Scanning, positional

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

In order to determine the sequence of the bioactive tripeptide, all the nine sub-libraries need to be tested. If those marked with + are the active ones in screening (H, G and C), then the sequence of the bioactive peptide (from N to C terminal) is white black gray. In deconvolution of a tripeptide library prepared from 20 amino acids, for example, 60 sub-libraries have to be synthesized and screened. For screening of hexapeptides, a set of 120 sub-libraries is needed. Once the set of sub-libraries is prepared in sufficient quantity, it can be used in many different screening experiments. 

---

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. 

In the cyclic voltammetry, the oxidation peaks of PH were clearly observed in positive scans for all the modified electrodes. In contrast, reduction peaks of Cgo were clearly observed in the absence of magnetic processing but not in the presence of magnetic processing. 

The VCTTM recorded with the LM cell of Eq. (1) and voltammograms at the Wl/ LM and LM/W2 interfaces are realized as curves 1, 2, and 3, respectively, in Fig. 1. A positive peak and a negative peak exist in voltammograms 1 and 2. The positive peak, the final rise, and the final descent in curve 2 are attributable to the transfer of from Wl to LM facilitated by dibenzo-18-crown-6, TPhB from LM to Wl, and CV+ from LM to Wl, respectively. The negative peak is due to the transfer of that has moved into LM during the positive scan from LM to Wl. The final rise and the final descent in curve 3 correspond to the transfer of CV from LM to W2 and that of TPhB from LM to W2, respectively. 

Backes BJ, Harris JL, Leonetti F, et al. Synthesis of positional-scanning hbraries of fluorogenic peptide substrates to define the extended substrate specificity of plasmin and thrombin. Nat Biotechnol 2000 18 187-93. 

Robust peptide-derived approaches aim to identify a small drug-like molecule to mimic the peptide interactions. The primary peptide molecule is considered in these approaches as a tool compound to demonstrate that small molecules can compete with a given interaction. A variety of chemical, 3D structural and molecular modeling approaches are used to validate the essential 3D pharmacophore model which in turn is the basis for the design of the mimics. The chemical approaches include in addition to N- and C-terminal truncations a variety of positional scanning methods. Using alanine scans one can identify the key pharmacophore points D-amino-acid or proline scans allow stabilization of (i-turn structures cyclic scans bias the peptide or portions of the peptide in a particular conformation (a-helix, (i-turn and so on) other scans, like N-methyl-amino-acid scans and amide-bond-replacement (depsi-peptides) scans aim to improve the ADME properties." ... 

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. 

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

After all four positive scans are completed (typically within 3 s), the polarity is switched and the fifth scan event records a negative-ion full-scan MS. If the expected protonated molecule is not detected in the positive mode, the second, third and fourth scan events are skipped and the fifth (negative-ion-mode) scan event is triggered. Similar to the positive-ion mode, if the expected [M-H]- ion is detected in the full-scan MS, IT data-dependent MS/MS (sixth), FT accurate MS (seventh), and FT MS/MS (eighth) scan events are acquired. Clearly demonstrated here is the ability of the LTQ-FT to handle multiple experiments on a chromatographic time scale. One might question the need for such an elaborate data-dependent scheme when apparently all that is needed is an accurate mass determination followed by a data-dependent accurate mass MS/MS spectmm. Apart from the fact that using the... 

---