Development of a High-Throughput Gene Expression Screen for Modulators of RAS-MAPK Signaling in a Mutant RAS Cellular Context

The RAS-MAPK pathway controls many cellular programs, including cell proliferation, differentiation, and apoptosis. In colorectal cancers, recurrent mutations in this pathway often lead to increased cell signaling that may contribute to the development of neoplasms, thereby making this pathway attractive for therapeutic intervention. To this end, we developed a 26-member gene signature of RAS-MAPK pathway activity utilizing the Affymetrix QuantiGene Plex 2.0 reagent system and performed both primary and confirmatory gene expression-based high-throughput screens (GE-HTSs) using KRAS mutant colon cancer cells (SW837) and leveraging a highly annotated chemical library. The screen achieved a hit rate of 1.4% and was able to enrich for hit compounds that target RAS-MAPK pathway members such as MEK and EGFR. Sensitivity and selectivity performance measurements were 0.84 and 1.00, respectively, indicating high true-positive and true-negative rates. Active compounds from the primary screen were confirmed in a dose-response GE-HTS assay, a GE-HTS assay using 14 additional cancer cell lines, and an in vitro colony formation assay. Altogether, our data suggest that this GE-HTS assay will be useful for larger unbiased chemical screens to identify novel compounds and mechanisms that may modulate the RAS-MAPK pathway.

[Multi-dose packaging of drugs as the causative vehicle for multidrug-resistant Enterobacter cloacae: new results from a case-control study]

Hospital hygiene faces cross-cutting and methodological challenges that are time consuming and require specialised knowledge. In outbreak situations German federal states can request assistance from infectious disease epidemiologists at the Robert Koch Institute (RKI). The presented study describes the successful collaboration of local hygienists, microbiologists, clinicians, health authorities and the epidemiologists of the RKI in the investigation of an outbreak of multidrug-resistant Enterobacter (E.) cloacae in 2009 in a children's hospital. The outbreak was discovered in July 2009 when E. cloacae was detected in 12 patients in the neonatal and paediatric intensive care unit (NICU). Hygiene measures were intensified for infection control, and the RKI was invited by the responsible regional health authorities in October 2009 to assist in the outbreak investigation. We conducted a retrospective matched case-control study to identify risk factors for E. cloacae colonisation and infection. We identified a case as any child in the NICU from 1st May to 5th October 2009 with laboratory confirmation of the outbreak clone. Controls were patients staying in the NICU (> 72 h before the case's diagnosis) and swab-negative for the outbreak clone. We used standardised questionnaires to collect demographic and medical information. Matched odds ratios (mOR) were calculated by bivariate and multivariable conditional logistic regression. Environmental investigations were conducted. We identified 28 colonised and 3 bacteraemic cases. 29 matched case-control pairs were included in the study. Multivariable analysis revealed an association between E. cloacae diagnosis and the receipt of oral drugs at the bed-side from multidose packaging (mOR=1.8/drug; p=0.006). No specific drug was identified; microbiological investigation of drugs was negative. This multiresistant E. cloacae outbreak was most likely distributed by oral application using contaminated multidose drug packaging extrinsically contaminated via hands of personnel. No further cases occurred for 6 weeks after protocols for handling oral drugs were changed (smaller packaging, patient-based storage, and limited circulation time). Special attention and thorough hygiene protocols are needed for the distribution of oral medication. In NICUs the use of multi-dose medications should be avoided. The cooperation between locally available expertise and infectious disease epidemiologists enabled the discovery of a previously unidentified risk factor.

Side chain SAR of bicyclic beta-lactamase inhibitors (BLIs). 1. Discovery of a class C BLI for combination with imipinem

Bridged monobactam beta-lactamase inhibitors were prepared and evaluated as potential partners for combination with imipenem to overcome class C beta-lactamase mediated resistance. The (S)-azepine analog 2 was found to be effective in both in vitro and in vivo assays and was selected for preclinical development.

Use of homogeneous time-resolved fluorescence energy transfer in the measurement of nuclear receptor activation

Nuclear receptors (NRs) are a superfamily of ligand-dependent transcription factors that mediate the effects of hormones and other endogenous ligands to regulate the expression of specific genes. NRs are clearly important targets for drug discovery. Ligand-dependent protein-protein interactions between NRs and NR coactivators (NRCoAs) are a critical step in regulation of transcription. Homogeneous time-resolved fluorescence (HTRF) energy transfer technology is sensitive, homogeneous, and nonradioactive. These characteristics make this approach attractive for developing high-throughput screening assays. The long-lived nature of the fluorescence of europium cryptate combined with a time delay in reading facilitates the homogeneous nature of the assay. Importantly, the introduction of lanthanides (with R0 values as great as 90 A in HTRF) make HTRF amenable to be used for protein-protein interactions. In this article we review, using peroxisome proliferator-activated receptor (PPAR)gamma as a model system, a novel approach for characterizing the ligand-dependent interaction between NR and NRCoA using HTRF technology and its potential uses in small-molecule screening, profiling selectivity of NR-NRCoA paired interactions, and profiling NR ligands as agonists versus partial agonists or antagonists.

