Janice M. Kerr

Proteolytic studies of homologous peptide and N-substituted glycine peptoid oligomers

Abstract Homologous L-amino acid, D-amino acid, and parallel and anit-parallel (retro) sequence N-substituted glycine peptide and peptoid oligomers were prepared and incubated with proteases from each major class. The L-amino acid containing peptides were readily cleaved by the appropriate enzymes, while equivalent D-amino acid containing and N-substituted glycine containing oligomers were essentially untouched. Homologous peptide and peptoid oligomers were prepared and incubated with proteases from each major class. All-L peptides were readily cleaved by the appropriate enzymes, while equivalent all-D and N-substituted glycine containing oligomers were not.

Simplified methods for construction, assessment and rapid screening of peptide libraries in bacteriophage

An efficient strategy has been devised for the construction of diverse peptide libraries in bacteriophage vectors. This strategy was used to generate a library of 4 x 10(8) random decapeptide inserts in the pIII protein of bacteriophage fd. A novel method for evaluating the genetic diversity of bacteriophage libraries based on colony hybridization with partially degenerate oligonucleotides has been developed. The decapeptide library was affinity-selected with a previously characterized monoclonal antibody specific for the V3 loop of the gp120 protein of HIV-1. Immunological screening, an efficient technique for the rapid identification of putative binding bacteriophage, is described. Hexapeptide sequences similar to those obtained from affinity selection of a hexapeptide bacteriophage library were obtained from the decapeptide library in all five frames. Immunological screening of 20,000 clones from the two libraries after two rounds of affinity selection rapidly identified antibody-binding sequences; 93% and 86% of the sequences obtained from the hexapeptide and decapeptide libraries, respectively, had IC50 values < or = 10 mM as free peptides.

Nmr Structural Characterization of Oligo-N-Substituted Glycine Lead Compounds from a Combinatorial Library

Synthesis and screening of combinatorial librariesfor pharmaceutical lead discovery is a rapidlyexpanding field. Oligo-N-substituted glycines (NSGs)were one of the earliest sources of moleculardiversity in combinatorial libraries. In one of thefirst demonstrations of the power of combinatorialchemistry, two NSG trimers, CHIR-2279 and CHIR-4531,were identified as nM ligands for two 7-transmembraneG-protein-coupled receptors. The NMR characterizationof these two lead compounds was undertaken to verifycovalent connectivity and to determine solutionconformations, if any. The sequential chemical shiftassignments were performed using a new strategy forassigning 1H and 13C resonances of NSGs. The conformational preferences were then determined inboth an aqueous co-solvent system and an organicsolvent to probe the effects of hydrophobic collapse. NSGs are expected to be more flexible than peptidesdue to the tertiary amide, with both cis andtrans amide bond conformations being accessible. Solution NMR studies indicate that although CHIR-2279and CHIR-4531 have identical backbones and termini,and very similar side chains, they do not display thesame solution conformational characteristics.

Identification of antibody mimotopes containing non-natural amino acids by recombinant and synthetic peptide library affinity selection methods

Abstract A 512-component synthetic hexapeptide library containing non-natural amino acids was generated based on a mimotope obtained from screening a diverse bacteriophage library with an anti-gp120 monoclonal antibody. Four peptides were identified by affinity selection with ≤ 2 μM IC 50 s, three of which contained non-natural amino acids.