Constrained epitopes

The following examples demonstrate the power of using constrained epitope libraries, for recognizing strongly binding motifs, which may represent the linear sequence of the normal ligand or mimic its steric structure, i.e. a so-called mimotope . 

Antibodies to the principal neutralizing determinant in the HIV gpl20 V3 loop prevent infection. The -Gly-Pro-Gly-Arg- sequence from residues 312 to 315 is found in 85-90% of HIV isolates and is believed to exist in reverse-turn conformation.1117 To determine the optimum construction of our B-cell epitope, a small library of restricted-turn constructs was screened against the V3 directed MAb 50.1. Based upon our previous analysis, both the B (before binding) and A (after binding) type constructions (Scheme 50) were incorporated into the constrained B-cell epitope library. 

B. Lead Finding Using Conformationally Constrained Peptides Mimicking Exposed Protein Epitopes... 

In Section II.C we will present novel tricyclic xanthene derived amino acid templates, which allow the construction of libraries of cyclic conformationally constrained peptide loop mimetics using the split-and-mix method without having to use tagging and deconvolution strategies. In Section III we will focus on parallel and combinatorial approaches devoted to the synthesis of small molecule, non-peptidic compound collections, which in addition offer the possibility to incorporate structural features derived from protein epitope mapping into conformationally constrained peptide mimetics. 

H. NOVEL AMINO ACID-DERIVED TEMPLATE MOLECULES FOR PROTEIN EPITOPE MAPPING USING CONFORMATIONALLY CONSTRAINED SMALL PEPTIDES... 

The innovative potential and the ingenuity which have gone into designing libraries, vectors and selection protocols are impressive. However, considerable input has come from structural modelling and design considerations, in the proliferation of phage-display scaffolds to provide constrained variable epitopes in different environments or contexts . In addition the method has been used to understand protein folding, protein-protein interactions and structure-function relationships in catalysis. I hope that, in this review,... 

Epitopes presented in constrained scaffolds may be prevented from optimal interactions with their target by local deleterious charge, hydrophobic, hydrophilic or steric interactions. Methods have, therefore, been developed which introduce hypervariability, not only into the highly variable epitopes but also into the framework which carries them. This has been achieved by the use of error-prone PCR or, more recently, in vivo hypermutation. Ouellette and Wright [100] in their review of PCR amplifiable DNA and RNA ligands,... 

The amino acid His-350 is located in a position similar to the general acid/base aspartic acid of exosialidases (Fig. 3a Nani 291) and has been mutated to alanine for co-crystaUization with DP5 [106]. In comparison to wild type endoNF, the alanine residue red in Fig. 3a) H350A perfectly superposes with the Ca and C(5 atoms of the histidine residue. Thus, the backbone of the p-propeller is not affected by this mutation. In the H350A mutant, a trimeric sialic acid (DP3) is bound in the active site coordinated by a network of water molecules and polar contacts (Fig. 3c). The geometry of the active site constrains the otherwise helical polysialic acid into an extended conformation (see Sect. 8 for heUcal epitopes). 

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