Detection of p56(lck) kinase activity using scintillation proximity assay in 384-well format and imaging proximity assay in 384- and 1536-well format

p56(lck) is a lymphocyte-specific tyrosine kinase that plays an important role in both T-cell maturation and activation. We have developed a homogeneous assay in which p56(lck) catalyzes the transfer of the gamma-phosphate group from [gamma-(33)P]ATP to a biotinylated peptide substrate. The labeled peptide is then captured on a streptavidin-coated scintillation proximity assay (SPA) bead or imaging proximity bead. The SPA is counted in a microplate scintillation counter and the imaging proximity assay is counted in a charge-coupled device-based imaging system called LEADseekertrade mark, recently launched as a homogeneous imaging system by Amersham Pharmacia Biotech. We show, via time-dependence assays and inhibitor studies, that this assay can be performed in 1536-well microplate format using imaging proximity as the method of detection. The results compare favorably with the same assay performed in 384-well microplate format using both SPA and imaging proximity as the detection methods. From this study, we conclude that a kinase assay can be performed in 384- and 1536-well format using imaging as the detection method, with significant time savings over standard scintillation counting. In addition, we show cost saving advantages of 1536- over 384-well format in terms of reagent usage, higher throughput, and waste disposal.

Molecular basis for p38 protein kinase inhibitor specificity

p38 is a member of the mitogen-activated protein (MAP) kinase family and is a critical enzyme in the proinflammatory cytokine pathway. Other MAP kinase group members that share both structural and functional homology to p38 include the c-Jun NH2-terminal kinases (JNKs or SAPKs) and the extracellular-regulated protein kinases (ERKs). In this study, we determined the molecular basis for p38alpha inhibitor specificity exhibited by five compounds in the diarylimidazole, triarylimidazole, and triarylpyrrole classes of protein kinase inhibitors. These compounds are significantly more potent inhibitors of p38 compared to the JNKs and ERKs. Three active site ATP-binding domain residues in p38, T106, M109, and A157, selected based on primary sequence alignment, molecular modeling, and X-ray crystal structure data, were mutated to assess their role in inhibitor binding and enzymatic catalysis. All mutants, with the exception of T106M, had kinase activity within 3-fold of wild-type p38. Mutation of T106 to glutamine, the residue present at the corresponding position in ERK-2, or methionine, the corresponding residue in p38gamma, p38delta, and the JNKs, rendered all five inhibitors ineffective. The diarylimidazoles had approximately a 6-fold decrease in potency toward M109A p38. For the mutant A157V, all diarylimidazoles and triarylimidazoles tested were 5-10-fold more potent compared with wild-type p38. In contrast, two triarylpyrroles were 15-40-fold less potent versus A157V p38. These results showed that the molecular basis for the specificity of the p38 inhibitors was attributed largely to threonine 106 in p38 and that methionine 109 contributes to increased binding affinity for imidazole based inhibitors.

High-yield expression, refolding, and purification of penicillin-binding protein 2a from methicillin-resistant Staphylococcus aureus strain 27R

The mecA-27R gene, which encodes PBP2a from methicillin-resistant Staphylococcus aureus strain 27R, was modified to remove the putative N-terminal membrane-spanning region, cloned into the T7 RNA polymerase expression vector pET11d, and used to transform Escherichia coli strain BL21(DE3). The majority of PBP2a was expressed in the form of inclusion bodies, which were extracted, denatured, and refolded. The protein was then purified by anion-exchange and size-exclusion chromatography. A 6-liter culture of induced E. coli provided 37 mg of purified PBP2a which was greater than 99% pure. Binding affinities for [3H]benzylpenicillin, imipenem, and L-695,256 (a beta-lactam with high affinity for PBP2a) were shown to be comparable to PBP2a found in membrane preparations of S. aureus strain 27R. A direct binding assay, using 14C-labeled L-695,256 was developed and used to show stoichiometric binding to the refolded, soluble PBP2a. In addition, electrospray mass spectrometry showed that 100% of the refolded PBP2a was covalently bound to the beta-lactam in a stoichiometric fashion. Finally, two mutations of the putative active-site serine showed the predicted loss of covalent binding of the beta-lactam to the PBP2a, demonstrating the high specificity of the soluble binding assay.

Endogenously synthesized peptide with an endoplasmic reticulum signal sequence sensitizes antigen processing mutant cells to class I-restricted cell-mediated lysis

The HLA-A2-positive human mutant cell line T2 is not lysed by influenza virus-specific HLA-A2-restricted cytotoxic lymphocytes after virus infection. However, lysis does occur when cells are incubated with the antigenic influenza matrix protein-derived peptide M57-68. To examine the nature of this defect, T2 cells were transfected with two different plasmids. One plasmid encoded the peptide M57-68, and the other encoded the same peptide preceded by an endoplasmic reticulum translocation signal sequence. Mutant T2 cells expressing the M57-68 peptide without the signal sequence were not susceptible to lysis by M57-68-specific HLA-A2-restricted cytotoxic T lymphocytes, whereas T2 cells expressing the M57-68 peptide plus signal sequence were lysed effectively. Lysis of parental T1 cells with either plasmid was equally effective. These results suggest that the T2 mutant cells are defective in the transport of antigenic peptides from the cytosol into the secretory pathway.