Oxidative Cleavage of Aromatic C-O Linkages by Oxoammonium Salts.

Oxidative cleavage of aromatic C(sp2)-O bond is important to the conversion of biomass and plastic wastes into value-added chemicals. Here we put forward the oxidative cleavage of para-C-O bonds in phenolic compounds in use of oxoammonium salts as oxidant and water as the oxygen source. The mechanism is that oxoammonium cation activates water to form hydroxy-oxoammonium adduct and thus realizes the ipso-substitution of 4-alkoxyphenol, which is proved by substituent effect, isotope labelling experiments, and kinetic analysis. Furthermore, this protocol is successfully applied into the depolymerization of both lignin model compounds with α-O-5 and 4-O-5 linkages and polyphenylene oxide (PPO).

Oxygenation of Phenols with Water as the Oxygen Source and Oxoammonium Salt as the Oxidant.

Aromatic C-H oxygenation is important in both industrial production and organic synthesis. Here we report a metal-free approach for phenol oxygenation with water as the oxygen source using oxoammonium salts as the renewable oxidant. Employing this protocol, various alkyl-substituted phenols were converted into benzoquinones in yields of 59-98%. On the basis of 18O-labeling and kinetic studies, the hydroxy-oxoammonium adduct was proposed to attack the aromatic ring similarly to electrophilic aromatic substitution. We suppose that the findings described here not only provide an efficient and highly selective protocol for aromatic C-H oxygenation but also may encourage further developments of possible transition-metal-free catalytic methods.

Highly Efficient Ruthenium-Catalyzed Semi-hydrogenation of Urea Derivatives to Formamides.

The utilization of CO2 as a non-toxic and cheap feedstock for C1 is a desirable route to achieve high value-added chemicals. In this context, we report a highly efficient ruthenium-catalyzed semi-hydrogenation reaction of CO2 -derived ureas. Various alkyl and aryl urea derivatives were successfully hydrogenated to obtain the corresponding recyclable amines and formamides (up to 97 % yield), highlighting the good substrate applicability of this method, which makes this method a sustainable alternative for the hydrogenation of CO2 to formamides in the presence of amines. In the meantime, we have discovered a new pathway that enables rapid hydrogenation of urea derivatives even at lower H2 pressure (<5 bar). This methodology might provide a new insight into the reduction functionalization of CO2 under mild pressure to form new C-N bond. Based on the control experiments and the observed intermediate products, we clarify the mechanism for selective semi-hydrogenation of ureas.

The diverse roles and dynamic rearrangement of vimentin during viral infection.

Epidemics caused by viral infections pose a significant global threat. Cytoskeletal vimentin is a major intermediate filament (IF) protein, and is involved in numerous functions, including cell signaling, epithelial-mesenchymal transition, intracellular organization and cell migration. Vimentin has important roles for the life cycle of particular viruses; it can act as a co-receptor to enable effective virus invasion and guide efficient transport of the virus to the replication site. Furthermore, vimentin has been shown to rearrange into cage-like structures that facilitate virus replication, and to recruit viral components to the location of assembly and egress. Surprisingly, vimentin can also inhibit virus entry or egress, as well as participate in host-cell defense. Although vimentin can facilitate viral infection, how this function is regulated is still poorly understood. In particular, information is lacking on its interaction sites, regulation of expression, post-translational modifications and cooperation with other host factors. This Review recapitulates the different functions of vimentin in the virus life cycle and discusses how they influence host-cell tropism, virulence of the pathogens and the consequent pathological outcomes. These insights into vimentin-virus interactions emphasize the importance of cytoskeletal functions in viral cell biology and their potential for the identification of novel antiviral targets.

Topology-independent and global protein structure alignment through an FFT-based algorithm.

