Structure-activity relationship of Ca2+ channel blockers: A study using conformational analysis and chemometric methods

Summary A structure-activity relationship study has been done on 8 compounds with the activity known as Ca²⁺ channel blockers. Conformational analysis was carried out using a molecular mechanics method. The 3D-QSAR approach was used and the most polar functional groups present in all the molecules were considered. Eight interatomic distances are necessary to define the relative spatial disposition of these relevant molecular fragments. The structure-activity relationship between interatomic distances and biological activity was performed using statistic and chemometric methods. In particular, with Principal Component Analysis, it was possible to reduce the number of interatomic distances: only six of the eight distances are sufficient to describe the system in a useful way. A classification method was iteratively used to select the most probable conformations linked to the biological activity and to build a model able to classify conformations according to their biological behaviour. Cluster analysis on the active selected conformations subsequently allowed the identification of two different geometrical patterns for the active compounds. Finally the validity of the model was verified by correctly predicting the activity of other molecules not used in the construction of the model but possessing known activity.     

Photolysis of 2-dialkylamino-3-amino(or alkylamino)-1,4-naphthoquinones

Using¹H and¹³C NMR spectroscopy, naphthodihydroimidazolediols were identified as the primary products of photolysis of 2-dialkylamino-3-amino(alkylamino)-1,4-naphthoquinones. Their further non-photochemical (thermal) transformations depend on their structure and on the photolysis conditions.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 358–362, February, 1993.     

Impact of biological factors on binding media identification in art objects: identification of animal glue in the presence of Aspergillus niger

The materials and especially organic materials used for creation of art objects can be utilized by various microorganisms for their growth and facilitate the microbial colonization of the object. An understanding of the chemical alterations in artefacts caused by the presence of microorganisms can be crucial for correct identification of the materials initially used for the artefact creation--nowadays an important step in restoration and/or art-historical investigation of the art object. The present article describes a model experiment in which we investigated the possible chemical alterations in animal glue films used as substrate for growth of the fungus Aspergillus niger. The sterilized animal glue solution was poured into Petri dishes, inoculated with Aspergillus niger, and subsequently incubated at 15 degrees C for 0, 7, 9, 14, and 28 days. After interruption of incubation, the content of the Petri dish was analyzed for amino acid composition by the GC-MS based method. It was found that the growth of Aspergillus niger on animal glue films did not cause significant changes in the amino acid composition of the film and had no impact on animal glue identification.     

The aliasing‐phenomenon in visual terms

In a recent paper it was shown that the aliasing phenomenon, which leads to a severe identification problem in the estimation of stochastic differential equations, can be overcome by using a polygonal (or higher) approximation for the time paths of the exogenous variables. This work attempts to visualize the problem and presents several simulated trajectories of a continuous time AR(2)‐process (Ornstein‐Uhlenbeck‐process) together with the observationally equivalent structures. Furthermore it is shown that aliasing can even change the analytical properties of the time paths of the system: whereas the first component of the Ornstein‐Uhlenbeck‐process is differentiable, the trajectories of the aliasing structures are continuous, but not differentiable any more.     

Unsupervised cell identification on multidimensional X‐ray fluorescence datasets

A novel approach to locate, identify and refine positions and whole areas of cell structures based on elemental contents measured by X‐ray fluorescence microscopy is introduced. It is shown that, by initializing with only a handful of prototypical cell regions, this approach can obtain consistent identification of whole cells, even when cells are overlapping, without training by explicit annotation. It is robust both to different measurements on the same sample and to different initializations. This effort provides a versatile framework to identify targeted cellular structures from datasets too complex for manual analysis, like most X‐ray fluorescence microscopy data. Possible future extensions are also discussed.     

