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.     

Prediction of an outcome using NETwork Clusters (NET-C)

Birth weight is a key consequence of environmental exposures and metabolic alterations and can influence lifelong health. While a number of methods have been used to examine associations of trace element (including essential nutrients and toxic metals) concentrations or metabolite concentrations with a health outcome, birth weight, studies evaluating how the coexistence of these factors impacts birth weight are extremely limited. Here, we present a novel algorithm NETwork Clusters (NET-C), to improve the prediction of outcome by considering the interactions of features in the network and then apply this method to predict birth weight by jointly modelling trace element and cord blood metabolite data. Specifically, by using trace element and/or metabolite subnetworks as groups, we apply group lasso to estimate birth weight. We conducted statistical simulation studies to examine how both sample size and correlations between grouped features and the outcome affect prediction performance. We showed that in terms of prediction error, our proposed method outperformed other methods such as (a) group lasso with groups defined by hierarchical clustering, (b) random forest regression and (c) neural networks. We applied our method to data ascertained as part of the New Hampshire Birth Cohort Study on trace elements, metabolites and birth outcomes, adjusting for other covariates such as maternal body mass index (BMI) and enrollment age. Our proposed method can be applied to a variety of similarly structured high-dimensional datasets to predict health outcomes.     

Exploration of the mechanism of Zisheng Shenqi decoction against gout arthritis using network pharmacology

BackgroundIn this study, the network pharmacological methods were used to predict the target of effective components of compounds in Zisheng Shenqi Decoction (ZSD, or Nourishing Kidney Qi Decoction) in the treatment of gouty arthritis (GA).MethodThe main effective components and corresponding key targets of herbs in the ZSD were discerned through the Traditional Chinese Medicine Systems Pharmacology Database and Analysis (TCMSP), Bioinformatics Analysis Tool for Molecular mechanism of Traditional Chinese Medicine (BATMAN-TCM) database. UniProt database and Swiss Target Prediction (STP) database was used to rectify and unify the target names and supply the target information. The targets related to GA were obtained by using GeneCards database. After we discovered the potential common targets between ZSD and GA, the interaction network diagram of “ZSD-component-GA-target” was constructed by Cytoscape software (Version 3.7.1). Subsequently, the Protein-protein interaction (PPI) network of ZSD effective components-targets and GA-related targets was constructed by Search Tool for the Retrieval of Interacting Genes Database (STRING). Bioconductor package “org.Hs.eg.db” and “cluster profiler” package were installed in R software (Version 3.6.0) which used for Gene Ontology analysis and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis.Results146 components and 613 targets of 11 herbal medicines in the ZSD were got from TCMSP database and BATMAN-TCM database. 987 targets of GA were obtained from GeneCards database. After intersected and removed duplications, 132 common targets between ZSD and GA were screened out by Cytoscape software (Version 3.7.1). These common targets derived from 81 effective components of 146 components, such as quercetin, stigmasterol and kaempferol. They were closely related to anti-inflammatory, analgesic and anti oxidative stress and the principal targets comprised of Purinergic receptor P2X, ligand-gated ion channel 7 (P2x7R), Nod-like receptor protein 3 (NLRP3) and IL-1β. GO enrichment analysis and KEGG pathway enrichment analysis by R software (Version 3.6.0) showed that the key target genes had close relationship with oxidative stress, reactive oxygen species (ROS) metabolic process and leukocyte migration in aspects of biological process, cell components and molecular function. It also indicated that ZSD could decrease inflammatory reaction, alleviate ROS accumulation and attenuate pain by regulating P2 × 7R and NOD like receptor signaling pathway of inflammatory reaction.ConclusionA total of 81 effective components and 132 common target genes between ZSD and GA were screened by network pharmacology. The PPI network, GO enrichment analysis and KEGG pathway enrichment analysis suggested that ZSD can exerte anti-inflammatory and analgesic effects on the treatment of GA by reducing decreasing inflammatory reaction, alleviating ROS accumulation, and attenuating pain. The possible molecular mechanism of it mainly involved multiple components, multiple targets and multiple signaling pathways, which provided a comprehensive understanding for further study. In general, the network pharmacological method applied in this study provides an alternative strategy for the mechanism of ZSD in the treatment of GA.     

In Silico Analysis of P450s and Their Role in Secondary Metabolism in the Bacterial Class Gammaproteobacteria

The impact of lifestyle on shaping the genome content of an organism is a well-known phenomenon and cytochrome P450 enzymes (CYPs/P450s), heme-thiolate proteins that are ubiquitously present in organisms, are no exception. Recent studies focusing on a few bacterial species such as Streptomyces, Mycobacterium, Cyanobacteria and Firmicutes revealed that the impact of lifestyle affected the P450 repertoire in these species. However, this phenomenon needs to be understood in other bacterial species. We therefore performed genome data mining, annotation, phylogenetic analysis of P450s and their role in secondary metabolism in the bacterial class Gammaproteobacteria. Genome-wide data mining for P450s in 1261 Gammaproteobacterial species belonging to 161 genera revealed that only 169 species belonging to 41 genera have P450s. A total of 277 P450s found in 169 species grouped into 84 P450 families and 105 P450 subfamilies, where 38 new P450 families were found. Only 18% of P450s were found to be involved in secondary metabolism in Gammaproteobacterial species, as observed in Firmicutes as well. The pathogenic or commensal lifestyle of Gammaproteobacterial species influences them to such an extent that they have the lowest number of P450s compared to other bacterial species, indicating the impact of lifestyle on shaping the P450 repertoire. This study is the first report on comprehensive analysis of P450s in Gammaproteobacteria.     

