The study of biomolecules in their native environments is a challenging task because of the vast complexity of cellular systems. Technologies developed in the last few years for the selective modification of biological species in living systems have yielded new insights into cellular processes. Key to these new techniques are bioorthogonal chemical reactions, whose components must react rapidly and selectively with each other under physiological conditions in the presence of the plethora of functionality necessary to sustain life. Herein we describe the bioorthogonal chemical reactions developed to date and how they can be used to study biomolecules.

/pdf/bioorthogonal-chemistry-fishing-for-selectivity-in-a-sea-of-125vhdfza6.pdf

Bioorthogonal Chemistry: Fishing for Selectivity in a Sea of Functionality

Selective chemical reactions enacted within a cellular environment can be powerful tools for elucidating biological processes or engineering novel interactions. A chemical transformation that permits the selective formation of covalent adducts among richly functionalized biopolymers within a cellular context is presented. A ligation modeled after the Staudinger reaction forms an amide bond by coupling of an azide and a specifically engineered triarylphosphine. Both reactive partners are abiotic and chemically orthogonal to native cellular components. Azides installed within cell surface glycoconjugates by metabolism of a synthetic azidosugar were reacted with a biotinylated triarylphosphine to produce stable cell-surface adducts. The tremendous selectivity of the transformation should permit its execution within a cell's interior, offering new possibilities for probing intracellular interactions.

Cell Surface Engineering by a Modified Staudinger Reaction

Dissecting complex cellular processes requires the ability to track biomolecules as they function within their native habitat. Although genetically encoded tags such as GFP are widely used to monitor discrete proteins, they can cause significant perturbations to a protein's structure and have no direct extension to other classes of biomolecules such as glycans, lipids, nucleic acids and secondary metabolites. In recent years, an alternative tool for tagging biomolecules has emerged from the chemical biology community—the bioorthogonal chemical reporter. In a prototypical experiment, a unique chemical motif, often as small as a single functional group, is incorporated into the target biomolecule using the cell's own biosynthetic machinery. The chemical reporter is then covalently modified in a highly selective fashion with an exogenously delivered probe. This review highlights the development of bioorthogonal chemical reporters and reactions and their application in living systems.

Chemistry in living systems.

13C NMR spectra of pentacyclic triterpenoids--a compilation and some salient features

https://chemistry.mdma.ch/hiveboard/rhodium/pdf/piper.phytochemistry.pdf

Phytochemistry of the genus Piper

A substantial portion of metabolism involves transformation of phosphate esters, including pathways leading to nucleotides and oligonucleotides, carbohydrates, isoprenoids and steroids, and phosphorylated proteins. Because the natural substrates bear one or more negative charges, drugs that target these enzymes generally must be charged as well, but small charged molecules can have difficulty traversing the cell membrane by means other than endocytosis. The resulting dichotomy has stimulated a great deal of effort to develop effective prodrugs, compounds that carry little or no charge to enable them to transit biological membranes, but able to release the parent drug once inside the target cell. This chapter presents recent studies on advances in prodrug forms, along with representative examples of their application to marketed and developmental drugs.

/pdf/prodrugs-of-phosphonates-and-phosphates-crossing-the-387agvhis4.pdf

Prodrugs of Phosphonates and Phosphates: Crossing the Membrane Barrier

Synthesis of Nonracemic Phosphonates

Foragers of the leafcutting ant, Atta cephalotes L (Formicidae, Attini) seldom or never attack many of the plant species available to them in nature In the semideciduous forests of lowland Guanacaste Province, Costa Rica, one of the tree species seldom cut is Hymenaea courbaril L (Leguminosae, Caesalpinioideae) We tested the hypothesis that this species is avoided by the ants because of the presence of ant-repellent secondary compounds in the leaves A bioassay to test repellency of leaf extracts was developed to guide the chemical isolation of ant repellents, using a laboratory colony of Atta cephalotesThe presence of one or more extractable ant repellents was quickly demonstrated Subsequent chemical isolation and identification revealed that there was essentially only one terpenoid responsible for the repellency: caryophyllene epoxide Tests with a concentration series of the pure compound demonstrated that the natural concentration of this terpenoid in Hymenaea could fully account for the observed repellency of intact leaves Field bioassays of the terpenoid in Costa Rica confirmed this result; leaves of a preferred species, Spondias purpurea L (Anacardiaceae), became as repellent as Hymenaea leaves when treated with caryophyllene epoxide at natural Hymenaea leaf concentrations Repellency of the epoxide was 20 times greater than that of caryophyllene, its sesquiterpene hydrocarbon precursor, which is also found in Hymenaea leavesAttine ants cut leaves to serve as substrate for culturing a specific fungus for food, principally for their larvae A reasonable hypothesis is that these ants selectively avoid plant species whose leaves contain compounds which are toxic to their fungus We tested caryophyllene epoxide for antifungal activity and found that it is an extremely potent compound, not only against the attine fungus, but other fungi as well We speculate that many of the other plant species avoided by these ants in nature may be similarly protected from ant attack by antifungal compounds in their leaves We further suggest that plant defense against leafcutting ants may be largely an incidental byproduct of selection for fungal resistance in plants

An antifungal terpenoid defends a neotropical tree (Hymenaea) against attack by fungus-growing ants (Atta).

Phosphonate and bisphosphonate analogues of farnesyl pyrophosphate as potential inhibitors of farnesyl protein transferase.

Synthesis of a phosphoantigen prodrug that potently activates Vγ9Vδ2 T-lymphocytes.

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