An integrative in silico approach to the structure of Omp33-36 in Acinetobacter baumannii

Omp33-36 in A. baumannii, a bacterium causing serious nosocomial infections, is a virulence factor associated with the pathogen metabolic fitness as well as its adherence and invasion to human epithelial cells. This protein is also involved in interaction of the bacteria with host cells by binding to fibronectin. Moreover, Omp33-36 renders cytotoxicity to A. baumannii in addition to inducing apoptosis and modulation of autophagy. In the present study, an integrated strategy is launched to pierce into the 3D structure of Omp33-36 protein. The signal peptide within the sequence was determined, then, topology as well as secondary and tertiary structures of the protein were predicted. The mature protein assigned as a 14-stranded barrel in which residues 1–19 is removed as signal peptide. The obtained 3D models were evaluated in terms of quality; and then, served as queries to find similar protein structures. The hits were analyzed regarding topology among which 14-stranded were considered. The most qualified model was refined and then its sequence aligned to its counterpart similar structure protein (CymA from Klebsiella oxytoca). The determined structure of Omp33-36 could justify its porin function and carbapenem-resistance associated with the loss of this protein.     

Comment on: “Topology identification and adaptive synchronization of uncertain complex networks with adaptive double scaling functions” [Commun Nonlinear Sci Numer Simul 2011;16:3337-43]

In this comment letter we point out that the main result of the recent paper [Xu Y, Zhou W, Fang J, Sun W. Topology identification and adaptive synchronization of uncertain complex networks with adaptive double scaling functions. Commun Nonlinear Sci Numer Simul 2011;16(18):3337-43] has certain errors. The mistakes are corrected and a correct version is presented in this letter. We further indicate that a sufficient condition has been neglected in a series of articles discussing the same topic of network topology identification; hence we hope this letter can help clarify some unclear concepts about this topic.     

A preliminary approach of dynamic identification of slender buildings by neuronal networks

The study of the dynamic behavior of slender masonry structures is usually related to the preservation of the historic heritage. This study, for bell towers and industrial masonry chimneys, is particularly relevant in areas with an important seismic hazard. The analysis of the dynamic behavior of masonry structures is particularly complex due to the multiple effects that can affect the variation of its main frequencies along the seasons of the year: temperature and humidity. Moreover, these dynamic properties also vary considerably in structures built in areas where land subsidence due to the variation of the phreatic level along the year is particularly evident: the stiffness of the soil–structure interaction also varies. This paper presents a study to evaluate the possibility of detecting the variation of groundwater level based on the readings obtained using accelerometers in different positions on the structure. To do this a general case study was considered: a 3D numerical model of a bellower. The variation of the phreatic level was evaluated between 0 and −20 m, and 81 cases studies were developed modifying the rigidity of the soil–structure interaction associated to a position of the phreatic level. To simulate the dispositions of accelerometers on a real construction, 16 points of the numerical model were selected along the structure to obtain modal displacements in two orthogonal directions. Through an adjustment by using neural networks, a good correlation has been observed between the predicted position of the water table and acceleration readings obtained from the numerical model. It is possible to conclude that with a discrete register of accelerations on the tower it is possible to predict the water table depth.     

Studies on oral bioavailability and first‐pass metabolism of withaferin A in rats using LC–MS/MS and Q‐TRAP

Withaferin A (WA) is one of the major bioactive steroidal lactones with extensive pharmacological activities present in the plant Withania somnifera. The absolute oral bioavailability of WA remains unknown and human‐related in vitro data are not available. Therefore, in the present study, the absolute oral bioavailability of WA in male rats and the in vitro screening of absorption factors by Q‐trap and LC–MS/MS analysis were conducted to explore possible clinical properties of WA. The developed and validated analytical methods were successfully applied to the pharmacokinetic studies and in vitro measurement of WA. The oral bioavailability was determined to be 32.4 ± 4.8% based on intravenous (5 mg/kg) and oral (10 mg/kg) administrations of WA in male rats. The in vitro results showed that WA could be easily transported across Caco‐2 cells and WA did not show as a substrate for P‐glycoprotein. Moreover, the stability of WA was similar between male rat and human in simulated gastric fluid (stable), in intestinal microflora solution (slow decrease) and in liver microsomes (rapid depletion, with a half‐life of 5.6 min). As such, the first‐pass metabolism of WA was further verified by rat intestine‐liver in situ perfusion, revealing that WA rapidly decreased and 27.1% remained within 1 h, while the content of three major metabolites (M1, M4, M5) identified by Q‐trap increased. This perfusion result is consistent with the oral bioavailability results in vivo. The first‐pass metabolism of WA might be the main barrier in achieving good oral bioavailability in male rats and it is predicted to be similar in humans. This study may hold clinical significance.