Catalytic Mechanism of Hyaluronate Lyase from <i>Spectrococcus pneumonia</i>: Quantum Mechanical/Molecular Mechanical and Density Functional Theory Studies

Hyaluronate lyase from <i>Spectrococcus pneumonia</i> can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. The major functions of hyaluronan are to regulate water balance and osmotic pressure and act as an ion-exchange resin. It has been suggested in our previous molecular dynamics simulation that the binding of the substrate molecule could lead to the ionization of Y408 and protonation of H399. Followed by our recent molecular dynamics simulation of the enzyme–substrate complex, a unified proton abstraction and donation mechanism for this enzyme can be established using a combined quantum mechanical and molecular mechanical approach and density functional theory method. Y408 is shown to serve as the general base in the proton abstraction, while general acid is the next proton donation step. Overall, this reaction can be classified into <i>syn</i>-elimination reaction mechanism. The neutralization effects of C5 carboxylate group by several polar residues such as N349 and H399 were also examined. Finally, in combination of our previous molecular dynamics simulations, a complete catalytic cycle for the degradation of hyaluronan tetrasaccharide catalyzed by the hyaluronate lyase from <i>Spectrococcus pneumonia</i> is proposed

New Delhi Metallo-β-Lactamase I: Substrate Binding and Catalytic Mechanism

Metallo-β-lactamases can hydrolyze and deactivate lactam-containing antibiotics, which is the major mechanism for causing drug resistance in the treatment of bacterial infections. This has become a global concern because of the lack of clinically approved inhibitors so far. The emergence of New Delhi metallo-β-lactamase I (NDM-1) makes the situation even more serious. In this work, first, the structure of NDM-1 in complex with the inhibitor molecule l-captopril is investigated by both density functional theory (DFT) and hybrid quantum mechanical/molecular mechanical (QM/MM) methods, and the theoretical results are in good agreement with the X-ray structure. The Michaelis structure with an antibiotic compound (ampicillin) bound in the active site is constructed from a recent X-ray structure of the NDM-1 enzyme with hydrolyzed ampicillin. It is further simulated using a QM/MM molecular dynamics method. One of the interesting binding features of ampicillin in the NDM-1 active site is that the conserved C3 carboxylate group is not ligated with Zn2 but rather is only hydrogen-bonded with N220 and K211. A bridging hydroxide ion is suggested to connect two zinc cofactors. This hydroxide ion is also hydrogen-bonded with D124. Subsequent reaction path calculations indicate that the initial step of lactam ring-opening occurs through a concerted step in which the cleavage of the C–N bond and the transfer of the hydrogen bond to D124 are nearly concerted. The ligand bond between Zn2 and the C3 carboxylate group forms after the first step of nucleophilic addition. The calculated activation energy barrier height is about 19.4 kcal/mol for the hydrolysis of ampicillin, which can be compared with the experimental value of 15.8 kcal/mol derived from <i>k</i>_cat = 15 s^–1. The overall mechanism is finally confirmed by a subsequent DFT study of a truncated active-site model

Initial Events in the Degradation of Hyaluronan Catalyzed by Hyaluronate Lyase from Spectrococcus pneumoniae: QM/MM Simulation

Hyaluronate lyase from Spectrococcus pneumonia can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. The major functions of hyaluronan are to regulate water balance and osmotic pressure and act as an ion-exchange resin. In this work, we focus on the prerequisite issue of the enzymatic reaction, i.e., the initial reactive conformer. Based on the quantum mechanical and molecular mechanical molecular dynamic simulations and free energy profiles, a near attack conformer was obtained for the degradation of hyaluronan catalyzed by the hyaluronate lyase. Along with the substrate binding, the phenylhydroxyl hydrogen atom of Tyr408 will transfer to nearby His399 via a near barrierless transition state, which results in a negatively charged Tyr408 and positively charged His399. The Tyr408, rather than the previously proposed His399, was suggested to act as the general base for the subsequent β-elimination reaction. The His399 was suggested to have the function of neutralizing the C5-carboxyl group

One-Step Synthesis of Nanoscale Zeolitic Imidazolate Frameworks with High Curcumin Loading for Treatment of Cervical Cancer

A straightforward nanoprecipitating method was developed to prepare water dispersible curcumin (CCM)-loaded nanoscale zeolitic imidazolate framework-8 (CCM@NZIF-8) nanoparticles (NPs). The as-synthesized CCM@NZIF-8 NPs possess high drug encapsulation efficiency (88.2%), good chemical stability and fast drug release in tumor acidic microenvironments. Confocal laser scanning microscopy and cytotoxicity experiments reveal that NZIF-8 based nanocarriers promote the cellular uptake of CCM and result in higher cytotoxicity of CCM@NZIF-8 than that of free CCM toward HeLa cells. The in vivo anticancer experiments indicate that CCM@NZIF-8 NPs exhibit much higher antitumor efficacy than free CCM. This work highlights the potential of using nanoscale metal organic framworks (NMOFs) as a simple and stable platform for developing a highly efficient drug delivery system in cancer treatment

Ester Formation via Nickel-Catalyzed Reductive Coupling of Alkyl Halides with Chloroformates

