Peptide combinatorial library screening approaches

Meldal and co-workers26,27 first described the fluorescence-quenching approach to screen the OBOC combinatorial libraries for protease substrates. A fluorescence-quench combinatorial library prepared from the porous PEGA bead resin (see above) is first inspected under a fluorescent microscope and the fluorescent beads are removed and discarded. After all of the false-positive beads have been removed, the peptide beads are transferred into an Eppendorf tube and washed 5 x with water, followed by a 5 x wash with the appropriate protease buffer. Protease is then added... 

Synthetic combinatorial chemistry approaches have created a vast new source of molecular diversity for the potential identification of lead compounds. This revolutionary field enables hundreds to thousands of times more compounds to be synthesized and screened in shorter periods of time relative to traditional approaches. In particular, novel antibacterials and/or antifungals as well as inhibitory peptides of either HIV proteases or HIV integrase proteins13 were identified following the screening of synthetic combinatorial libraries (SCLs). As described below, SCLs have been used by this laboratory to develop antimicrobial and antifungal compounds, as well as novel treatments for HIV infection. 

In collaboration with University of Trieste, we have developed rational approaches for the design and synthesis of peptidomimetic and non-peptidic inhibitors of HIV PR, utilizing structure-based [12-15], as well as combinatorial, library design methods [16, 17]. In this paper, we survey computer-assisted studies on the design, focusing and in silico screening of virtual combinatorial libraries of peptidomimetics and cyclic ureas, as potential anti-HIV agents, that were carried out in our laboratory. 

A positional scanning combinatorial library (Fig. 3) can be used in place of iterative synthesis and screening [9]. In this approach, all library mixtures are synthesized and assayed for activity. The most active mixture from each positional library reveals the preferred residue at each position. Because all possible combinations of residues are represented in one of the sublibraries, the approach should be insensitive to synergistic effects associated with the structure. The orthogonal combinatorial library consists of two different libraries made up of the same compounds and synthesized in a way that mixtures from each library will only share one peptide or subunit [10]. In this way, these libraries are nonoverlapping, or orthogonal. 

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