Cyclic Changes in Active Site Polarization and Dynamics Drive the 'Ping-pong' Kinetics in NRH:Quinone Oxidoreductase 2: An Insight from QM/MM Simulations

Computational Study on Flavin-Catalyzed Aerobic Dioxygenation of Alkenyl Thioesters: Decomposition of Anionic Peroxides

Flavin-dependent catalysts are widely applied to aerobic monooxygenation/oxidation reactions. In contrast, flavin-catalyzed aerobic dioxygenation reactions exhibit higher atomic economy but are less reported, not to mention the relevant mechanistic studies. Herein, a density functional theory study on flavin-catalyzed aerobic epoxidation-oxygenolysis of alkenyl thioesters was performed for the first time. Different from the previous mechanistic proposal, a pathway featuring two catalytic stages, monoanionic flavin-C(4a)-peroxide/oxide intermediates, and a reverse reaction sequence (epoxidation goes prior to oxygenolysis) was revealed. In comparison, the pathways involving dianionic flavin catalysts, monoanionic flavin-N(5)-(hydro)peroxide/C(10a)-peroxide, or neutral flavin-C(4a)-hydroperoxide/hydroxide/N(5)-oxide, and the pathways where oxygenolysis goes prior to epoxidation are less favored. Epoxidation goes through intramolecular substitution of the O-O bond of anionic flavin-C(4a)-peroxide by β-carbon, while the resulting flavin-C(4a)-oxide accomplishes the oxygenolysis. Furthermore, two other reaction modes, i.e., concerted O-O cleavage/1,2-shift of α-substituents and dyotropic rearrangement were discovered for the decomposition of other anionic peroxides, and preliminary rules were summarized for understanding the chemoselectivity for this process. This study sheds light on the different reaction features of numerous flavin-dioxygen derivatives, providing deeper insights into flavin-catalyzed dioxygenation reactions, and is expected to inspire experimental design based on unconventional anionic peroxides.

Virtual Screening of Molecules via Neural Fingerprint-based Deep Learning Technique

A machine learning-based drug screening technique has been developed and optimized using convolutional neural network-derived fingerprints. The optimization of weights in the neural network-based fingerprinting technique was compared with fixed Morgan fingerprints in regard to binary classification on drug-target binding affinity. The assessment was carried out using six different target proteins using randomly chosen small molecules from the ZINC15 database for training. This new architecture proved to be more efficient in screening molecules that less favorably bind to specific targets and retaining molecules that favorably bind to it.

Scientific contribution

We have developed a new neural fingerprint-based screening model that has a significant ability to capture hits. Despite using a smaller dataset, this model is capable of mapping chemical space similar to other contemporary algorithms designed for molecular screening. The novelty of the present algorithm lies in the speed with which the models are trained and tuned before testing its predictive capabilities and hence is a significant step forward in the field of machine learning-embedded computational drug discovery.

Polymorphisms and Pharmacogenomics of NQO2: The Past and the Future

The flavoenzyme N-ribosyldihydronicotinamide (NRH):quinone oxidoreductase 2 (NQO2) catalyzes two-electron reductions of quinones. NQO2 contributes to the metabolism of biogenic and xenobiotic quinones, including a wide range of antitumor drugs, with both toxifying and detoxifying functions. Moreover, NQO2 activity can be inhibited by several compounds, including drugs and phytochemicals such as flavonoids. NQO2 may play important roles that go beyond quinone metabolism and include the regulation of oxidative stress, inflammation, and autophagy, with implications in carcinogenesis and neurodegeneration. NQO2 is a highly polymorphic gene with several allelic variants, including insertions (I), deletions (D) and single-nucleotide (SNP) polymorphisms located mainly in the promoter, but also in other regulatory regions and exons. This is the first systematic review of the literature reporting on NQO2 gene variants as risk factors in degenerative diseases or drug adverse effects. In particular, hypomorphic 29 bp I alleles have been linked to breast and other solid cancer susceptibility as well as to interindividual variability in response to chemotherapy. On the other hand, hypermorphic polymorphisms were associated with Parkinson's and Alzheimer's disease. The I and D promoter variants and other NQO2 polymorphisms may impact cognitive decline, alcoholism and toxicity of several nervous system drugs. Future studies are required to fill several gaps in NQO2 research.

