On the hydrolysis mechanisms of amides and peptides

Disulfide/α-Amide-Bridged Doxorubicin Dimeric Prodrug: Effect of Aggregation Structures on pH/GSH Dual-Triggered Drug Release

Disulfide bonding has attracted intense interest in the tumor intracellular microenvironment-activated drug delivery systems (DDSs) in the last decades. Although various molecular structures of redox-responsive disulfide-containing DDSs have been developed, no investigation was reported on the effect of aggregation structures. Here, the effect of aggregation structures on pH/GSH dual-triggered drug release was investigated with the simplest pH/GSH dual-triggered doxorubicin-based drug self-delivery system (DSDS), the disulfide/α-amide-bridged doxorubicin dimeric prodrug (DDOX), as a model. By fast precipitation or slow self-assembly, DDOX nanoparticles were obtained. With similar diameters, they exhibited different pH/GSH dual-triggered drug releases, demonstrating the effect of aggregation structures. The π-π stacking in different degrees was revealed by the UV-vis, fluorescence, and BET analysis of the DDOX nanoparticles. The effect of the π-π stacking between the dimeric prodrug and its activated products on drug release was also explored with the molecular simulation approach. The finding opens new ideas in the design of high-performance DDSs for future precise tumor treatment.

Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling

The formation of an amide bond is an essential step in the synthesis of materials and drugs, and in the assembly of amino acids to form peptides. The mechanism of this reaction has been studied extensively, in particular to understand how it can be catalyzed, but a representation capable of explaining all the experimental data is still lacking. Numerical simulation should provide the necessary molecular description, but the solvent involvement poses a number of challenges. Here, we combine the efficiency and accuracy of neural network potential-based reactive molecular dynamics with the extensive and unbiased exploration of reaction pathways provided by transition path sampling. Using microsecond-scale simulations at the density functional theory level, we show that this method reveals the presence of two competing distinct mechanisms for peptide bond formation between alanine esters in aqueous solution. We describe how both reaction pathways, via a general base catalysis mechanism and via direct cleavage of the tetrahedral intermediate respectively, change with pH. This result contrasts with the conventional mechanism involving a single pathway in which only the barrier heights are affected by pH. We show that this new proposal involving two competing mechanisms is consistent with the experimental data, and we discuss the implications for peptide bond formation under prebiotic conditions and in the ribosome. Our work shows that integrating deep potential molecular dynamics with path sampling provides a powerful approach for exploring complex chemical mechanisms.

Recycling and Degradation of Polyamides

As one of the five major engineering plastics, polyamide brings many benefits to humans in the fields of transportation, clothing, entertainment, health, and more. However, as the production of polyamide increases year by year, the pollution problems it causes are becoming increasingly severe. This article reviews the current recycling and treatment processes of polyamide, such as chemical, mechanical, and energy recovery, and degradation methods such as thermal oxidation, photooxidation, enzyme degradation, etc. Starting from the synthesis mechanism of polyamide, it discusses the advantages and disadvantages of different treatment methods of polyamide to obtain more environmentally friendly and economical treatment schemes. Finding enzymes that can degrade high-molecular-weight polyamides, exploring the recovery of polyamides under mild conditions, synthesizing environmentally degradable polyamides through copolymerization or molecular design, and finally preparing degradable bio-based polyamides may be the destination of polyamide.

Molecular Retention Limitations for Prevascularized Subcutaneous Sites for Islet Transplantation

Beta cell replacement therapies utilizing the subcutaneous space have inherent advantages to other sites: the potential for increased accessibility, noninvasive monitoring, and graft extraction. Site prevascularization has been developed to enhance islet survivability in the subcutaneous zone while minimizing potential foreign body immune responses. Molecular communication between the host and prevascularized implant site remains ill-defined. Poly(ethylene oxide)s (PEOs) of various hydrated radii (i.e., ∼11-62 Å) were injected into prevascularized subcutaneous sites in C57BL/6 mice, and the clearance and organ biodistribution were characterized. Prevascularization formed a barrier that confined the molecules compared with the unmodified site. Molecular clearance from the prevascularized site was inversely proportional to the molecular weight. The upper limit in molecular size for entering the vasculature to be cleared was determined to be 35 kDa MW PEO. These findings provide insight into the impact of vascularization on molecular retention at the injection site and the effect of molecular size on the mobility of hydrophilic molecules from the prevascularized site to the host. This information is necessary for optimizing the transplantation site for increasing the beta cell graft survival.

