 1 and 2 displayed 84 - 91% turn-off emission responses selectively with Fe³⁺ ion in aqueous buffer (MeCN/H₂O, 1:4, v/v, pH = 7.4) solution. Chemosensors 1 and 2 exhibited remarkable sensing ability towards Fe³⁺ ion over other metal ions with limit of detection (LOD) of 4.28 and 4.33 μM, respectively. The binding stoichiometry of 1 and 2 with Fe³⁺ ion was studied by Benesi-Hildebrand fitting, Stern-Volmer plot and Job's plots, revealing that both chemosensors (1 - 2) bind with Fe³⁺ metal ion in 1:1 stoichiometric ratio with the apparent association constant (K_a) 8.90 × 10³ and 11.16 × 10³ M^-1, respectively. Furthermore, the interactions of chemosensors (1 - 2) with metal ion were also investigated by using density functional theory (DFT) at B3LYP hybrid functional using 6-31G and LanL2DZ basis sets.

Coordination among Bond Formation/Cleavage in a Bifunctional-Catalyzed Fast Amide Hydrolysis: Evidence for an Optimized Intramolecular N-Protonation Event

A density functional theory (DFT) computational analysis, using the ωB97X-D functional, of a rapid amide cleavage in 2-carboxyphthalanilic acid (2CPA), where the amide group is flanked by two catalytic carboxyls, reveals key mechanistic information: (a) General base catalysis by a carboxylate coupled to general acid catalysis by a carboxyl is not operative. (b) Nucleophilic attack by a carboxylate on the amide carbonyl coupled to general acid catalysis at the amide oxygen can also be ruled out. (c) A mechanistic pathway that remains viable involves general acid proton delivery to the amide nitrogen by a carboxyl, while the other carboxylate engages in nucleophilic attack upon the amide carbonyl; a substantially unchanged amide carbonyl in the transition state; two concurrent bond-forming events; and a spatiotemporal-base rate acceleration. This mechanism is supported by molecular dynamic simulations which confirm a persistent key intramolecular hydrogen bonding. These theoretical conclusions, although not easily verified by experiment, are consistent with a bell-shaped pH/rate profile but are at odds with hydrolysis mechanisms in the classic literature.

Influence of Block Length on Articular Cartilage Lubrication with a Diblock Bottle-Brush Copolymer

We report how the tribological properties of a class of diblock copolymers with architecture and function inspired by the lubricating glycoprotein lubricin correlate to chemical composition. This class of diblock copolymers, consisting of a cationic cartilage-binding block and a brush-lubricating block, demonstrates that boundary lubrication of articular cartilage more strongly depends on the cartilage-binding block than the lubrication block. Specifically, the cartilage-binding functional groups (tertiary or quaternary amines) and cartilage-binding block length significantly influence the degree of lubrication under boundary mode experimental conditions. An optimal number (∼24 in this case) of cartilage-binding groups led to the lowest coefficient of friction, and an increase or decrease in the number of cations in the binding block led to partial (>24, and between 12 and 24) or complete (=12) loss of lubricating ability. The length of the lubricating block (DP = 200 or 400) chosen in this study had no effect on the degree of lubrication. These results are put into context in terms of binding affinity to the cartilage and the spatial packing density of the polymer on the cartilage surface and can serve as a useful guide for future designs of synthetic lubricants that rival the efficacy of natural lubricants.

Dynamic Ureas with Fast and pH-Independent Hydrolytic Kinetics

Low cost, high performance hydrolysable polymers are of great importance in biomedical applications and materials industries. While many applications require materials to have a degradation profile insensitive to external pH to achieve consistent release profiles under varying conditions, hydrolysable chemistry techniques developed so far have pH-dependent hydrolytic kinetics. This work reports the design and synthesis of a new type of hydrolysable polymer that has identical hydrolysis kinetics from pH 3 to 11. The unprecedented pH independent hydrolytic kinetics of the aryl ureas were shown to be related to the dynamic bond dissociation controlled hydrolysis mechanism; the resulting hindered poly(aryl urea) can be degraded with a hydrolysis half-life of 10 min in solution. More importantly, these fast degradable hindered aromatic polyureas can be easily prepared by addition polymerization from commercially available monomers and are resistant to hydrolysis in solid form for months under ambient storage conditions. The combined features of good stability in solid state and fast hydrolysis at various pH values is unprecedented in polyurea material, and will have implications for materials design and applications, such as sacrificial coatings and biomaterials.