1,3,5-Triaza-7-Phosphaadamantane (PTA) as a 31P NMR Probe for Organometallic Transition Metal Complexes in Solution

Due to the rigid structure of 1,3,5-triaza-7-phosphaadamantane (PTA), its ³¹P chemical shift solely depends on non-covalent interactions in which the molecule is involved. The maximum range of change caused by the most common of these, hydrogen bonding, is only 6 ppm, because the active site is one of the PTA nitrogen atoms. In contrast, when the PTA phosphorus atom is coordinated to a metal, the range of change exceeds 100 ppm. This feature can be used to support or reject specific structural models of organometallic transition metal complexes in solution by comparing the experimental and Density Functional Theory (DFT) calculated values of this ³¹P chemical shift. This approach has been tested on a variety of the metals of groups 8–12 and molecular structures. General recommendations for appropriate basis sets are reported.     

Trehalose-protected lipid membranes for determining membrane protein structure and insertion

Trehalose preserves lipid bilayers during dehydration and rehydration by replacing water to form hydrogen bonds between its own OH groups and lipid headgroups. We compare the lipid conformation and dynamics between trehalose-protected lyophilized membranes and hydrated membranes, to assess the suitability of the trehalose-containing membrane as a matrix for membrane protein structure determination. (31)P spectra indicate that the lipid headgroup of trehalose-protected dry POPC membrane (TRE-POPC) have an effective phase transition temperature that is approximately 50K higher than that of the hydrated POPC membrane. In contrast, the acyl chains have similar transition temperatures in the two membranes. Intramolecular lipid (13)C'-(31)P distances are the same in TRE-POPC and crystalline POPC, indicating that the lipid headgroup and glycerol backbone conformation is unaffected by trehalose incorporation. Intermolecular (13)C-(31)P distances between a membrane peptide and the lipid headgroups are 10% longer in the hydrated membrane at 226 K than in the trehalose-protected dry membrane at 253 K. This is attributed to residual motions in the hydrated membrane, manifested by the reduced (31)P chemical shift anisotropy, even at the low temperature of 226 K. Thus, trehalose lyoprotection facilitates the study of membrane protein structure by allowing experiments to be conducted at higher temperatures than possible with the hydrated membranes.     

In vivo (31)P MRS study of skeletal muscle metabolism in patients with postpolio residual paralysis

The muscle metabolism of at-rest patients with varying degrees of postpolio residual paralysis (PPRP) was studied and compared with that of controls using in vivo phosphorus magnetic resonance spectroscopy. The phosphocreatine (PCr)/inorganic phosphate (Pi) and PCr/adenosine triphosphate ratios were lower in patients than in controls. Reduction in PCr/Pi suggests abnormalities in oxidative phosphorylation. A significant increase was observed in the phosphomonoester/PCr ratio in patients, indicating the accumulation of intermediary compounds of the glycolytic pathway. Furthermore, the phosphodiester/PCr ratio was also significantly increased in patients. In general, the observed changes in metabolite ratios were found to be related to the degree of residual paralysis, suggesting that metabolic changes are secondary to chronic neurogenic processes. These metabolic alterations appear to be the possible cause of energy deficit and underlying muscle fatigue in PPRP patients. The present results provide an insight into the metabolic impairment and degree of muscle damage in patients with PPRP.     

面向对象的三维对流扩散问题有限元程序设计

根据三维对流扩散问题的有限元分析,采用面向对象的程序设计语言C ,建立向量类、矩阵类、单元类、结点类、材料类和有限元方法类等,实现三维对流扩散问题的有限元分析程序开发,对相关的对流扩散问题进行数值模拟.结果表明与用结构化语言开发的传统有限元程序相比,程序更易重用、维护、扩充,并且可以融入用C 编制的大型通用有限元科学和工程计算软件.     

摩托车车架瞬态强度分析与改进设计

针对摩托车车架结构复杂,并且在摩托车工作过程中受到路面激励力作用的特点,在考虑整车各零部件相互作用的前提下,建立了较详细的摩托车整车瞬态强度分析有限元模型,模拟了摩托车整车在实际工作过程中的动态强度变化历程.研究表明:根据瞬态分析结果再结合车架的结构特征及应力分布情况,能更准确、深入地揭示摩托车在实际工作过程中车架动态强度随时间的变化关系,为摩托车车架动态结构强度设计提供可靠依据.     

阻抗测量法及梁的阻抗应答分析

提出了利用压电陶瓷的阻抗测量法的概念,即用压电陶瓷作为驱动源产生动态阻抗信息.测试系统由阻抗分析仪、计算机、压电陶瓷片、铝梁组成.实验将铝梁作为测试对象,在其上粘贴压电陶瓷,通过对阻抗应答、振动模型和压电陶瓷片的粘贴位置的分析,研究梁的阻抗频率特性.实验结果表明,利用阻抗法,容易得到构造物的频率响应特性,应答分析也简单.