Synthesis and structure investigation of stabilized aromatic oligoamides and their interaction with g quadruplex structures 1

Foldamers were defined as oligomers that fold into a conformationally ordered state in solution, the structures of which are stabilized by a collection of noncovalent interactions among

Chapter 1

Introduction

1.1 Background

In nature, most of the amazing functions carried out by biomacromolecules, such as molecular recognition, catalysis and information storages, involve compact and stable solution structures approaching conformational uniqueness In order to gain deeper insight into the operation of the nature’s biomacromolecules as well as to identify new molecules that display bio-functional performances, developing new molecules that adopt well-defined conformations have been the object of very active research during the last twenty years This field of study has come to be known as foldamers Foldamers were defined as oligomers that fold into a conformationally ordered state

in solution, the structures of which are stabilized by a collection of noncovalent interactions among monomer units.1

To design foldamers rationally, several issues within the field of protein folding should be taken into consideration Predictability is the primary consideration in the design of secondary motifs to determine the potential usefulness of foldamers In addition, stability, tunability and ease of synthesis are also essential features for designing foldamers Until now, two major categories of foldamers have been studied: single-stranded foldamers that fold (peptidomimetics and their abiotic analogues) as well as multiple-stranded foldamers that both fold and associate (nucleotidomimeitics

and their abiotic analogues) Generally, single-stranded abiotics are unnatural backbones that mimic secondary structures, such as folding and helices, while multi-stranded foldamers simulate such as double-helical conformations existing in oligonucleotides

Since the pioneering work of Gellman,2 single-stranded oligomers that fold into well-defined secondary structures have been extensively investigated In the earlier studies, a large number of artificial peptidomimetic systems such as aliphatic α-, β-,

γ-, and δ-peptides3 were designed and synthesized With the development of structurally unique folding patterns, the applications of such synthesized secondary structures in discrete areas have been broadened For example, several folded

α-peptides have been revealed to display strong antibacterial and antimicrobial activity.4,5

Recently, there has been increasing interest in identification of novel and unnatural backbones which fold into secondary structures akin to those found in proteins The advantages of these foldamers include rigidity inherent in aromatic units, torsional flexibility of the linkers and various nonconvalent interactions that enforce discrete folded conformation Considering these advantages, single-stranded foldamers with various abiotic backbones have been studied, including backbones utilizing bipyridine segments,6 solvophobic interaction,7 hydrogen-binding interactions8 and metal coordination.9 However, the challenges in designing synthetic folding oligomers exist

in terms of folding stability, tunability, and the control of conformational changes under distinct conditions in which molecules adopt various secondary structures

Among the artificial foldamers reported, aromatic oligoamides utilizing hydrogen bonding to control the folding conformations have been proven to substantially alleviate these challenges These foldamers aryl amide has been used very often to connect building blocks together In general, most oligoamides make use of in H-bonding interactions between adjacent monomer units Although interactions between remote units in the sequence may also contribute to the stability of the structure, it was not the predominant factor that determines how the molecule may fold In this way, these foldamers often contain a few sets of distinct monomer building blocks that make up regularly ordered backbone

1.2 Literature Review

1.2.1 Linear Aromatic Oligoamides

The simplest structural motif of aromatic oligoamides is the linear strand In a linear oligomer, there is almost no contact between aromatic units remote from each other Several building blocks allowing the construction of linear conformation are shown in Figure 1.1 Oligoamides of anthranilic acid was first reported by Hamilton

2,5-bis(2-aminophenylene) pyrazine (Figure 1.1b).11

Usually, those oligomers exhibit good linearity due to the formation of the hydrogen bonds on both sides of the molecular strand In contrast, some linear strands are not expected to be strictly linear and a curvature in backbone could be observed due to the presence of hydrogen bond located at only one side of the strand For

example, oligoamides of 6-alkoxy-5-aminopicolinic acid form linear motif in which the amide protons hydrogen-bond to both the ether oxygen atom and the endocyclic pyridine nitrogen atom at the same side (Figure 1.1c).12 Due to the slight curvature, the facial polarity of those strands was reported to be useful for molecular recognition

For example, Ishu Saraogi et al reported a family of oligoamide with controlled

curvature serving as α-helix mimetics.15 Another α-helix proteomimetics is N-alkylated aromatic oligoamides reported by Frederick Campbell.17 Further modification of those partially linear structures leads to bend structures For example,