DehydroalanylGly, a new post translational modification resulting from the breakdown of glutathione

BACKGROUND

The human body contains numerous long-lived proteins which deteriorate with age, typically by racemisation, deamidation, crosslinking and truncation. Previously we elucidated one reaction responsible for age-related crosslinking, the spontaneous formation of dehydroalanine (DHA) intermediates from phosphoserine and cysteine. This resulted in non-disulphide covalent crosslinks. The current paper outlines a novel posttranslational modification (PTM) in human proteins, which involves the addition of dehydroalanylglycine (DHAGly) to Lys residues.

METHODS

Human lens digests were examined by mass spectrometry for the presence of (DHA)Gly (+144.0535 Da) adducts to Lys residues. Peptide model studies were undertaken to elucidate the mechanism of formation.

RESULTS

In the lens, this PTM was detected at 18 lysine sites in 7 proteins. Using model peptides, a pathway for its formation was found to involve initial formation of the glutathione degradation product, γ-Glu(DHA)Gly from oxidised glutathione (GSSG). Once the Lys adduct formed, the Glu residue was lost in a hydrolytic mechanism apparently catalysed by the ε-amino group of the Lys.

CONCLUSIONS

This discovery suggests that within cells, the functional groups of amino acids in proteins may be susceptible to modification by reactive metabolites derived from GSSG.

GENERAL SIGNIFICANCE

Our finding demonstrates a novel +144.0535 Da PTM arising from the breakdown of oxidised glutathione.

A computational study of the glycylserine hydrolysis at physiological pH: a zwitterionic versus anionic mechanism

The hydrolysis of GlySer at physiological pH was investigated by modeling the most feasible reaction mechanisms in aqueous phase at the MP2/6-311+(2df,2p)//SMD-M06/6-311+(2df,2p) level of the theory. To refine the energies of the most relevant transition states along the reaction paths the cluster-continuum concept was adopted. The hydrolytic process could proceed through two competitive mechanisms involving either the zwitterionic or the anionic form of GlySer. The calculations suggest that at physiological pH the actual mechanism is most probably mixed, anionic-zwitterionic. In this reaction scheme the first stage of N→O acyl transfer involves the anionic form whereas the second stage, during which the resultant ester is hydrolyzed, most likely involves the zwitterionic ester form of GlySer. The energy requirement for the first reaction stage is estimated to be slightly lower than for the second one. The calculated activation parameters (e.g. ΔG(#) = 27.8 kcal mol(-1)) for the nucleophilic addition of a water molecule to the ester carbonyl group of the zwitterionic ester are in good agreement with the experimentally determined values at pD 7.4 (ΔG(#) = 28.7 kcal mol(-1)).

Poly(ethylene glycol)-block-cationic polylactide nanocomplexes of differing charge density for gene delivery

Representing a new type of biodegradable cationic block copolymer, well-defined poly(ethylene glycol)-block-cationic polylactides (PEG-b-CPLAs) with tertiary amine-based cationic groups were synthesized by thiol-ene functionalization of an allyl-functionalized diblock precursor. Subsequently the application of PEG-b-CPLAs as biodegradable vectors for the delivery of plasmid DNAs (pDNAs) was investigated. Via the formation of PEG-b-CPLA:pDNA nanocomplexes by spontaneous electrostatic interaction, pDNAs encoding luciferase or enhanced green fluorescent protein were successfully delivered to four physiologically distinct cell lines (including macrophage, fibroblast, epithelial, and stem cell). Formulated nanocomplexes demonstrated high levels of transfection with low levels of cytotoxicity and hemolysis when compared to a positive control. Biophysical characterization of charge densities of nanocomplexes at various polymer:pDNA weight ratios revealed a positive correlation between surface charge and gene delivery. Nanocomplexes with high surface charge densities were utilized in an in vitro serum gene delivery inhibition assay, and effective gene delivery was observed despite high levels of serum. Overall, these results help to elucidate the influence of charge, size, and PEGylation of nanocomplexes upon the delivery of nucleic acids in physiologically relevant conditions.