MOTIVATION: Protein structure alignment is one of the fundamental problems in computational structure biology. A variety of algorithms have been developed to address this important issue in the past decade. However, due to their heuristic nature, current structure alignment methods may suffer from suboptimal alignment and/or over-fragmentation and thus lead to a biologically wrong alignment in some cases. To overcome these limitations, we have developed an accurate topology-independent and global structure alignment method through an FFT-based exhaustive search algorithm, which is referred to as FTAlign. RESULTS: Our FTAlign algorithm was extensively tested on six commonly used datasets and compared with seven state-of-the-art structure alignment approaches, TMalign, DeepAlign, Kpax, 3DCOMB, MICAN, SPalignNS and CLICK. It was shown that FTAlign outperformed the other methods in reproducing manually curated alignments and obtained a high success rate of 96.7 and 90.0% on two gold-standard benchmarks, MALIDUP and MALISAM, respectively. Moreover, FTAlign also achieved the overall best performance in terms of biologically meaningful structure overlap (SO) and TMscore on both the sequential alignment test sets including MALIDUP, MALISAM and 64 difficult cases from HOMSTRAD, and the non-sequential sets including MALIDUP-NS, MALISAM-NS, 199 topology-different cases, where FTAlign especially showed more advantage for non-sequential alignment. Despite its global search feature, FTAlign is also computationally efficient and can normally complete a pairwise alignment within one second. AVAILABILITY AND IMPLEMENTATION: http://huanglab.phys.hust.edu.cn/ftalign/.

Aerobic α-hydroxylation of 2-Me-1-tetralone in 1-alkyl-3-methylimidazolium ionic liquids.

The aerobic α-hydroxylation of 2-Me-1-tetralone was investigated in imidazol-based ionic liquids (ILs), where reactions in 1-alkyl-3-methylimidazolium tetrafluoroborates were found to generate considerable products. By correlating the conversion at 2 h with viscosity, relative permittivity and the ET(30) value of ILs, we found that the local polarity in ILs represented by the ET(30) value or the chemical shift of α-proton at the substrate was the critical factor influencing the reaction rate. Furthermore, two-dimensional nuclear Overhauser effect spectroscopy (2D NOESY) was used to characterize the distribution of 2-Me-1-tetralone in ILs. As a result, the mesoscopic structures in ILs were recommended to have crucial influences on the distribution of the substrate in ILs, and the caused local polarity could affect the activation of 2-Me-1-tetralone. These findings revealed the solvent effects of ILs with different structures on the α-hydroxylation of 2-Me-1-tetralone, and may encourage the explorations of more types of aerobic oxidations in ILs.

PepBDB: a comprehensive structural database of biological peptide-protein interactions.

Summary: A structural database of peptide-protein interactions is important for drug discovery targeting peptide-mediated interactions. Although some peptide databases, especially for special types of peptides, have been developed, a comprehensive database of cleaned peptide-protein complex structures is still not available. Such cleaned structures are valuable for docking and scoring studies in structure-based drug design. Here, we have developed PepBDB-a curated Peptide Binding DataBase of biological complex structures from the Protein Data Bank (PDB). PepBDB presents not only cleaned structures but also extensive information about biological peptide-protein interactions, and allows users to search the database with a variety of options and interactively visualize the search results. Availability and implementation: PepBDB is available at http://huanglab.phys.hust.edu.cn/pepbdb/.

Determination of an effective scoring function for RNA-RNA interactions with a physics-based double-iterative method.

RNA-RNA interactions play fundamental roles in gene and cell regulation. Therefore, accurate prediction of RNA-RNA interactions is critical to determine their complex structures and understand the molecular mechanism of the interactions. Here, we have developed a physics-based double-iterative strategy to determine the effective potentials for RNA-RNA interactions based on a training set of 97 diverse RNA-RNA complexes. The double-iterative strategy circumvented the reference state problem in knowledge-based scoring functions by updating the potentials through iteration and also overcame the decoy-dependent limitation in previous iterative methods by constructing the decoys iteratively. The derived scoring function, which is referred to as DITScoreRR, was evaluated on an RNA-RNA docking benchmark of 60 test cases and compared with three other scoring functions. It was shown that for bound docking, our scoring function DITScoreRR obtained the excellent success rates of 90% and 98.3% in binding mode predictions when the top 1 and 10 predictions were considered, compared to 63.3% and 71.7% for van der Waals interactions, 45.0% and 65.0% for ITScorePP, and 11.7% and 26.7% for ZDOCK 2.1, respectively. For unbound docking, DITScoreRR achieved the good success rates of 53.3% and 71.7% in binding mode predictions when the top 1 and 10 predictions were considered, compared to 13.3% and 28.3% for van der Waals interactions, 11.7% and 26.7% for our ITScorePP, and 3.3% and 6.7% for ZDOCK 2.1, respectively. DITScoreRR also performed significantly better in ranking decoys and obtained significantly higher score-RMSD correlations than the other three scoring functions. DITScoreRR will be of great value for the prediction and design of RNA structures and RNA-RNA complexes.

