Development Of New Library Research Articles

A Strategy for Combinatorial Cavity Design in De Novo Proteins.

Protein sequence space is vast; nature uses only an infinitesimal fraction of possible sequences to sustain life. Are there solutions to biological problems other than those provided by nature? Can we create artificial proteins that sustain life? To investigate these questions, we have created combinatorial collections, or libraries, of novel sequences with no homology to those found in living organisms. Previously designed libraries contained numerous functional proteins. However, they often formed dynamic, rather than well-ordered structures, which complicated structural and mechanistic characterization. To address this challenge, we describe the development of new libraries based on the de novo protein S-824, a 4-helix bundle with a very stable 3-dimensional structure. Distinct from previous libraries, we targeted variability to a specific region of the protein, seeking to create potential functional sites. By characterizing variant proteins from this library, we demonstrate that the S-824 scaffold tolerates diverse amino acid substitutions in a putative cavity, including buried polar residues suitable for catalysis. We designed and created a DNA library encoding 1.7 × 106 unique protein sequences. This new library of stable de novo α-helical proteins is well suited for screens and selections for a range of functional activities in vitro and in vivo.

New ligands for nickel catalysis from diverse pharmaceutical heterocycle libraries.

Ligands are essential for controlling the reactivity and selectivity of transition metal-catalyzed reactions. Access to large phosphine ligand libraries has become an essential tool for the application of metal-catalyzed reactions industrially, but these existing libraries are not well suited to new catalytic methods based on non-precious metals (i.e., Ni, Cu, Fe). The development of the requisite nitrogen- and oxygen-based ligand libraries lags far behind phosphines and the development of new libraries is anticipated to be time consuming. Here we show that this process can be dramatically accelerated by mining a typical pharmaceutical compound library that is rich in heterocycles for new ligands. Using this approach, we were able to screen a structurally diverse set of compounds with minimal synthetic effort and identify several new ligand classes for nickel-catalyzed cross-electrophile coupling. These new ligands gave improved yields for challenging cross-couplings of pharmaceutically relevant substrates compared to previously published ligands.

Functionalized Orthoesters as Powerful Building Blocks for the Efficient Preparation of Heteroaromatic Bicycles

By combining substituted anilines with functionalized orthoesters, an efficient and connective methodology for the preparation of benzoxazole, benzothiazole, and benzimidazole derivatives has been established. The versatility of this approach enables the development of new libraries of heterocycles containing multifunctional sites.

Reductionism and library and information science philosophy

PurposeThe purpose of this article is to consider the meaning of “reductionism” within the context of renewed efforts to make library and information science philosophy.Design/methodology/approachThis article argues that the question of reductionism, as discussed in other traditions of thought, is relevant to the conversation about development of new library and information science (LIS) philosophy. Based on the viewpoint that one can be opposed to philosophical reductionism yet still be in favour of science, some forms of reductionism are described and links are drawn to library and information science by way of examples.FindingsHow reductionism is defined and understood should be addressed in the efforts to make new LIS philosophy.Originality/valueBeing “non‐reductionist” can be a stance in its own right, as evidenced by broader transdisciplinary conversations, but this is yet to be considered at any depth in LIS.

Analysis of surface properties of human cancer cells using derivatized beads

Standard histochemical analysis of cells and tissues generally involves procedures that utilize a relatively small number of probes such as dyes, and generally requires hours or days to process. Our laboratory has developed a novel method for histochemical surveys of cell surface properties that utilizes a large number of probes (derivatized agarose beads) and takes seconds or minutes to accomplish. In this study, 4 human cell lines (CCL-255 (LS123) human colon cancer cells that are non-tumorigenic in nude mice; CRL-1459 (CCD-18CO) human colon endothelial cells that are non-malignant; CCL-220 (COLO 320DM) human colon cancer cells that are tumorigenic in nude mice; and HTB-171 (NCI H446) human lung carcinoma cells) were tested for their ability to bind to agarose beads derivatized with 51 different molecules. There were statistically significant differences in binding of the 4 cell types to all of the 51 types of beads, but 15 types of beads showed dramatic differences in binding to one or more of the 4 cell types. For example, only HTB-171 (NCI H446) bound to p-aminophenyl-beta-D-glucopyranoside-derivatized beads and only CCL-220 (COLO 320DM) bound to L-tyrosine-derivatized beads. The specificity of cell-bead binding was examined by performing assays in the presence or absence of exogenously added compounds in hapten-type of inhibition experiments. This assay, that utilizes large numbers of novel probes, may help in the development of new libraries of surface properties of specific cell types, with differing degrees of malignancy, that at this time could not be developed by using other available technologies.