Strategies Towards Capturing Nitrogenase Substrates and Intermediates via Controlled Alteration of Electron Fluxes

Nitrogenase utilizes an ATP-dependent reductase to deliver electrons to its catalytic component to enable two important reactions: the reduction of N₂ to NH₄⁺, and the reduction of CO to hydrocarbons. The two nitrogenase-based reactions parallel the industrial Haber–Bosch and Fischer–Tropsch processes, yet they occur under ambient conditions. As such, understanding the enzymatic mechanism of nitrogenase is crucial for the future development of biomimetic strategies for energy-efficient production of valuable chemical commodities. Mechanistic investigations of nitrogenase has long been hampered by the difficulty to trap substrates and intermediates relevant to the nitrogenase reactions. Recently, we have successfully captured CO on the Azotobacter vinelandii V-nitrogenase via two approaches that alter the electron fluxes in a controlled manner: one approach utilizes an artificial electron donor to trap CO on the catalytic component of V-nitrogenase in the resting state; whereas the other employs a mismatched reductase component to reduce the electron flux through the system and consequently accumulate CO on the catalytic component of V-nitrogenase. Here we summarize the major outcome of these recent studies, which not only clarified the catalytic relevance of the one-CO (lo-CO) and multi-CO (hi-CO) bound states of nitrogenase, but also pointed to a potential competition between N₂ and CO for binding to the same pair of reactive Fe sites across the sulfur belt of the cofactor. Together, these results highlight the utility of these strategies in poising the cofactor at a well-defined state for substrate- or intermediate-trapping via controlled alteration of electron fluxes, which could prove beneficial for further elucidation of the mechanistic details of nitrogenase-catalyzed reactions.     

Targeting the Substrate Binding Site of E. coli Nitrile Reductase QueF by Modeling,Substrate and Enzyme Engineering

Nitrile reductase QueF catalyzes the reduction of 2‐amino‐5‐cyanopyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₀) to 2‐amino‐5‐aminomethylpyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₁) in the biosynthetic pathway of the hypermodified nucleoside queuosine. It is the only enzyme known to catalyze a reduction of a nitrile to its corresponding primary amine and could therefore expand the toolbox of biocatalytic reactions of nitriles. To evaluate this new oxidoreductase for application in biocatalytic reactions, investigation of its substrate scope is prerequisite. We report here an investigation of the active site binding properties and the substrate scope of nitrile reductase QueF from Escherichia coli. Screenings with simple nitrile structures revealed high substrate specificity. Consequently, binding interactions of the substrate to the active site were identified based on a new homology model of E. coli QueF and modeled complex structures of the natural and non‐natural substrates. Various structural analogues of the natural substrate preQ₀ were synthesized and screened with wild‐type QueF from E. coli and several active site mutants. Two amino acid residues Cys190 and Asp197 were shown to play an essential role in the catalytic mechanism. Three non‐natural substrates were identified and compared to the natural substrate regarding their specific activities by using wild‐type and mutant nitrile reductase.     

Structure-based bioisosteric design,synthesis and biological evaluation of novel pyrimidines as antiplasmodial antifolate agents

The efficacy of most marketed antimalarial drugs has been compromised by the development of parasite resistance, underscoring an urgent need to find new drugs with new mechanisms of action. This article describes the synthesis and the in vitro antimalarial profiling of antifolate P218 analogues, by exploring a bioisosteric replacement of the carboxylic group by a phosphinic moiety as well as structural isomerization of P218. The detailed synthetic route employed to access the title compounds is described. The listed compounds exhibited low antimalarial activity against drug-resistant strains of P. falciparum including chloroquine-resistant W2.     

Identification of 3-Methoxycarpachromene and Masticadienonic Acid as New Target Inhibitors against Trypanothione Reductase from Leishmania Infantum Using Molecular Docking and ADMET Prediction

Polyphenolic and Terpenoids are potent natural antiparasitic compounds. This study aimed to identify new drug against Leishmania parasites, leishmaniasis’s causal agent. A new in silico analysis was accomplished using molecular docking, with the Autodock vina program, to find the binding affinity of two important phytochemical compounds, Masticadienonic acid and the 3-Methoxycarpachromene, towards the trypanothione reductase as target drugs, responsible for the defense mechanism against oxidative stress and virulence of these parasites. There were exciting and new positive results: the molecular docking results show as elective binding profile for ligands inside the active site of this crucial enzyme. The ADMET study suggests that the 3-Methoxycarpachromene has the highest probability of human intestinal absorption. Through this work, 3-Methoxycarpachromene and Masticadienonic acid are shown to be potentially significant in drug discovery, especially in treating leishmaniasis. Hence, drug development should be completed with promising results.     