Evaluation of the regioselective delactonization of tri-sialic acid lactone by in-solution molecular dynamics simulation

An approximate model for the delactonization of tri-sialic acid lactone is presented with two water-layers that led to neutral hydrolysis of δ-lactone. The hydrolytic reactivity was studied with a 10-ns in-solution molecular dynamics simulation. The initial step of this hydrolysis involves a reactant water nucleophile complex via a proton transfer with another water molecule. Therefore, the probability of water molecules localized at the hydrolytic center correlates to the hydrolysis of δ-lactone. The stepwise delactonization of α2,8-(NeuAc)(3) lactone results/resulted from water concentration discrepancy near the carbonyl carbon of lactones in two water oxygen···carbonyl carbon shells, and the distances of OC···O(water) layers were 2.8 Å and 5.1 Å. Based on in-solution molecular dynamics study, the motion of water molecules over the re-face of the carbonyl groups was used for the quantitative description of the residence probability, p, whose value is 0.11 for lactone I and 0.33 for lactone II. The geometric criteria used to determine the residence statistics are (1) the distance of water-oxygen···carbonyl carbon in less than 5.1 Å and (2) the cone angle, θ, of carbonyl OC···O(water) in the range of 85-115°. As expected, a higher residence probability at lactone II led to its faster hydrolysis. Both the radial g(r) and angular p(θ) pair distribution functions of water oxygen and carbonyl groups of lactones ensure a better surrounding hydration encounter for lactone II. In contrast, water molecules around lactone I are deduced due to a steric hindrance by the turn structure of α2,8-(NeuAc)(3) lactone.

Protein autoproteolysis: conformational strain linked to the rate of peptide cleavage by the pH dependence of the N --> O acyl shift reaction

Nucleophilic attack by a side chain nucleophile on the adjacent peptide bond followed by N --> O or N --> S acyl shift is the primary step in protein autoproteolysis. Precursor structures of autoproteolytic proteins reveal strained (or twisted) amides at the site of cleavage, and we previously showed that SEA domain autoproteolysis involves substrate destabilization by approximately 7 kcal/mol. However, the precise chemical mechanism by which conformational energy is converted into reaction rate acceleration has not been understood. Here we show that the pH dependence of autoproteolysis in a slow-cleaving mutant (1G) of the MUC1 SEA domain is consistent with a mechanism in which N --> O acyl shift proceeds after initial protonation of the amide nitrogen. Unstrained amides have pK(a) values of 0 with protonation on the oxygen, and autoproteolysis is therefore immeasurably slow at neutral pH. However, conformational strain forces the peptide nitrogen into a pyramidal conformation with a significantly increased pK(a) for protonation. We find that pK(a) values of approximately 4 and approximately 6, as in model compounds of twisted amides, reproduce the rate of autoproteolysis in the 1G and wild-type SEA domains, respectively. A mechanism involving strain, nitrogen protonation, and N --> O shift is also supported by quantum-chemical calculations. Such a reaction therefore constitutes an alternative to peptide cleavage that is utilized in autoproteolysis, as opposed to a classical mechanism involving a structurally conserved active site with a catalytic triad and an oxyanion hole, which are not present at the SEA domain cleavage site.

Synthesis of Degradable Functional Poly(ethylene glycol) Analogs as Versatile Drug Delivery Carriers

Poly(ethylene glycol) (PEG) is widely used as a water soluble carrier for polymer-drug conjugates. Herein, we report degradable linear PEG analogs (DPEGs) carrying multifunctional groups. The DPEGs were synthesized by a Michael addition based condensation polymerization of dithiols and PEG diacrylates (PEGDA) or dimethacrylates (PEGDMA). They were stable at pH 7.4 but quickly degraded at pH 6.0 and 5.0. Thus, DPEGs could be used as drug carriers without concern for their retention in the body. DPEGs could be made to carry such functional groups as terminal thiol or (meth)acrylate and pendant hydroxyl groups. The functional groups were used for conjugation of drugs and targeting groups. This new type of PEG analog will be useful for drug delivery and the PEGylation of biomolecules and colloidal particles.

