Mapping small molecule binding data to structural domains.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Large-scale bioactivity/SAR Open Data has recently become available, and this has allowed new analyses and approaches to be developed to help address the productivity and translational gaps of current drug discovery. One of the current limitations of these data is the relative sparsity of reported interactions per protein target, and complexities in establishing clear relationships between bioactivity and targets using bioinformatics tools. We detail in this paper the indexing of targets by the structural domains that bind (or are likely to bind) the ligand within a full-length protein. Specifically, we present a simple heuristic to map small molecule binding to Pfam domains. This profiling can be applied to all proteins within a genome to give some indications of the potential pharmacological modulation and regulation of all proteins. RESULTS: In this implementation of our heuristic, ligand binding to protein targets from the ChEMBL database was mapped to structural domains as defined by profiles contained within the Pfam-A database. Our mapping suggests that the majority of assay targets within the current version of the ChEMBL database bind ligands through a small number of highly prevalent domains, and conversely the majority of Pfam domains sampled by our data play no currently established role in ligand binding. Validation studies, carried out firstly against Uniprot entries with expert binding-site annotation and secondly against entries in the wwPDB repository of crystallographic protein structures, demonstrate that our simple heuristic maps ligand binding to the correct domain in about 90 percent of all assessed cases. Using the mappings obtained with our heuristic, we have assembled ligand sets associated with each Pfam domain. CONCLUSIONS: Small molecule binding has been mapped to Pfam-A domains of protein targets in the ChEMBL bioactivity database. The result of this mapping is an enriched annotation of small molecule bioactivity data and a grouping of activity classes following the Pfam-A specifications of protein domains. This is valuable for data-focused approaches in drug discovery, for example when extrapolating potential targets of a small molecule with known activity against one or few targets, or in the assessment of a potential target for drug discovery or screening studies

Influence of misonidazole on the incidence of radiation-induced intestinal tumours in mice.

C57BL mice were given local irradiation to 2 cm2 of the lower abdomen in the dose range 16--24 Gy. There were some early deaths, but mice dying between 50--240 days predominantly developed invasive adenocarcinomas of the intestine. When the radiosensitizer misonidazole was given in a single dose shortly before irradiation the proportion of mice developing tumours was higher, but the difference was not statistically significant. However, there was a significant increase in the incidence of multiple tumours, largely attributable to tumours arising in the rectum

Computational fluid dynamics study of crec riser simulator: mixing patterns

The CREC Riser Simulator Reactor is a novel mini-fluidized reactor. This novel device was invented by de Lasa 1. The applications of this unit has shown to be of great value to establish catalyst performance and kinetic models for a diversity of gas phase catalytic reactions. This has been the case, given that the CREC Riser Simulator is excellent with respect to particle and fluid mixing2. This study establishes using CFD (Computational Fluid Dynamics), the CREC Riser Simulator mixing flow patterns. CFD simulations were developed using the COMSOL Multiphysics® module. Fig.1a reports the geometric characteristics of the CREC Riser Simulator including the impeller, the basket containing the catalyst and the external baffles.The proposed CFD model was validated using experimental data obtained in a basket as shown in Fig.1a. For instance, for an impeller speed of 4000 rpm, the outer annulus experimental gas velocity2 was ~0.9 m/s and the simulated CFD gas velocity2 was ~1.3 m/s. Please click Additional Files below to see the full abstract

Improved immune-suppression techniques for the exongrafting of human tumours.

The transplantability of a xenografted human adenocarcinoma has been examined in mice that had been immune-suppressed by thymectomy and whole-body irradiation and the results have been compared with transplantation into athymic (nude) mice. Two alternative techniques were used to prevent marrow failure following whole-body irradiation: reconstituting the animals with a marrow graft, or protecting them by an injection of cytosine arabinoside (Ara-C) 2 days before the irradiation. The results show that the Ara-C-prepared mice were more receptive to transplantation than marrow-grafted or nude mice, and they were the only animals that developed regional metastases from implanted xenografts. Some recovery of immunity occurred in both types of immune-suppressed mice, which was evident more than 5 weeks after immune-suppression and which was more marked in females than in males. It was concluded that the immune-suppressed mice were superior to nude mice for short-term experiments but they may be less satisfactory for long-term experiments

Geometric model of quantum navigation during (anti-)search on a plane

A model of joint random walk of two agents on an infinite plane is considered. The agents possess no means of mutual classical communication, but have access to quantum entanglement resource which is used according to a pre-arranged protocol. Depending on the details of the protocol, an effective force of attraction or repulsion emerges between the two agents. The emergence of this force from quantum entanglement is interpreted in terms of spherical or hyperbolic geometries for attraction or repulsion, respectively.Comment: 4 pages, 3 figure

