Light Activation of a Cysteine Protease Inhibitor: Caging of a Peptidomimetic Nitrile with Ru

A photocaged protease inhibitor was designed using a synthesized peptidomimetic molecule with a nitrile group used for attachment to the 'cage', a ruthinium-based complex in this case. The aim is to develop this technology as a cancer drug that can be activated in proximity to the cancerous tissue with light. The protease inhibitor is meant to target a cysteine cathepsin, which is overexpressed in many cancers. Additionally, the ruthinium molecule also has potential bioactivity since it can covalently bind DNA. This complex showed excellent stability in the dark and rapid release of the inhibitor upon irradiation with light.

Manipulating the munchies in mice

This "news and views" paper gives a summary of this article about using a bump-and-hole method to create ion channels which are activated by drugs rather than by their native substrates. (We were talking in class today about how difficult it is to make a protein with this degree of orthogonality.) The ligand-binding extracellular domain was linked to cation- or anion-selective transmembrane and intracellular domains so that nerve cells could be selectively inhibited or excited. I chose this article mainly because I thought it had a funny title, but also because it was a good summary of the research that had been done.

DNA hybridization of pathogenicity island of vancomycin-resistant Enterococcus faecalis with discretely functionalized gold nanoparticles in organic solvent mixtures

Researchers joined short DNA sensors to gold nanoparticles in an organic solvent mixture.  The 10 base-pair DNA fragments were able to anneal to the target DNA and label it.  Such technology could be used in disease detection.  The researchers went on to see the effects changes to the solvent had on the annealing.  The study is lacking in a couple of areas, but the overall idea seems as though it could prove useful

Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase

This paper analyzes with the hydrophobic in an attempt to better model it.  Current modeling of the hydrophobic effect for biological application is incomplete and these researchers find it may be partially wrong.  They find that the effect stretches further than just the water molecules adjacent to the hydrophobic components and also analyze the effects on the binding pocket.

Architecture of human telomerase RNA

I was at an RNA symposium this weekend and Qi Zhang presented an interesting structural analysis of the telomerase RNA. This article discusses how the structure of the RNA component of telomerase core domain is important for template recognition. The core domain has a 39 degree angle of motion that correlates well with moving across the template DNA during telomere extension. It is a nice example of using structural information to understand the mechanism of action for biologically relevant enzymes. Additionally, the structural data could be used to develop specific SM inhibitors as we previously learned.

Rapid Multitarget Immunomagnetic Separation through Programmable DNA Linker Displacement

The authors describe a technique for magnetic selection of multiple targets in less time than previous studies.  Antibodies on the magnetic beads selectively bind their targets and then a first sort can occur.  The magnetic beads can then be selectively cleaved in a short amount of time and additional sorts can be used to sort all targets from one another.  The purity was high, but the yield of each target was low.  For sorting of four different groups this process took 1.5 hours compared to 5 hours by the standard method.

Cytocompatible click-based hydrogels with dynamically tunable properties through orthogonal photoconjugation and photocleavage reactions

The authors present a hydrogel network with two orthogonal light controlled functions. Thiol containing molecules can be covalently attached by the radical mediated thiol-ene reaction with visible light. The gel matrix can also be degraded by photocleaving at a nitrobenzyl moiety using UV light. These reactions are bioorthogonal and spatiotemporally controlled, allowing the material's properties to be regulated in real time. They demonstrated the utility of this matrix by encapsulating human mesenchymal stem cells. The cells were allowed to grow through regions of the hydrogel that had been modified by the thiol-ene reaction to contain integrin binding peptide ligands. The photocleaving reaction was then used to liberate cells at specific areas of the gel. Also, the authors encapsulated a cell-laden fibrin clot. Cell migration from the clot was controlled by both of the the photochemical reactions.

Metabolic engineering of microorganisms for isoprenoid production

This 2008 article gives a nice (if somewhat dated, now) overview of isoprenoid engineering advances. In Dr. Williams course we recently looked at mevalonate pathway optimization for increased amorpha-4,11-diene production and I touched upon taxadiene production as well. Both drug precursors rely on isoprenoid engineering for useful semisynthetic production versus extraction from plants, which is costly, time consuming, and environmentally adverse (in the case of Taxol). Though not the thorough review of Keasling's work that Dr. Williams hopes that one of us turns up, this could serve as a starting point for further investigation of isoprenoid production in microbial hosts.

Structure-Based Identification and Neutralization Mechanism of Tyrosine Sulfate Mimetics That Inhibit HIV-1 Entry

HIV-1 entry occurs when CD4 binds to the HCV-1 gp120 glycoprotein on the cell surface which induces a conformational change to trigger additional co-receptor CCR5 to interact. In this paper, P.D. Kwong and co-workers identified CCR5-N terminus mimetic small molecule inhibitors using in silico screening and further characterized in viral entry inhibition assay.  

RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites

This paper describes the development of a new independent E. Coli strain JX 33 that allows to reassign the stop codon UAG into a sense codon, in order to facilitate the introduction of unnatural amino acids in live cells.In JX33, the release factor 1 has been knocked-out to overcome the current issues associated with low level of incorporation. Also, their method can be used to incorporate several unnatural amino acids at different sites within the same protein. They tested the incorporation of up to 6 mutations in the EGFP gene and obtained similar level of fluorescence among all mutants.

This is an interesting article. It may open up the possibility to introduce different unnatural amino acids within the same protein with high level of incorporation.