Addressing recent docking challenges: A hybrid strategy to integrate template-based and free protein-protein docking.

Protein-protein docking is an important computational tool for predicting protein-protein interactions. With the rapid development of proteomics projects, more and more experimental binding information ranging from mutagenesis data to three-dimensional structures of protein complexes are becoming available. Therefore, how to appropriately incorporate the biological information into traditional ab initio docking has been an important issue and challenge in the field of protein-protein docking. To address these challenges, we have developed a Hybrid DOCKing protocol of template-based and template-free approaches, referred to as HDOCK. The basic procedure of HDOCK is to model the structures of individual components based on the template complex by a template-based method if a template is available; otherwise, the component structures will be modeled based on monomer proteins by regular homology modeling. Then, the complex structure of the component models is predicted by traditional protein-protein docking. With the HDOCK protocol, we have participated in the CPARI experiment for rounds 28-35. Out of the 25 CASP-CAPRI targets for oligomer modeling, our HDOCK protocol predicted correct models for 16 targets, ranking one of the top algorithms in this challenge. Our docking method also made correct predictions on other CAPRI challenges such as protein-peptide binding for 6 out of 8 targets and water predictions for 2 out of 2 targets. The advantage of our hybrid docking approach over pure template-based docking was further confirmed by a comparative evaluation on 20 CASP-CAPRI targets. Proteins 2017; 85:497-512. © 2016 Wiley Periodicals, Inc.

Comparative pharmacokinetics of free doxorubicin and a liposomal formulation in cats following intravenous administration.

Doxorubicin, a potent chemotherapeutic agent used extensively in cancer treatment, displays complex pharmacokinetic behavior, especially across various formulations. With a rising incidence of cancer cases in cats, understanding the drug's pharmacokinetics in feline subjects remains a critical yet unexplored area. Hence, this study investigated the pharmacokinetic profile of doxorubicin after slow intravenous administration of doxorubicin hydrochloride (DOX·HCl) or doxorubicin hydrochloride pegylated liposome (DOX·HCl-PLI) in twelve cats at a single dose of 20 mg/m2. Blood samples collected at pretreatment time (0 h) and over 192 h were analyzed using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS). The obtained pharmacokinetic parameters of doxorubicin revealed significant differences between the two formulations and were as follows: elimination half-life (T1/2λz) of 5.00 ± 3.20 h (DOX·HCl) and 17.62 ± 8.13 h (DOX·HCl-PLI), area under the concentration/time curve from 0 to last point (AUClast) of 0.67 ± 0.12 µg hr./mL (DOX·HCl) and 783.09 ± 267.29 µg hr./mL (DOX·HCl-PLI), and total body clearance (CL_obs) of 27098.58 ± 5205.19 mL/h/m2 (DOX·HCl) and 28.65 ± 11.09 mL/h/m2 (DOX·HCl-PLI). Additionally, differences were also detected in the apparent volume of distribution (Vz_obs) with 178.56 ± 71.89 L/m2 (DOX·HCl) and 0.64 ± 0.20 L/m2 (DOX·HCl-PLI), and the maximum plasma concentration (Cmax) with 2.25 ± 0.30 µg/mL (DOX·HCl) and 24.02 ± 5.45 µg/mL (DOX·HCl-PLI). Notably, low concentration of doxorubicinol, the metabolite of doxorubicin, was detected in plasma after administration of DOX·HCl, with even less present when DOX·HCl-PLI was administered. This investigation provides valuable insights into the distinct pharmacokinetic behaviors of DOX·HCl and DOX·HCl-PLI in cats, contributing essential groundwork for future studies and potential clinical applications in feline oncology.

Key Roles of Free Cations in Modulating the Reaction Rate in Imidazolium Ionic Liquid-Dimethyl Sulfoxide Mixtures.