Comparison of Transcriptomic Profiles of MiaPaCa-2 Pancreatic Cancer Cells Treated with Different Statins

Statins have been widely used for the treatment of hypercholesterolemia due to their ability to inhibit HMG-CoA reductase, the rate-limiting enzyme of de novo cholesterol synthesis, via the so-called mevalonate pathway. However, their inhibitory action also causes depletion of downstream intermediates of the pathway, resulting in the pleiotropic effects of statins, including the beneficial impact in the treatment of cancer. In our study, we compared the effect of all eight existing statins on the expression of genes, the products of which are implicated in cancer inhibition and suggested the molecular mechanisms of their action in epigenetic and posttranslational regulation, and in cell-cycle arrest, death, migration, or invasion of the cancer cells.     

新型嘧啶单环类非经典叶酸拮抗剂的合成及抗肿瘤活性研究

以课题组前期设计合成的非经典叶酸拮抗剂6-(4'-甲基苯乙基)-N5-氯乙酰基-2,4-二氨基哌啶并[3,2-d]嘧啶(wm-8.2)为先导化合物,将wm-8.2中的哌啶并嘧啶双环结构简化为嘧啶单环结构,以提高分子柔韧性并简化分子结构,根据6-位空间占位设计6-H和6-甲基两个系列,考察了不同桥链长度和不同芳香杂环侧链对抗肿瘤活性的影响.同时对具有叶酸抑制剂分子结构特征的关键中间体进行活性对比测定,研究了N(5)位氯乙酰基对活性的影响.两个系列目标化合物和关键中间体共36个化合物的结构均经1H NMR,13C NMR和MS确证.生物活性测定表明,6位为甲基的化合物中,具有三碳桥链及对甲基苯环侧链的6-甲基-2,4-二氨基-5-(N-(4-甲基苯基)丙基-N-(2-氯乙酰基))氨基嘧啶(6b-3)具有最好的HL-60、A549和HCT116细胞增殖抑制活性,IC50分别为0.25,0.83和0.63μmol?L^-1.化合物6b-3在N(5)位氯乙酰基取代之前的关键中间体6-甲基-2,4-二氨基-5-(N-(4-甲基苯基)丙基)氨基嘧啶(5b-3)具有最优的二氢叶酸还原酶抑制活性.总结了化合物的构效关系,并用计算机模拟进行了阐释.     

Enzymatic Conversion of Flavonoids using Bacterial Chalcone Isomerase and Enoate Reductase

Flavonoids are a large group of plant secondary metabolites with a variety of biological properties and are therefore of interest to many scientists, as they can lead to industrially interesting intermediates. The anaerobic gut bacterium Eubacterium ramulus can catabolize flavonoids, but until now, the pathway has not been experimentally confirmed. In the present work, a chalcone isomerase (CHI) and an enoate reductase (ERED) could be identified through whole genome sequencing and gene motif search. These two enzymes were successfully cloned and expressed in Escherichia coli in their active form, even under aerobic conditions. The catabolic pathway of E. ramulus was confirmed by biotransformations of flavanones into dihydrochalcones. The engineered E. coli strain that expresses both enzymes was used for the conversion of several flavanones, underlining the applicability of this biocatalytic cascade reaction.     

Peptide prefractionation is essential for proteomic approaches employing multiple‐reaction monitoring of fruit proteomic research

Off‐gel? IEF has become a popular tool in proteomics research to fractionate peptides or proteins. We conducted a detailed investigation on the fruit proteomics of apple, banana, and strawberry fruit employing Off‐gel? electrophoresis (OGE) as a crucial step to improve the proteome coverage and quantitative proteomic workflows including multiple‐reaction monitoring (MRM). We provide technical details concerning the application of Off‐gel?IEF, nano‐LC–MS detection, and MRM optimization and analysis. Our results demonstrated that the application of OGE is an effective method for peptide fractionation and increased significantly the number of proteins identified by at least ten times, with more total peptides detected and collected. Furthermore, we developed a protocol combining OGE and MRM studies to identify and quantitatively investigate monodehydroascorbate reductase, a key enzyme in the redox and antioxidant system of apple fruit during fruit ripening. Using this method, the quantitative changes in this protein during ripening and in response to ethylene treatment was investigated. Our results provide direct and comprehensive evidence demonstrating the benefits of OGE and its application for both shotgun and quantitative proteomics research.     

Nickel(II)-Mediated Reversible Thiolate/Disulfide Conversion as a Mimic for a Key Step of the Catalytic Cycle of Methyl-Coenzyme M Reductase

According to the well-accepted mechanism, methyl-coenzyme M reductase (MCR) involves Ni-mediated thiolate-to-disulfide conversion that sustains its catalytic cycle of methane formation in the energy saving pathways of methanotrophic microbes. Model complexes that illustrate Ni-ion mediated reversible thiolate/disulfide transformation are unknown. In this paper we report the synthesis, crystal structure, spectroscopic properties and redox interconversions of a set of Ni^II complexes comprising a tridentate N₂S donor thiol and its analogous N₄S₂ donor disulfide ligands. These complexes demonstrate reversible Ni^II-thiolate/Ni^II-disulfide (both bound and unbound disulfide-S to Ni^II) transformations via thiyl and disulfide monoradical anions that resemble a primary step of MCR's catalytic cycle.