Kinetic and Theoretical Studies on the Mechanism of Intramolecular Catalysis in Phenyl Ester Hydrolysis

The kinetic study of the hydrolysis reaction of Z-substituted phenyl hydrogen maleates (Z = H, m-CH3, p-CH3, m-Cl, p-Cl and m-CN) was carried out in aqueous solution, and the results were complemented with theoretical studies. Under some experimental conditions, two kinetic processes were observed. One of them was ascribed to maleic anhydride formation and the other to the anhydride hydrolysis. The Brönsted-type plot for the leaving-group dependence was linear with slope beta(lg) = -1. The experimental results are consistent with a mechanism that involves significant bond breaking in the rate-limiting transition state (alpha(lg) = 0.64). Theoretical results for the reaction in the gas phase showed an excellent Brönsted-type dependence with a beta(lg) of -1.03. A tetrahedral intermediate (TI) could not be found through DFT gas-phase studies (B3LYP/6-311+G*). Calculations carried out within a continuous solvation model or with discrete water molecules failed to find a stable TI. With both models, a flat region on the potential-energy surface is found and a tight optimization of the structures led back to starting materials. The theoretical results do not discard the possible existence of an unstable intermediate on the free-energy surface, but the analysis of the whole body of results compared with other acyl transfer reactions lead us to suggest that an enforced concerted mechanism is the most appropriate to describe these reactions.

Mechanism of Hydrolysis and Aminolysis of Homocysteine Thiolactone

Homocysteine thiolactone (tHcy) is deemed a risk factor for cardiovascular diseases and strokes, presumably because it acylates the side chain of protein lysine residues ("N-homocysteinylation"), thereby causing protein damage and autoimmune responses. We analysed the kinetics of hydrolysis and aminolysis of tHcy and two related thiolactones (gamma-thiobutyrolactone and N-trimethyl-tHcy), and we have thereby described the first detailed mechanism of thiolactone aminolysis. As opposed to the previously studied (thio and oxo)esters and (oxo)lactones, aminolysis of thiolactones was found to be first order with respect to amine concentration. Anchimeric assistance by the alpha-amino group of tHcy (through general acid/base catalysis) could not be detected, and the Brønsted plot (nucleophilicity versus pK(a)) for aminolysis yielded a slope (beta(nuc)) value of 0.66. These data support a mechanism of aminolysis where the rate-determining step is the formation of a zwitterionic tetrahedral intermediate. The beta(nuc) value and steric factors dictate a regime whereby, at physiological pH values (pH 7.4), maximal reactivity of tHcy is exhibited with primary amine groups with a pK(a) value of 7.7; this allows the reactivity of various protein amino groups towards N-homocysteinylation to be predicted.

Kinetics and Mechanism of the Reactions of S-2,4-Dinitrophenyl 4-Substituted Thiobenzoates with Secondary Alicyclic Amines

[reaction: see text] The title reactions, in 44 wt % ethanol-water at 25.0 degrees C, exhibit slightly curved Brønsted-type plots (log kN versus pKa of amines) with slopes beta1 = 0.1-0.44 (at high pKa) and beta2 ca. 0.7 (at low pKa). The magnitude of some of these slopes, together with the fact that the curvature center (pKa(0) = 9.5-10.8) does not change with the electronic effects of the benzoyl substituent, suggests that these reactions are not stepwise, but concerted.

A safety catch linker for Fmoc-based assembly of constrained cyclic peptides

A new safety-catch linker for Fmoc solid-phase peptide synthesis of cyclic peptides is reported. The linear precursors were assembled on a tert-butyl protected catechol derivative using optimized conditions for Fmoc-removal. After activation of the linker using TFA, neutralization of the N-terminal amine induced cyclization with concomitant cleavage from the resin yielding the cyclic peptides in DMF solution. Several constrained cyclic peptides were synthesized in excellent yields and purities.