Imidazolium ionic liquids (ILs) are widely utilized in various fields due to their distinctive properties. However, their high viscosity limits their application in specific reactions, and mixing ILs with organic components is a way to solve this problem. While previous studies mainly focused on the structural changes of ILs after adding organic molecules, no studies elucidated the influence of their existing species on chemical reactions. In this study, aerobic α-hydroxylation of 2-methylcyclohexanone was chosen as a model reaction, and the reaction rate was found to be adjusted by varying imidazolium concentration in its mixtures with dimethyl sulfoxide. To elucidate the mechanism, the distribution of species in an IL solution and its change with concentration were studied by molecular dynamics simulations, and the results revealed the significant impact of the concentration of free cations on the reaction rate. The interaction between the ionic species and reaction intermediate, as calculated by density functional theory, highlighted the crucial role of free cations in this reaction. This study demonstrates the feasibility of tuning the concentration of free cations by varying the concentration of the IL solution, establishing the relationship between its microstructure and chemical reaction efficiency, thus providing vital information for the design and application of ILs.

Relation Between Calcium-Phosphorus Product and Total Coronary Artery Occlusion in a Nonchronic Kidney Disease Population: A Cross-Sectional Study.

Excessive calcium-phosphorus product (Ca-P product) in patients with chronic kidney disease (CKD) is associated with coronary artery calcification and coronary artery disease, but the relation between Ca-P product and coronary artery disease in non-CKD populations has rarely been reported. Therefore, we designed a cross-sectional study to investigate the role of Ca-P product in total coronary artery occlusion (TCAO) in a non-CKD population. We reviewed 983 patients who underwent coronary angiography at Guangyuan Central Hospital from February 2018 to January 2020. Ca-P product (mg2/dl2) was calculated as Ca (mmol/L) × 4 × P (mmol/L) × 3.1 and was analyzed as a continuous and tertiary variable. TCAO was defined as complete occlusion of any coronary artery by coronary angiography (thrombolysis in myocardial infarction flow grade 0). Statistical analysis was performed using univariate and multivariate logistic regression models and restricted cubic splines. Univariate logistic regression analysis showed a statistically significant association between Ca-P product and TCAO (odds ratio [OR] 0.97, 95% confidence interval [CI] 0.95 to 0.99, p <0.001). After stepwise adjustment for covariates, the risk of TCAO was reduced by 40% in the high versus low Ca-P group (OR 0.6, 95% CI 0.38 to 0.95, p = 0.031), and the risk of TCAO was predicted to decrease by 4% (OR 0.96, 95% CI 0.94 to 0.99, p = 0.006) for each unit increase in Ca-P product. Restricted cubic splines showed a nonlinear relation between Ca-P product and TCAO, with a significant decrease in the risk of TCAO after reaching 27.46 (nonlinear p = 0.047). In conclusion, in non-CKD populations, a higher Ca-P product (≥27.46 mg2/dl2) may help avoid TCAO.

Development of a UPLC-MS/MS method for quantifying KPT-335 (Verdinexor) in feline plasma for a study of PK.

KPT-335 (Verdinexor) is a novel SINE that potently inhibits the nucleoprotein Exportin 1 (XPO1/CRM1) of tumor cell lines and reduces the replication level of the influenza virus. KPT-335 is mainly used for the treatment of canine tumors. Drugs for the effective treatment of feline tumors are currently unavailable in China. KPT-335 may have potential in the treatment of cat tumors. However, the effects of KPT-335 in cats are unreported, and no relevant methodology has been established for pharmacokinetic studies. In this study, a UPLC-MS/MS method was developed to determine KPT-335 concentrations in cat plasma, followed by pharmacokinetic studies. Briefly, plasma proteins are precipitated with acetonitrile, and the supernatant was collected for detection after centrifugation. The linearity for KPT-335 in cat plasma was in the range of 5-1,000 ng/mL. Satisfactory accuracy and precision were obtained. The intra-day accuracy was between -4.10% and 10.48%, the precision was ≤4.65%; the inter-day accuracy was between -0.11% and 8.09%, and the precision was ≤5.85%. Intra-day and inter-day accuracy and precision were within regulatory limits. The results of preliminary pharmacokinetic studies were as follows: Tmax was 1.46 ± 0.51 h; Cmax was 239.54 ± 190.60 ng·mL-1; T1/2 was 5.16 ± 2.30 h; AUC0-t was 1439.85 ± 964.64 ng·mL-1·h. The AUC0-∞ was 1589.82 ± 1003.75 ng·mL-1·h. The purpose of this study was to develop a rapid and simple UPLC-MS/MS method to detect KPT-335 concentration in cat plasma and to conduct preliminary pharmacokinetic studies to support the future application of KPT-335 in felines.

