Towards the sequence-specific multivalent molecular recognition of cyclodextrin oligomers

Towards the sequence-specific multivalent molecular recognition of cyclodextrin oligomers Michael Kurlemann and Bart Jan Ravoo* Full Research Paper Address: Organic Chemistry Institute, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany Email: Bart Jan Ravoo* - * Corresponding author Keywords: cooperativity; cyclodextrins; molecular recognition; multivalency; sequence specificity Open Access Beilstein J. Org. Chem. 2014, 10, 2428–2440. doi:10.3762/bjoc.10.253 Received: 11 July 2014 Accepted: 19 September 2014 Published: 20 October 2014 This article is part of the Thematic Series "Superstructures with cyclodextrins: Chemistry and applications II". Guest Editor: G. Wenz © 2014 Kurlemann and Ravoo; licensee Beilstein-Institut. License and terms: see end of document. Abstract Sequence-specific multivalent molecular recognition has been recognized to play a major role in biological processes. Furthermore, sequence-specific recognition motifs have been used in various artificial systems in the last years, e.g., to emulate biological processes or to build up new materials with highly specific recognition domains. In this article, we present the preparation of cyclodextrin (CD)-based strands and complementary and non-complementary strands modified with guest molecules and the investigation of their complexation behavior towards each other by isothermal titration calorimetry (ITC). As complementary binding motifs n-butyl and α-CD and adamantane and β-CD were selected. It was found that it is possible to realize sequencespecific molecular recognition by the use of host–guest chemistry, but the recognition motifs as well as the linkages have to be chosen very carefully. In the case of trivalent systems one adamantane moiety must be included to induce preferred formation of 1:1 adducts. Due to the too weak interaction between n-butyl and α-CD these systems have a negative chelate cooperativity and open adducts are preferentially formed. As soon as two adamantane moieties are present, the complementary systems have a positive chelate cooperativity and double-stranded structures are favored over open adducts. In this system the n-butyl moiety provides insufficient discrimination towards α- and β-CD and no sequence specificity is observed. By the combination of three adamantane moieties sequence specificity can be generated. Exclusively with the complementary CD sequence double-stranded structures are formed, with non-complementary strands aggregates of higher stoichiometry are generated. Introduction Multivalency is the interaction of a receptor and a ligand with at least two recognition motifs on each binding partner [1]. In recent years multivalency has been recognized to play a major role in almost all biological processes, e.g., the recognition of cells by other cells, bacteria or viruses, the adhesion of cells or signal transduction pathways [2]. By the combination of 2428 Beilstein J. Org. Chem. 2014, 10, 2428–2440. multiple, rather weak non-covalent interactions stable yet reversible systems are generated, which are responsive to external stimuli. These advantages have made synthetic multivalent systems interesting for a broad field of applications. In the case of medicinal applications multivalent molecules have been used as inhibitors of toxins or viruses and for imaging and targeted drug delivery [3]. Hydrogels which are built up by multivalent host–guest interactions and vesicles of amphiphilic host molecules have been intensively studied for their ability to function as drug delivery systems as well [4-9]. Additionally, such vesicles can be modified with bio-active ligands and serve as model systems to mimic biological processes on cell membranes [10,11]. In the field of materials science multivalency has been used to create functional polymers [12-14] and self-assembled electronic [15-20] or biofunctional materials [21-27]. Even the molecular recognition of macroscopic gel blocks by multivalent host–guest interactions has been realized [28-32]. Besides the number of receptor–ligand interactions their spatial distribution is crucial for the highly selective molecular recognition as well. The most important natural example of sequence specific, multivalent molecular recognition is the hybridization of complementary DNA strands via the base pairing of adenosine and thymine respectively guanine and cytosine. Within the last years these binding motifs have been transferred to artificial systems like peptide nucleic acids (PNA) [33] and extensively used to mimic biological processes [34,35] or to generate functional materials [36]. Host–guest chemistry has been studied in the field of sequence-specific molecular recognition as well. The selective recognition of short peptides made of natural amino acids with aromatic side chains by different host moieties like coordination cages [37] and cucurbiturils [38,39] has been demonstrated. For cyclodextrins (CD) a similar approach is reported, but by using CD strands and different model peptides of natural and artificial amino acids no significant selectivity was observed [40]. In this work we present an alternative approach to realize the hybridization of complementary strands mediated by multivalent host–guest interaction. We used α- and β-CD because of their well-known and regiospecific modifiability for the preparation of di- and trivalent host sequences and investigated their binding behavior towards complementary and non-complementary di- and trivalent guest sequences which were modified with n-butyl and 1-adamantyl moieties. Such structures can be used for the self-assembly of complicated molecular architectures. Furthermore, the results foster the understanding of the basic principles of sequencespecific molecular recognition, which is ubiquitous in nature. Results and Discussion The divalent CD sequences 1–3 (Figure 1A) were synthesized by the amide coupling of peracetylated α- and β-CD, bearing an amine respectively a carboxylic acid function at the primary side, followed by complete deprotection under Zemplén conditions (Figure 2). The trivalent CD sequences 4–7 (Figure 1B) were prepared by amide coupling of peracetylated 6 A,D -diamine functionalized α- and β-CD with monocarboxylic acid functionalized α- and β-CD, again followed by complete deprotection under Zemplén conditions (Figure 2). Based on MALDI mass spectra of the protected and unprotected cyclodextrin strands impurities by monomeric building blocks respectively dimeric species in the case of trivalent strands can be excluded (see Supporting Information File 1). The di- and trivalent guest strands 8–14 (Figure 1C, D) were synthesized by solid phase peptide synthesis using a standard Fmoc-protocol (Figure 3). Therefore the serine derivatives 15 and 16 (Figure 1E) and a water-soluble linker molecule were used. The purity of the guest strands is estimated to be >95% based on 1 H NMR spectra (see Supporting Information (...truncated)