An overview of activity-based probes for glycosidases

As the scope of modern genomics technologies increases, so does the need for informative chemical tools to study functional biology. Activity-based probes (ABPs) provide a powerful suite of reagents to probe the biochemistry of living organisms. These probes, featuring a specificity motif, a reactive chemical group and a reporter tag, are opening-up large swathes of protein chemistry to investigation in vitro, as well as in cellular extracts, cells and living organisms in vivo. Glycoside hydrolases, by virtue of their prominent biological and applied roles, provide a broad canvas on which ABPs may illustrate their functions. Here we provide an overview of glycosidase ABP mechanisms, and review recent ABP work in the glycoside hydrolase field, encompassing their use in medical diagnosis, their application for generating chemical genetic disease models, their fine-tuning through conformational and reactivity insight, their use for high-throughput inhibitor discovery, and their deployment for enzyme discovery and dynamic characterization.Medical BiochemistryBio-organic Synthesi

Identification of widespread Adenosine nucleotide dinding in Mycobacterium tuberculosis.

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Glycoconjugated Site-Selective DNA-Methylating Agent Targeting Glucose Transporters on Glioma Cells

DNA-alkylating drugs continue to remain an important weapon in the arsenal against cancers. However, they typically suffer from several shortcomings because of the indiscriminate DNA damage that they cause and their inability to specifically target cancer cells. We have developed a strategy for overcoming the deficiencies in current DNA-alkylating chemotherapy drugs by designing a site-specific DNA-methylating agent that can target cancer cells because of its selective uptake via glucose transporters, which are overexpressed in most cancers. The design features of the molecule, its synthesis, its reactivity with DNA, and its toxicity in human glioblastoma cells are reported here. In this molecule, a glucosamine unit, which can facilitate uptake via glucose transporters, is conjugated to one end of a bispyrrole triamide unit, which is known to bind to the minor groove of DNA at A/T-rich regions. A methyl sulfonate moiety is tethered to the other end of the bispyrrole unit to serve as a DNA-methylating agent. This molecule produces exclusively N3-methyladenine adducts upon reaction with DNA and is an order of magnitude more toxic to treatment resistant human glioblastoma cells than streptozotocin is, a Food and Drug Administration-approved, glycoconjugated DNA-methylating drug. Cellular uptake studies using a fluorescent analogue of our molecule provide evidence of uptake via glucose transporters and localization within the nucleus of cells. These results demonstrate the feasibility of our strategy for developing more potent anticancer chemotherapeutics, while minimizing common side effects resulting from off-target damage

The changing landscape of microbial biodiversity exploration and its implications for systematics

A vast diversity of Bacteria and Archaea exists in nature that has evaded axenic culture. Advancements in single-cell genomics, metagenomics, and molecular microbial ecology approaches provide ever-improving insight into the biology of this so-called “microbial dark matter”; however, due to the International Code of Nomenclature of Prokaryotes, yet-uncultivated microorganisms are not accommodated in formal taxonomy regardless of the quantity or quality of data. Meanwhile, efforts to calibrate the existing taxonomy with phylogenetic anchors and genomic data are increasingly robust. The current climate provides an exciting opportunity to leverage rapidly expanding single-cell genomics and metagenomics datasets to improve the taxonomy of Bacteria and Archaea. However, this opportunity must be weighted carefully in light of the strengths and limitations of these approaches. We propose to expand the definition of the Candidatus taxonomy to include taxa, from the phylum level to the species level, that are described genomically, particularly when genomic work is coupled with advanced molecular ecology approaches to probe metabolic functions in situ. This system would preserve the rigor and value of traditional microbial systematics while enabling growth of a provisional taxonomic structure to facilitate communication about “dark” lineages on the tree of life