A chemical-genetic screen reveals a mechanism of resistance to PI3K inhibitors in cancer

The authors of this paper have developed a method to detect synthetic lethal drug-gene interactions in tumor models. They introduce a single genetic modification into a normal cell line such as healthy breast cells. With that modification they also introduce a barcode , which is a short, nontranscribed stretch of DNA which can be selectively quantified by PCR. The number of PCR reads corresponds to how much of that barcode is present, which corresponds to numbers of cells carrying that particular genetic modification in a population of cells.

Structure-Guided Design of a Methyl Donor Cofactor That Controls a Viral Histone H3 Lysine 27 Methyltransferase Activity

This paper uses a "bump and hole" approach to study a vSET methyltransferase mutant and SAM analog pair. This pair is responsible for histone methylation and affects gene transcription. To create the "bumped" SAM analog (16c) and "hole" protein (vSET-L116A), the crystal structure was used. The vSET-L116A/16c combination was shown to have decreased activity as compared to wild type/SAM and mutant/SAM combinations.

Ligand-induced sequestering of branchpoint sequence allows conditional control of splicing

Both 795 classes are crossing over with discussions on riboswitches and RNA splicing. I think it is very interesting to see the application from both the chemical biology and engineering standpoints. These switches are a very nice way to control gene expression, but can also be modified to create new biosensors! In Gavin's class we only discussed protein sensing aptamers, but not any small molecule sensors. For Deiters' class this is a another example of a small molecule switch. This paper describes the use of the theophylline riboswitch to control mRNA splicing. They have previously shown that the theophylline switch can inhibit splicing when attached to the 3' end of the pre-mRNA. This paper tries to improve splicing control by inserting the branch point sequence inside the theophylline aptamer.

ATP-induced helicase slippage reveals highly coordinated subunits

This paper discusses the T7 helicase enzyme, which unwinds DNA using dTTP. The authors found that adding ATP would also allow unwinding but caused the helicase to 'slip' along the DNA. Enzyme kinetics were also discussed to determine the effect of slippage frequency. Further discussion on the binding of the enzyme to DNA is also included.

Control of tumor and microenvironment cross-talk by miR-15a and miR-16 in prostate cancer

In this paper, Musumeci and co-workers found new miR-15a/16 targets responsible for tumor promoting activity in non-neoplastic associated fibroblasts. They have shown miR-15a/16 are downregulated in fibroblast cells that are surrounded by tumor cells. Downregulation of these microRNAs induced the expression of growth factor FGF-2 which promotes tumor growth and progression via microenvironment cross talk. I found this article interesting that microRNAs are involved in cell-cell interactions.

Fluorescent DNA chemosensors: identification of bacterial species by their volatile metabolites

DNA-like fluorescent sensors are reported to identify M. tuberculosis, E. coli and P. putida bacterial strains in culture based on volatile metabolites. These DNA based chemosensors are able to differentiate bacterial strains of interest due to unique fluorescent profiles produced when exposed to the bacterial cultures. This method allows for quick detection of pathogenic bacteria in clinical samples through a fluorescent readout.

An efficient platform for genetic selection and screening of gene switches in Escherichia coli

In Gavin's class we discussed Gallivan's system for evolving a riboswitch using a motility selection. I raised the question whether a genetic selection would be better in this case. As described in the introduction of this paper, there are several problems with genetic selections for riboswitches. Two of these problems include the handling of hundreds of agar plates and the difficulty of quantitatively monitoring the selection. This paper describes a dual selection and screen that uses a TetA-GFP fusion protein to genetically select for riboswitches and quantitatively monitor the process.

Discovery of Pazopanib, a Novel and Potent Vascular Endothelial Growth Factor Receptor Inhibitor

In Alex's class we recently discussed small molecule inhibitors of DNA. One of the small molecules targeted the VEGF pathway in the hope of reducing tumor growth. As we discussed, DNA small molecule inhibitors must be able to not only penetrate the cell and nucleus, but also access the DNA wrapped around the histones.
Small molecules that can inhibit cellular receptors are the most widely used therapeutic on the market due to the easy accessibly of the receptor on the outside of the cell. This paper from GlaxoSmithKline (RTP) describes the discovery of a kinase inhibitor that targets a VEGF receptor, which has been approved by the FDA to treat renal cell carcinoma (RCC).

Structural basis for the bifunctionality of fructose-1,6-bisphosphate aldolase/phosphatase

In contrast to this conventional concept, archaeal fructose-1,6-bisphosphate (FBP) aldolase/phosphatase (FBPA/P) consists of a single catalytic domain, but catalyses two chemically distinct reactions of gluconeogenesis: (1) the reversible aldol condensation of dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (GA3P) to FBP; (2) the dephosphorylation of FBP to fructose-6-phosphate (F6P)². Thus, FBPA/P is fundamentally different from ordinary enzymes whose active sites are responsible for a specific reaction. However, the molecular mechanism by which FBPA/P achieves its unusual bifunctionality remains unknown. Here we report the crystal structure of FBPA/P at 1.5-Å resolution in the aldolase form, where a critical lysine residue forms a Schiff base with DHAP. A structural comparison of the aldolase form with a previously determined phosphatase form³ revealed a dramatic conformational change in the active site, demonstrating that FBPA/P metamorphoses its active-site architecture to exhibit dual activities. Thus, our findings expand the conventional concept that one enzyme catalyses one biochemical reaction.

Largazole and Analogues with Modified Metal-Binding Motifs Targeting Histone Deacetylases: Synthesis and Biological Evaluation

Inhibitors of Histone Deacetylases represent promising anti-cancer agents. HDAC proteins are a familly of 18 enzymes and they exhibit a high homology within their catalytic sites, rendering specific targeting of one protein really challenging. They developed an efficient route to largazole analogues. They investigated the properties of chelation with Zinc cation.
The compounds they made were less active than largazole, however they show some selectivity toward the class I of HDACs.