Corrigendum: Development of a UPLC-MS/MS method for quantifying KPT-335 (Verdinexor) in feline plasma for a study of PK.

[This corrects the article DOI: 10.3389/fvets.2024.1438295.].

Control of Selectivity in FeCl3 -Catalyzed Aerobic Oxidation of Cycloketones.

The FeCl3 -catalyzed aerobic oxidation of ketones always gives rise to the α-C-C cleavage product, having challenges to afford hydroxyl keto compounds. Here we report an effective control of the main product from keto acid to α-hydroxyl ketone, by reducing the concentration of FeCl3 catalyst, together with the use of DMSO as the solvent. In addition, mechanistic investigations suggested the same FeCl3 -coordinated peroxide intermediate for both hydroxylation and C-C cleavage routes, and emphasize the role of DMSO as both ligand and reductant. This work provides a new approach for selective aerobic oxidation under Lewis acid catalysis.

Salmonella effector SopB reorganizes cytoskeletal vimentin to maintain replication vacuoles for efficient infection.

A variety of intracellular bacteria modulate the host cytoskeleton to establish subcellular niches for replication. However, the role of intermediate filaments, which are crucial for mechanical strength and resilience of the cell, and in bacterial vacuole preservation remains unclear. Here, we show that Salmonella effector SopB reorganizes the vimentin network to form cage-like structures that surround Salmonella-containing vacuoles (SCVs). Genetic removal of vimentin markedly disrupts SCV organization, significantly reduces bacterial replication and cell death. Mechanistically, SopB uses its N-terminal Cdc42-binding domain to interact with and activate Cdc42 GTPase, which in turn recruits vimentin around SCVs. A high-content imaging-based screening identified that MEK1/2 inhibition led to vimentin dispersion. Our work therefore elucidates the signaling axis SopB-Cdc42-MEK1/2 as mobilizing host vimentin to maintain concrete SCVs and identifies a mechanism contributing to Salmonella replication. Importantly, Trametinib, a clinically-approved MEK1/2 inhibitor identified in the screen, displayed significant anti-infection efficacy against Salmonella both in vitro and in vivo, and may provide a therapeutic option for treating drug-tolerant salmonellosis.

Computational investigation of potent inhibitors against SARS-CoV-2 2'-O-methyltransferase (nsp16): Structure-based pharmacophore modeling, molecular docking, molecular dynamics simulations and binding free energy calculations.

The Coronavirus Disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has created unprecedented public health and economic crises around the world. SARS-CoV-2 2'-O-methyltransferase (nsp16) adds a "cap" to viral RNA to maintain the stability of viral RNA, and inhibition of nsp16 activity may reduce viral proliferation, making this protein an attractive drug target. Here, we report the identification of several small molecule inhibitors of nsp16 by virtual screening. First, the nsp16-sinefungin complex (PDB ID: 6WKQ) was selected from the protein data bank. Asp6912, Cys6913, Asp6897 and Asp6928 were determined to be the key amino acids for sinefungin binding in the crystal structure of nsp16-sinefungin complex by molecular dynamics simulation. The complex structures in the stable binding trajectory of nsp16-sinefungin were than clustered through molecular dynamics RMSD analysis. Six clusters were generated, and six representative structures were selected to construct the pharmacophore based on the structure. These six pharmacophores were superimposed on the binding pocket to simplify and pick the common characteristics. The compounds obtained by the pharmacophore screening from Bionet and Chembiv databases were docked into the nsp16 active pocket. The candidate compounds were selected according to the molecular docking score and then screened by MM/GBSA. Finally, four candidate compounds were obtained. Four sets of 150ns molecular dynamics simulations were performed to determine whether candidate compounds could maintain stable interactions with key amino acids. The results of MD and MM/PBSA energy decomposition indicated that C1 and C2 could form a stable complex system with nsp16, and could form strong hydrogen bonds and salt bridges with the key amino acid Asp6897 and Asp6928. This study thus identifies and attempts to validate for the first time the potential inhibitory activities of C1 and C2 against nsp16, allowing the development of potent anti-COVID-19 drugs and unique treatment strategies.

