Positional scanning library

Because of their ease of synthesis and their structural similarity to peptides, many laboratories have used peptoids as the basis for combinatorial drug discovery. Peptoids were among the first non-natural compounds used to establish the basic principles and practical methods of combinatorial discovery [17]. Typically, diverse libraries of relatively short peptoids (< 10 residues) are synthesized by the mix-and-split method and then screened for biological activity. Individual active compounds can then be identified by iterative re-synthesis, sequencing of compounds on individual beads, or indirect deduction by the preparation of positional scanning libraries. 

Experimental Procedure for the Parallel Synthesis of Heterocyclic Positional Scanning Libraries 47 to 51... 

A special type of combinatorial library is the positional scanning library (43, 49,58). This array contains a set of combinatorial libraries with one or more (two positions = dual positional scan (4, 59))deconvoluted positions. In each of the synthesized libraries the deconvoluted positions are different. After screening one can combine the positions of the spot with the peptides of highest activity of each library to obtain the complete sequence of a peptide with most likely the greatest activity. 

Fig. 4. Positional scan library format three diversity positions, three elements per position. 0=Exed position, X = equimolar random position.

For heterocychc libraries in a positional scan format, a key factor is in being able to devise a method for efficiendy carrying out the construction of the library in the positional scan format. For peptide hbraries, the Houghten laboratory was able to employ mixtures of building blocks where the molar ratios had been adjusted to account for reactivity (kinetic rate) differences of incoming building blocks and thereby achieve equimolar mixtures. A non-peptide, two-dimensional positional scan library, identified as an indexed combinatorial library, was reported recently [63], In this work a novel acetyl-... 

A hybrid of the one-bead-one-peptide and positional-scanning library formats (see Section 4.3.V.3.2.2) is presented by an approach termed library of libraries ,which is directed toward the identification of pharmacophore motifs, i.e. structural motifs necessary for the bioactivity of interest, rather than the complete structures of individual active compounds. This library format enables the identification of specific, i.e. nonreplaceable, positions of a peptide with a bioactivity of interest versus unspecific positions, which can be replaced by a variety of different amino acids without loss in activity. In the example presented,a hexapeptide library is generated as 160000 (20 x20) sublibraries (beads), which represent all possible combinations of three defined and three mixture positions within the hexapeptide framework, i.e. 8000 (20 ) different combinations of three amino acids at the defined positions within a given arrangement of the hexapeptide multiphed by 20 possible different arrangements of three defined and three mixture positions. While the defined positions are coupled using the DCR method,01 the mixture positions are introduced by the coupling of amino acid mixtures. 

Backes BJ, Harris JL, Leonetti F, Craik CS, Ellman JA. Synthesis of positional-scanning libraries of fluorogenic peptide substrates to define the extended substrate specificity of plasmin and thrombin. Nature Biotechnol 2000 18 187-93. 

Figure 3.7. Positional scanning libraries where R1 to R4 represent single amino acids and X represents a mixture of those amino acids.

Dooley, C., Houghten, R. (1993) The use of positional scanning synthetic peptide combinatorial libraries for the rapid determination of opioid receptor ligands. Life Sci 52, 1509-1517. 

Dooley, . T., Ny, P, Bidlack, J. M., Houghten, R. A. (1998) Selective ligands for the i, S, and opioid receptors identified from a single mixture based tetrapeptide positional scanning combinatorial library. / Biol Chem 273, 18848-18856. 

Positional scanning with phage libraries were used to discover the amino acid residues in peptides responsible for binding to the calciumbinding protein calmodulin.18 In this case, the binding polypeptide needed Trp as a key residue located in the fourteenth position from the N-terminus for strong binding. 

Although not identical, both the orthogonal and positional scan formatted libraries share the features that all mixtures are made at the start of the library process and only individual compound synthesis is required after the first screening of mixtures. This is an extra initial effort with regard to the synthesis of mixtures when compared to an iterative method. The advantage is that no intermediate mixture syntheses will be required. If prepared in sufficient quantity, the library can be screened over a large number of assays, and the added effort of initial mixture syntheses will be translated into an efficiency in deconvolution relative to the continual resynthesis of mixtures with iterative deconvolution. 

Fig. 2. Mixture libraries - position scanning. (AA) =one of 20 amino acids (AAA) = all 20 amino acids simultaneously incorporated.

FIGURE 2.6 Positional scanning. A full library B-J a full set of first order sub-libraries. 

Pinilla C, Appel JR, Houghten RA, Positional scanning synthetic peptide combinatorial libraries, In Schneider CH, Eberle AN eds., Peptides 1992, ESCOM, Leiden, 1993, p. 65-66. 

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