Privileged substructures are of potentially great importance in medicinal chemistry. These scaffolds are characterized by their ability to promiscuously bind to a multitude of receptors through a variety of favorable characteristics. This may include presentation of their substituents in a spatially defined manner and perhaps also the ability to directly bind to the receptor itself, as well as exhibiting promising characteristics to aid bioavailability of the overall molecule. It is believed that some privileged substructures achieve this through the mimicry of common protein surface elements that are responsible for binding, such as β- and gamma;-turns. As a result, these structures represent a promising means by which new lead compounds may be identified.

The combinatorial synthesis of bicyclic privileged structures or privileged substructures

9-Fluorenylmethoxycarbonyl (Fmoc) amino acids were first used for solid phase peptide synthesis a little more than a decade ago. Since that time, Fmoc solid phase peptide synthesis methodology has been greatly enhanced by the introduction of a variety of solid supports, linkages, and side chain protecting groups, as well as by increased understanding of solvation conditions. These advances have led to many impressive syntheses, such as those of biologically active and isotopically labeled peptides and small proteins. The great variety of conditions under which Fmoc solid phase peptide synthesis may be carried out represents a truly "orthogonal" scheme, and thus offers many unique opportunities for bioorganic chemistry.

Solid phase peptide synthesis utilizing 9‐fluorenylmethoxycarbonyl amino acids

Fundamental and applied research in chemistry and biology benefits from opportunities provided by droplet-based microfluidic systems. These systems enable the miniaturization of reactions by compartmentalizing reactions in droplets of femoliter to microliter volumes. Compartmentalization in droplets provides rapid mixing of reagents, control of the timing of reactions on timescales from milliseconds to months, control of interfacial properties, and the ability to synthesize and transport solid reagents and products. Droplet-based microfluidics can help to enhance and accelerate chemical and biochemical screening, protein crystallization, enzymatic kinetics, and assays. Moreover, the control provided by droplets in microfluidic devices can lead to new scientific methods and insights.

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Reactions in Droplets in Microfluidic Channels

One of the initial steps in the development of therapeutic agents is the identification of lead compounds that bind to the receptor or enzyme target of interest. Many analogs of these lead compounds are then synthesized to define the key recognition elements for maximal activity. In general, many compounds must be evaluated in both the lead identification and optimization steps. Increasing burdens have been placed on these efforts due to the large number of new therapeutic targets that continue to be identified thorough modern molecular biology methods.1 To address this demand, very powerful chemical and biological methods have been developed for the generation of large combinatorial libraries of peptides2 and oligonucleotides3 that are then screened against a receptor or enzyme to identify high-affinity ligands or potent inhibitors, respectively. While these studies have clearly demonstrated the power of library synthesis and screening strategies, peptides and oligonucleotides generally have poor oral activities and rapid in vivo clearance;4 therefore their utility as bioavailable therapeutic agents is often limited. Due to the favorable pharmacokinetic properties of many small organic molecules (<600-700 molecular weight),5 the design, synthesis, and evaluation of libraries of these compounds6 has rapidly become a major frontier in organic chemistry. Lorin A. Thompson was born in Lexington, KY, in 1970. He received the Bachelor of Science degree from the University of North Carolina, Chapel Hill, in 1992 where he worked under the guidance of Joseph Desimone. He is currently pursuing his doctorate in the laboratory of Jonathan Ellman at UC Berkeley where he is the 1994 Glaxo-Wellcome fellow. His research interests include the development of synthetic methodology for organic library construction.

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Synthesis and Applications of Small Molecule Libraries.

A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker.

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Peptide nucleic acids

1. Peptoids 419 2. Oligocarbamates 420 3. Oligoureas 420 4. Vinylogous Sulfonyl Peptides 420 5. Peptidosulfonamides 420 6. Azatides 420 7. Ketides 420 D. Small Molecule Libraries 420 1. Acyclic Libraries 422 2. Libraries on Preformed Scaffolds 422 3. Heterocyclic Libraries 423 4. Structurally Heterogeneous Libraries 427 E. Cleavable Linkers 428 1. Single Cleavable Linkers 428 2. Multiply Cleavable Linkers 429 IV. Screening Methods 432 A. On-Bead Screening 432 1. Binding Assay 432 2. Functional Assay 434 B. Solution-Phase Screening 434 1. The 96-Well Two-Stage Releasable Assays 435

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The “One-Bead-One-Compound” Combinatorial Library Method

http://www.5z.com/mlebl/publications/TetLett1995_Krchnak.pdf

Polymer-Supported Mitsunobu Ether Formation and its Use in Combinatorial Chemistry

The development of multidrug resistant (MDR) and extensively drug resistant (XDR) forms of tuberculosis (TB) has stimulated research efforts globally to expand the new drug pipeline. Nitroaromatic compounds, including 1,3-benzothiazin-4-ones (BTZs) and related agents, are a promising new class for the treatment of TB. Research has shown that the nitroso intermediates of BTZs that are generated in vivo cause suicide inhibition of decaprenylphosphoryl-β-d-ribose 2′ oxidase (DprE1), which is responsible for cell wall arabinogalactan biosynthesis. We have designed and synthesized novel anti-TB agents inspired from BTZs and other nitroaromatic compounds. Computational studies indicated that the unsubstituted aromatic carbons of BTZ043 and related nitroaromatic compounds are the most electron-deficient and might be prone to nucleophilic attack. Our chemical studies on BTZ043 and the additional nitroaromatic compounds synthesized by us and others confirmed the postulated reactivity. The results indicate that nuc...

/pdf/thiolates-chemically-induce-redox-activation-of-btz043-and-5du1l8hya2.pdf

Thiolates Chemically Induce Redox Activation of BTZ043 and Related Potent Nitroaromatic Anti-Tuberculosis Agents

Noninvasive continuous monitoring of solid-phase peptide synthesis by acid-base indicator.

Peptides generated on polymeric beads that are attached to the support via cleavable linkers are released into solution in equimolecular amounts in several independent steps and screening of the «peptide libraries» can be performed in the usual manner used for testing peptides in solution

Viktor Krchňák

Papers

The “One-Bead-One-Compound” Combinatorial Library Method

Polymer-Supported Mitsunobu Ether Formation and its Use in Combinatorial Chemistry

Thiolates Chemically Induce Redox Activation of BTZ043 and Related Potent Nitroaromatic Anti-Tuberculosis Agents

Noninvasive continuous monitoring of solid-phase peptide synthesis by acid-base indicator.

Multiple release of equimolar amounts of peptides from a polymeric carrier using orthogonal linkage-cleavage chemistry