Feedback-Driven Mechanisms Between Phosphorylated Caveolin-1 and Contractile Actin Assemblies Instruct Persistent Cell Migration.

The actin cytoskeleton and membrane-associated caveolae contribute to active processes, such as cell morphogenesis and motility. How these two systems interact and control directional cell migration is an outstanding question but remains understudied. Here we identified a negative feedback between contractile actin assemblies and phosphorylated caveolin-1 (CAV-1) in migrating cells. Cytoplasmic CAV-1 vesicles display actin-associated motilities by sliding along actin filaments or/and coupling to do retrograde flow with actomyosin bundles. Inhibition of contractile stress fibers, but not Arp2/3-dependent branched actin filaments, diminished the phosphorylation of CAV-1 on site Tyr14, and resulted in substantially increased size and decreased motility of cytoplasmic CAV-1 vesicles. Reciprocally, both the CAV-1 phospho-deficient mutation on site Tyr14 and CAV-1 knockout resulted in dramatic AMPK phosphorylation, further causing reduced active level of RhoA-myosin II and increased active level of Rac1-PAK1-Cofilin, consequently led to disordered contractile stress fibers and prominent lamellipodia. As a result, cells displayed depolarized morphology and compromised directional migration. Collectively, we propose a model in which feedback-driven regulation between actin and CAV-1 instructs persistent cell migration.

Cytoskeleton-a crucial key in host cell for coronavirus infection.

The emerging coronavirus (CoV) pandemic is threatening the public health all over the world. Cytoskeleton is an intricate network involved in controlling cell shape, cargo transport, signal transduction, and cell division. Infection biology studies have illuminated essential roles for cytoskeleton in mediating the outcome of host‒virus interactions. In this review, we discuss the dynamic interactions between actin filaments, microtubules, intermediate filaments, and CoVs. In one round of viral life cycle, CoVs surf along filopodia on the host membrane to the entry sites, utilize specific intermediate filament protein as co-receptor to enter target cells, hijack microtubules for transportation to replication and assembly sites, and promote actin filaments polymerization to provide forces for egress. During CoV infection, disruption of host cytoskeleton homeostasis and modification state is tightly connected to pathological processes, such as defective cytokinesis, demyelinating, cilia loss, and neuron necrosis. There are increasing mechanistic studies on cytoskeleton upon CoV infection, such as viral protein‒cytoskeleton interaction, changes in the expression and post-translation modification, related signaling pathways, and incorporation with other host factors. Collectively, these insights provide new concepts for fundamental virology and the control of CoV infection.

Multifaceted Functions of Host Cell Caveolae/Caveolin-1 in Virus Infections.

Virus infection has drawn extensive attention since it causes serious or even deadly diseases, consequently inducing a series of social and public health problems. Caveolin-1 is the most important structural protein of caveolae, a membrane invagination widely known for its role in endocytosis and subsequent cytoplasmic transportation. Caveolae/caveolin-1 is tightly associated with a wide range of biological processes, including cholesterol homeostasis, cell mechano-sensing, tumorigenesis, and signal transduction. Intriguingly, the versatile roles of caveolae/caveolin-1 in virus infections have increasingly been appreciated. Over the past few decades, more and more viruses have been identified to invade host cells via caveolae-mediated endocytosis, although other known pathways have been explored. The subsequent post-entry events, including trafficking, replication, assembly, and egress of a large number of viruses, are caveolae/caveolin-1-dependent. Deprivation of caveolae/caveolin-1 by drug application or gene editing leads to abnormalities in viral uptake, viral protein expression, or virion release, whereas the underlying mechanisms remain elusive and must be explored holistically to provide potential novel antiviral targets and strategies. This review recapitulates our current knowledge on how caveolae/caveolin-1 functions in every step of the viral infection cycle and various relevant signaling pathways, hoping to provide a new perspective for future viral cell biology research.