A suture-free, shape self-adaptive and bioactive PEG-Lysozyme implant for Corneal stroma defect repair and rapid vision restoration

Corneal transplantation is a prevailing treatment to repair injured cornea and restore vision but faces the limitation of donor tissue shortage clinically. In addition, suturing-needed transplantation potentially causes postoperative complications. Herein, we design a PEG-Lysozyme injective hydrogel as a suture-free, shape self-adaptive, bioactive implant for corneal stroma defect repair. This implant experiences a sol-gel phase transition via an in situ amidation reaction between 4-arm-PEG-NHS and lysozyme. The physicochemical properties of PEG-Lysozyme can be tuned by the components ratio, which confers the implant mimetic corneal modulus and provides tissue adhesion to endure increased intraocular pressure. In vitro tests prove that the implant is beneficial to Human corneal epithelial cells growth and migration due to the bioactivity of lysozyme. Rabbit lamellar keratoplasty experiment demonstrates that the hydrogel can be filled into defect to form a shape-adaptive implant adhered to native stroma. The implant promotes epithelialization and stroma integrity, recovering the topology of injured cornea to normal. A newly established animal forging behavior test prove a rapid visual restoration of rabbits when use implant in a suture free manner. In general, this work provides a promising preclinical practice by applicating a self-curing, shape self-adaptive and bioactive PEG-Lysozyme implant for suture-free stroma repair.

Utilization of a kinetic isotope effect to decrease decomposition of ceftriaxone in a mixture of D2O/H2O

The discovery of cephalosporin and demonstration of its improved stability in aqueous solution, as well as enhanced in vitro activity against penicillin-resistant organisms, were major breakthroughs in the development of β-lactam antibiotics. Although cephalosporins are more stable with respect to hydrolytic degradation than penicillins, they still experience a variety of chemical transformations. The present study offers an insight into the rates and mechanisms of ceftriaxone degradation at the therapeutic concentration in water, a mixture of water and deuterium oxide, and deuterium oxide itself at the neutral pH. Specific ceftriaxone degradation products were observed in aged samples (including a previously unreported dimer-type species), and by comparing the degradation rates in H₂O and D₂O, the observation of a kinetic isotope effect provided some valuable insight as to the nature of the initial ceftriaxone degradation. The effect of protium to deuterium isotope change on the degradation kinetics of ceftriaxone was evaluated using the method of initial rates based on HPLC analysis as well as by quantitative ¹H NMR spectroscopy. Moreover, computational analysis was utilized to get a molecular insight into chemical processes governing the ceftriaxone degradation and to rationalize the stabilizing effect of replacing H₂O with D₂O.

Reconstructing Reactivity in Dynamic Host-Guest Systems at Atomistic Resolution: Amide Hydrolysis Under Confinement in the Cavity of a Coordination Cage

Spatial confinement is widely employed by nature to attain unique efficiency in controlling chemical reactions. Notable examples are enzymes, which selectively bind reactants and exquisitely regulate their conversion into products. In an attempt to mimic natural catalytic systems, supramolecular metal–organic cages capable of encapsulating guests in their cavity and of controlling/accelerating chemical reactions under confinement are attracting increasing interest. However, the complex nature of these systems, where reactants/products continuously exchange in-and-out of the host, makes it often difficult to elucidate the factors controlling the reactivity in dynamic regimes. As a case study, here we focus on a coordination cage that can encapsulate amide guests and enhance their hydrolysis by favoring their mechanical twisting towards reactive molecular configurations under confinement. We designed an advanced multiscale simulation approach that allows us to reconstruct the reactivity in such host–guest systems in dynamic regimes. In this way, we can characterize amide encapsulation/expulsion in/out of the cage cavity (thermodynamics and kinetics), coupling such host–guest dynamic equilibrium with characteristic hydrolysis reaction constants. All computed kinetic/thermodynamic data are then combined, obtaining a statistical estimation of reaction acceleration in the host–guest system that is found in optimal agreement with the available experimental trends. This shows how, to understand the key factors controlling accelerations/variations in the reaction under confinement, it is necessary to take into account all dynamic processes that occur as intimately entangled in such host–guest systems. This also provides us with a flexible computational framework, useful to build structure–dynamics–property relationships for a variety of reactive host–guest systems.

