Scaffold optimization in discontinuous epitope containing protein mimics of gp120 using smart libraries

Abstract

A diversity of protein surface discontinuous epitope mimics is now rapidly and efficiently accessible. Despite the important role of protein-protein interactions involving discontinuous epitopes in a wide range of diseases, mimicry of discontinuous epitopes using peptide-based molecules remains a major challenge. Using copper(I) catalyzed azide-alkyne cycloaddition (CuAAC), we have developed a general and efficient method for the synthesis of collections of discontinuous epitope mimics. Up to three different cyclic peptides, representing discontinuous epitopes in HIV-gp120, were conjugated to a selection of scaffold molecules. Variation of the scaffold molecule, optimization of the ring size of the cyclic peptides and screening of the resulting libraries for successful protein mimics led to an HIV gp120 mimic with an IC50 value of 1.7 μM. The approach described here provides rapid and highly reproducible access to clean, smart libraries of very complex bio-molecular constructs representing protein mimics for use as synthetic vaccines and beyond.

Cyclotriveratrylene‐Based Glycoclusters as High Affinity Ligands of Bacterial Lectins from Pseudomonas aeruginosa and Burkholderia ambifaria

“…The trivalent CTV‐based glycocluster was obtained from the readily available trimethoxy‐triallyl precursor 1 in a few synthetic steps (Scheme ). Pd‐catalyzed removal of the allyl ethers afforded the triphenol 2 in good yield and subsequent etherification with propargyl bromide led to the desired tri‐propargylated CTV‐based core 3 . Conjugation with the azido‐functionalized carbohydrates 4 under Meldal's conditions afforded the trivalent acetylated glycoclusters 5 in high yields and final removal of the acetates provided the trivalent glycoclusters 6 .…”

An orthogonally protected CycloTriVeratrylene (CTV) as a highly pre-organized molecular scaffold for subsequent ligation of different cyclic peptides towards protein mimics

“…We have provided bases for realization of molecular construction of protein mimics by (1) the development of syntheses of different scaffolds for attachment of (cyclic) peptides, [1][2][3][4] (2) synthetic approaches for attachment of different (cyclic) peptides to scaffolds, [5][6][7][8][9][10] and (3) the generation of collections of the resulting protein mimics. 9,11,12 The latter aspect is especially note worthy since design of an optimal protein mimic is often hardly possible even when a significant amount of structural data is available, so there has to be a versatile approach to prepare collections or libraries of protein mimics, which can be screened to find protein mimic "hits" 9,12 For this purpose a non-orthogonally protected scaffold is used, providing direct access to the required unprotected protein mimics, which can be screened as mixtures or as single compounds, followed by MS-identification of the hit(s). 11,12 However, this/these hit(s) then have to be re-synthesized using the an orthogonally protected scaffold to obtain appreciable quantities of single protein mimic compounds for validation of the hit and subsequent structural and biological activity studies Thus, a scalable (re)synthesis approach for any individual hit is absolutely essential.…”

“…9,11,12 The latter aspect is especially note worthy since design of an optimal protein mimic is often hardly possible even when a significant amount of structural data is available, so there has to be a versatile approach to prepare collections or libraries of protein mimics, which can be screened to find protein mimic "hits" 9,12 For this purpose a non-orthogonally protected scaffold is used, providing direct access to the required unprotected protein mimics, which can be screened as mixtures or as single compounds, followed by MS-identification of the hit(s). 11,12 However, this/these hit(s) then have to be re-synthesized using the an orthogonally protected scaffold to obtain appreciable quantities of single protein mimic compounds for validation of the hit and subsequent structural and biological activity studies Thus, a scalable (re)synthesis approach for any individual hit is absolutely essential. So far, we have developed semiorthogonally protected TAC, ATAC and TACO scaffolds, 1,3,4 Figure 1.…”

“…2 More recently, preparation of collections of gp120 protein mimics, using these different scaffolds, showed that CTV-scaffolded gp120 epitope mimics were the most powerful protein mimics (IC50-values of the gp120-CD4 interaction in ELISA of 1.7 and 2.2 μM). 12 Therefore, we felt it was necessary to develop an orthogonally protected CTV derivative, so that the selected protein mimics can be re-synthesized. In this research we describe the synthesis of the highly pre-organized semi-orthogonally protected CTV scaffold as well as an example of sequential introduction of three different cyclic peptides towards individual protein mimics.…”

Untapped Opportunities of Resin‐to‐Resin Transfer Reactions (RRTR) for the Convergent Assembly of Multivalent Peptide Conjugates

“…ad esired target, it now offers an ew option besides (solidphase) chemical ligations (SPCL). Through combinations of scaffolds [80][81][82][83] as well as appendages, [84][85][86] RRTR allows for a fast and modular increase of diversity from al imited amount of immobilizedb uildingb locks. Amenable to library and highthroughput formats, [87,88] this earlier untapped strategy to facilitate the synthesis of multivalent peptidea ssemblies can further be exploited in this newly proposed direction.…”