Use of Non-Steroidal Anti-Inflammatory Drugs That Elevate Cardiovascular Risk: An Examination of Sales and Essential Medicines Lists in Low-, Middle-, and High-Income Countries

PMCID: PMC3570554This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Single-cell transcriptomics to explore the immune system in health and disease

The immune system varies in cell types, states, and locations. The complex networks, interactions, and responses of immune cells produce diverse cellular ecosystems composed of multiple cell types, accompanied by genetic diversity in antigen receptors. Within this ecosystem, innate and adaptive immune cells maintain and protect tissue function, integrity, and homeostasis upon changes in functional demands and diverse insults. Characterizing this inherent complexity requires studies at single-cell resolution. Recent advances such as massively parallel single-cell RNA sequencing and sophisticated computational methods are catalyzing a revolution in our understanding of immunology. Here we provide an overview of the state of single-cell genomics methods and an outlook on the use of single-cell techniques to decipher the adaptive and innate components of immunity.National Institute of Allergy and Infectious Diseases (U.S.) (Grant U24AI118672)National Institute of Allergy and Infectious Diseases (U.S.) (Grant R24AI072073

3-Amino-1-(3,4-dimeth­oxy­phen­yl)-9,10-dihydro­phenanthrene-2,4-dicarbonitrile

In the title compound, C24H19N3O2, the partially saturated ring adopts a distorted half-chair conformation with the methyl­ene-C atom closest to the amino­benzene ring lying 0.664 (3) Å out of the plane defined by the five remaining atoms (r.m.s. deviation = 0.1429 Å. The dihedral angle [32.01 (10)°] between the benzene rings on either side of this ring indicates a significant fold in this part of the mol­ecule. The dimeth­oxy-substituted benzene ring is almost orthogonal to the benzene ring to which it is attached [dihedral angle = 72.03 (9)°]. The mol­ecule has been observed previously as the major component of a 1:19 co-crystal with 2-amino-4-(3,4-dimeth­oxy­phen­yl)-5,6-dihydro­benzo[ha]quinoline-3-carbonitrile [Asiri et al. (2011). Acta Cryst. E67, o2873–o2873]. Supra­molecular chains with base vector [201] are formed in the crystal structure via N—H⋯O hydrogen bonds between the amino H atoms of one mol­ecule inter­acting with the meth­oxy O atoms of a neighbouring mol­ecule. The chains are linked into a three-dimensional architecture by C—H⋯π inter­actions

A second monoclinic polymorph for 3-amino-1-(4-meth­oxy­phen­yl)-9,10-dihydro­phenanthrene-2,4-dicarbonitrile

The title compound, C23H17N3O, has been previously described in a monoclinic P21/c polymorph with Z = 4 [Asiri, Al-Youbi, Faidallah, Ng & Tiekink (2011). Acta Cryst. E67, o2449]. In the new monoclinic P21/n form, with Z = 8, there are two independent mol­ecules, A and B, in the asymmetric unit. In both mol­ecules, the cyclo­hexa-1,3-diene ring has a screw-boat conformation, whereas it is a distorted half-chair in the original polymorph. There is a fold in each mol­ecule, as indicated by the dihedral angle between the benzene rings of the 1,2-dihydro­naphthalene and aniline residues of 33.19 (10)° (mol­ecule A) and 30.6 (10)° (mol­ecule B). The meth­oxy­benzene ring is twisted out of the plane of the aniline residue to which it is connected [dihedral angles = 49.22 (10) and 73.27 (10)°, in A and B respectively]. In the crystal, the two independent mol­ecules self-associate via N—H⋯N hydrogen bonds, generating a 12-membered {⋯HNC3N}2 synthon. These are connected into a supra­molecular tape in the (-101) plane by N—H⋯O(meth­oxy) inter­actions. In the P21/c polymorph, supra­molecular layers are formed by N—H⋯N and N—H⋯O inter­actions

Optimizing Medium Components to Enhance High Cell Mass Production of Biotherapeutic Strain Lactobacillus reuteri DSM 20016T by Statistical Method

798-803Probiotics referred to a group of living microorganisms which highly influence the human health. A number of studies have highlighted on the bio-therapeutic potential of Lactobacillus reuteri strains, especially in treating eradication of Helicobacter pylori. Therefore, in present investigation, statistical methods were applied to optimize medium composition for high cell mass production of L. reuteri strain DSM 20016T. Most influencing medium components were screened by using Plackett-Burman and optimized using Box-Bhenken experimental design. The concentration of lactose, yeast extract and phosphate in cultivation medium has shown significant effect on the cell mass production. The highest cell mass obtained after 48h incubation was 3.96 ± 0.02 gL−1 in RSM-optimized medium compared to 1.76 ± 0.17 gL−1 in un-optimized medium