The synthesis of alkyl esters from readily available alkyl halides and chloroformates was achieved for the first time using a mild Ni-catalyzed reductive coupling protocol. Unactivated primary and secondary alkyl iodides as well as glycosyl, benzyl, and aminomethyl halides were successfully employed to yield products in moderate to excellent yields with high functional group tolerance

Styrene as 4π-Component in Zn(II)-Catalyzed Intermolecular Diels–Alder/Ene Tandem Reaction

A mild Zn-catalyzed intermolecular Diels–Alder/ene tandem reaction with styrene as a 4π-component is reported. A variety of dihydro­naphthalene products could be prepared in moderate to good yields. Moreover, a combination of DFT calculations and experiments was performed to further understand the mechanism of this unique tandem reaction

“Amide Resonance” in the Catalysis of 1,2-α‑l‑Fucosidase from Bifidobacterium bifidum

Bifidobacterium is a genus of Gram-positive bacteria, which is important in the absorption of nourishment from the human milk oligosaccharides (HMO). We present here the detailed simulation of the enzymatic hydrolysis of 2′-fucosyllactose catalyzed by 1,2-α-l-fucosidase from Bifidobacterium bifidum using the combined quantum mechanical and molecular mechanical approach. Molecular dynamics simulations and free energy profiles support that the overall reaction is a stepwise mechanism. The first step is the proton transfer from N423 to D766, and the second step involves the hydrolysis reaction via the inversion mechanism catalyzed by the amide group of N423. Assisted by D766, N423 serves as the general base to activate the water molecule to attack the anomeric carbon center. E566 is the general acid to facilitate the cleavage of glycosidic bond between l-fucose and galactose units. The intrinsic resonance structure for the side chain amide group of the asparagine residue is shown to be the origin to the catalytic activity, which is also confirmed by the mutagenesis simulation of N423G

Thermodynamic Functions for the Solubility of 3‑Nitrobenzonitrile in 12 Organic Solvents from <i>T</i>/K = (278.15 to 318.15)

The solubilities of 3-nitrobenzonitrile in 12 organic solvents including methanol, ethanol, <i>n</i>-propanol, isopropanol, acetone, <i>n</i>-butanol, 2-methyl-1-propanol, acetonitrile, acetic acid, ethyl acetate, cyclohexane, and toluene were measured by the static method within the temperature range from (278.15 to 318.15) K under atmospheric pressure of 101.1 kPa. The mole fraction solubility of 3-nitrobenzonitrile in the selected solvents increased with a rise in temperature. In general, they ranked as acetone > (acetonitrile, ethyl acetate) > toluene > acetic acid > methanol > ethanol > <i>n</i>-propanol > <i>n</i>-butanol > isopropanol >2-methyl-1-propanol > cyclohexane. The achieved solubilities of 3-nitrobenzonitrile were correlated via the <i>λh</i> equation, modified Apelblat equation, NRTL model, and Wilson model. The maximum relative average deviation and root-mean-square deviation were 1.87% and 2.399 × 10^–3, respectively. Finally, the mixing properties, e.g., change in Gibbs energy, enthalpy, entropy, activity coefficient at infinitesimal concentration, and reduced excess enthalpy, were also derived on the basis of the Wilson model. The mixing process of 3-nitrobenzonitrile in these solvents was endothermic and spontaneous

Additional file 1: Figure S1. of Size Control and Growth Process Study of Au@Cu2O Particles

(a) TEM image. (b) Particle size histograms and UV-is spectra of the Au triangular nanoplate (TN) colloids. Figure S2. Photograph of colloidal suspensions of the samples. (DOCX 443 kb

Ultrasonic Treatment Enhanced Ammonia-Oxidizing Bacterial (AOB) Activity for Nitritation Process

Oxidation of ammonia to nitrite rather than nitrate is critical for nitritation process for wastewater treatment. We proposed a promising approach by using controlled ultrasonic treatment to enhance the activity of ammonia-oxidizing bacteria (AOB) and suppress that of nitrite-oxidizing bacteria (NOB). Batch activity assays indicated that when ultrasound was applied, AOB activity reached a peak level and then declined but NOB activity deteriorated continuously as the power intensity of ultrasound increased. Kinetic analysis of relative microbial activity versus ultrasonic energy density was performed to investigate the effect of operational factors (power, sludge concentration, and aeration) on AOB and NOB activities and the test parameters were selected for reactor tests. Laboratory sequential batch reactor (SBR) was further used to test the ultrasonic stimulus with 8 h per day operational cycle and synthetic waste urine as influent. With specific ultrasonic energy density of 0.09 kJ/mg VSS and continuously fed influent containing above 200 mg NH₃–N/L, high AOB reproductive activity was achieved and nearly complete conversion of ammonia-N to nitrite was maintained. Microbial structure analysis confirmed that the treatment changed community of AOB, NOB, and heterotrophs. Known AOB <i>Nitrosomonas</i> genus remained at similar level in the biomass while typical NOB <i>Nitrospira</i> genus disappeared in the SBR under ultrasonic treatment and after the treatment was off for 30 days