Neuroprotective Properties of Quinone Reductase 2 Inhibitor M-11, a 2-Mercaptobenzimidazole Derivative

The ability of NQO2 to increase the production of free radicals under enhanced generation of quinone derivatives of catecholamines is considered to be a component of neurodegenerative disease pathogenesis. The present study aimed to investigate the neuroprotective mechanisms of original NQO2 inhibitor M-11 (2-[2-(3-oxomorpholin-4-il)-ethylthio]-5-ethoxybenzimidazole hydrochloride) in a cellular damage model using NQO2 endogenous substrate adrenochrome (125 µM) and co-substrate BNAH (100 µM). The effects of M-11 (10-100 µM) on the reactive oxygen species (ROS) generation, apoptosis and lesion of nuclear DNA were evaluated using flow cytometry and single-cell gel electrophoresis assay (comet assay). Results were compared with S29434, the reference inhibitor of NQO2. It was found that treatment of HT-22 cells with M-11 results in a decline of ROS production triggered by incubation of cells with NQO2 substrate and co-substrate. Pre-incubation of HT-22 cells with compounds M-11 or S29434 results in a decrease of DNA damage and late apoptotic cell percentage reduction. The obtained results provide a rationale for further development of the M-11 compound as a potential neuroprotective agent.

Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase

Prolyl-tRNA synthetases (ProRSs) catalyze the covalent attachment of proline onto cognate tRNAs, an indispensable step for protein synthesis in all living organisms. ProRSs are modular enzymes and the "prokaryotic-like" ProRSs are distinguished from "eukaryotic-like" ProRSs by the presence of an editing domain (INS) inserted between motifs 2 and 3 of the main catalytic domain. Earlier studies suggested the presence of coupled-domain dynamics could contribute to catalysis; however, the role that the distal, highly mobile INS domain plays in catalysis at the synthetic active site is not completely understood. In the present study, a combination of theoretical and experimental approaches has been used to elucidate the precise role of INS domain dynamics. Quantum mechanical/molecular mechanical simulations were carried out to model catalytic Pro-AMP formation by Enterococcus faecalis ProRS. The energetics of the adenylate formation by the wild-type enzyme was computed and contrasted with variants containing active site mutations, as well as a deletion mutant lacking the INS domain. The combined results revealed that two distinct types of dynamics contribute to the enzyme's catalytic power. One set of motions is intrinsic to the INS domain and leads to conformational preorganization that is essential for catalysis. A second type of motion, stemming from the electrostatic reorganization of active site residues, impacts the height and width of the energy profile and has a critical role in fine tuning the substrate orientation to facilitate reactive collisions. Thus, motions in a distal domain can preorganize the active site of an enzyme to optimize catalysis.

Colloidal-sized zirconium porphyrin metal-organic frameworks with improved peroxidase-mimicking catalytic activity, stability and dispersity

Metal-organic frameworks (MOFs) have attracted great attention as enzyme mimic materials in colorimetric hydrogen peroxide (H₂O₂) detection. At present, it is highly desirable but remains challenging to prepare MOFs with high stability and dispersity to further improve their peroxidase-mimicking catalytic activity. In this work, we developed a new and facile method for the synthesis of a sub-100 nm peroxidase-mimicking zirconium porphyrin metal-organic framework (Zr-PorMOF) via a solvothermal method. The experimental results indicated that compared with the micron-sized crystals obtained using a classical synthesis method, the catalytic activity, stability and dispersity in water of the colloidal Zr-PorMOF were obviously enhanced. The as-synthesized colloidal Zr-PorMOF was further successfully applied in colorimetric H₂O₂ detection, and satisfactory detection performance was obtained. Furthermore, the colloidal Zr-PorMOF was also successfully employed in the construction of a peroxidase-based tandem catalysis system. Taking glucose oxidase as an example, this system was successfully applied for glucose sensing in real human serum samples, which proved its practical feasibility in diabetes diagnosis and indicates its high potential feasibility in peroxidase-related applications in complex biomatrix.