Encapsulation of guests in metal–organic cages allows control over chemical reactivity. Focusing on the hydrolysis of amides, here we show an effective molecular simulation approach to reconstruct reactivity in host–guest systems in dynamic regimes.

Achieving an Order of Magnitude Speedup in Hybrid-Functional- and Plane-Wave-Based Ab Initio Molecular Dynamics: Applications to Proton-Transfer Reactions in Enzymes and in Solution

Ab initio molecular dynamics (MD) with hybrid density functionals and a plane wave basis is computationally expensive due to the high computational cost of exact exchange energy evaluation. Recently, we proposed a strategy to combine adaptively compressed exchange (ACE) operator formulation and a multiple time step integration scheme to reduce the computational cost significantly [J. Chem. Phys. 2019, 151, 151102 ]. However, it was found that the construction of the ACE operator, which has to be done at least once in every MD time step, is computationally expensive. In the present work, systematic improvements are introduced to further speed up by employing localized orbitals for the construction of the ACE operator. By this, we could achieve a computational speedup of an order of magnitude for a periodic system containing 32 water molecules. Benchmark calculations were carried out to show the accuracy and efficiency of the method in predicting the structural and dynamical properties of bulk water. To demonstrate the applicability, computationally intensive free-energy computations at the level of hybrid density functional theory were performed to investigate (a) methyl formate hydrolysis reaction in neutral aqueous media and (b) proton-transfer reaction within the active-site residues of the class C β-lactamase enzyme.

Studies on the synthesis and stability of α-ketoacyl peptides

Oxidative stress, an excess of reactive oxygen species (ROS), may lead to oxidative post-translational modifications of proteins resulting in the cleavage of the peptide backbone, known as α-amidation, and formation of fragments such as peptide amides and α-ketoacyl peptides (α-KaP). In this study, we first compared different approaches for the synthesis of different model α-KaP and then investigated their stability compared to the corresponding unmodified peptides. The stability of peptides was studied at room temperature or at temperatures relevant for food processing (100 °C for cooking and 150 °C as a simulation of roasting) in water, in 1% (m/v) acetic acid or as the dry substance (to simulate the thermal treatment of dehydration processes) by HPLC analysis. Oxidation of peptides by 2,5-di-tert-butyl-1,4-benzoquinone (DTBBQ) proved to be the most suited method for synthesis of α-KaPs. The acyl side chain of the carbonyl-terminal α-keto acid has a crucial impact on the stability of α-KaPs. This carbonyl group has a catalytic effect on the hydrolysis of the neighboring peptide bond, leading to the release of α-keto acids. Unmodified peptides were significantly more stable than the corresponding α-KaPs. The possibility of further degradation reactions was shown by the formation of Schiff bases from glyoxylic or pyruvic acids with glycine and proven through detection of transamination products and Strecker aldehydes of α-keto acids by HPLC–MS/MS. We propose here a mechanism for the decomposition of α-ketoacyl peptides.

Glutamine as an Ammonia Donor in Catabolism of the Glucosinolate, Sinalbin, in Biosynthesis of 4-Hydroxybenzylamine

Amines synthesized by plants may be considered a dietary source of bioactive compounds, which are of interest due to possible health promoting effects. Developing Sinapis alba sprouts are known to produce 4-hydroxybenzylamine, but the reaction mechanism has not yet been established. We propose here a suggested metabolic pathway for the formation of 4-hydroxybenzylamine in S. alba plants. The catabolic sequence starts with a reaction between l-glutamine (Gln) as ammonia donor and 4-hydroxybenzyl carbocation, the enzymatic catalyzed hydrolysis product from sinalbin (4-hydroxybenzylglucosinolate). The suggested reactions are compared with alternative plant metabolic reactions used in the biosynthesis of biogenic amines.