Gong et al prepared an oligoamides adopting bend structure by replacing the

endocyclic nitrogen atom of 6-alkoxy-5-aminopicolinic acid with an exocyclic methoxy hydrogen-bond acceptors (Figure 1.1d).13

a) b) c)

d)

Figure 1.1 Aromatic Oligoamides adopting linear conformations (a,b,c)

However, aromatic oligoamide foldmer may undergo conformational changes via a syn-to-anti or anti-to-syn 180º rotation For example, A transition between linear to turn conformational switch of unsymmetrically linked phenolic oligoamides has been

reported through deprotonation.22 The deprotonation of a hydroxyl group in each unit induces a rearrangement of the hydrogen-bonding mode within the unit from OH…O=C to NH…O (oxyanion), which leads to linear-to-turn conformational switching

Figure 1.2 Proposed conformational change of aromatic oligoamides in solution

1.2.2 Crescent and Helical Aromatic Oligoamides

Among all aromatic oligomers, crescent-shaped oligomers or helices have received particular interests Usually, these oligomers consist of a single repeating unit Some examples are shown in Figure 1.1 Curvature of aromatic oligoamide is resulted when amine and acid substituents define an angle smaller than 180o For short oligomers having a rigid, curved backbone, the structures are planar and crescent- shaped since there is no sufficient repulsive interactions between end units As its chain length extends, oligomers are deviated from planarity so as to form helices Based on this principle, the group of Hamilton,29 Lehn,28 Gong,13 Huc15 and Li16 made a great contribution in developing crescent and helical structures containing cavtities with tunable sizes since 1999

Gong’s group firstly designed a hydrogen-binding rigidified crescent aromatic oligoamides containing benzene residues meta-linked by amide linkages, as shown in Figure 1.1d.13a The reliability of the three-center H-bonds in rigidifying the oligoamide backbone was demonstrated by the well-defined crescent conformation of dimer, trimer and tetramer According on this three-center H-bonding, a 9-mer and a 11-mer were synthesized and structures were investigated.13b-d The longer oligoamides adopt, both in the solid state and in the chloroform solution, a helical structure with approximately seven benzene rings per turn and an inner diameter of 10 Å

Huc’group has researched extensively into the helical structures enforced by aromatic pyridine oligoamides They first reported an elegant system of double helical aromatic oligoamides consisting of pyridine residues, with backbones rigidified by intramolecular H-bonds in 2000.14a,14o The X-ray crystal structure demonstrated the presence of ellipsoid helices with an inner diameter of 5.5 Å (n=2) and 8 Å (n=4) In addition, these oligoamide helices can also further dimerize at higher concentrations, forming a stable double helix in solution Within the double helix, the two oligomer strands are held together by arene-arene interactions between pyridine rings lying opposite each other (Figure 1.3b) In addition, sequences comprised of quinoline,14f-h 8-fluoroquinoline14e and pyridoquinoline monomers,14g as well as combinations thereof,14i-l were reported to adopt double helices with a large diameter Among these studied, the most prominent finding is the observation of a tetramer composed of fluoroqinolinecarboxamide-based oligomers that adopt a helical conformation with a large pitch, which allows the formation of a quadruple helix both in solution and the

solid state (Figure 1.3c and 1.3d) Also, they found that naphthyridine oligoamides can spontaneously assemble in parallel and antiparallel triple helices.14m

Figure 1.3.14e Crystal structures of Huc’s aromatic oligoamides: (a) a single helix made of 7-amino-8-fluoro-2-quinolinecarboxylic acid building blocks with the fluorine atoms shown as blue spheres that converge towards the helix hollow space, (b) a narrow double helix composed of pyridine rings only, 14b (c) a quadruple helix composed of four identical single helices shown in (a), a string of sites partially occupied by water molecules is shown as spheres, (d) octameric amides of 7-amino-8-fluoro-2-quinolinecarboxylic acid, as a double helix

Other than above foldamers, aromatic oligoamides based on other monomeric units

or linkages have also been reported recently For example, alternating aromatic heterocycles and methyl-substituted aromatic carbocycles connected together through urea linkage have been synthesized.16 In addition, Li et al reported a folding

architecture utilizing F···H-N hydrogen bonds.25d

Figure 1.4 Helix formation by intramolecular hydrogen bond.13c

The deviation of helices from planarity is achieved by slight changes of the torsional angles involving every aryl-amide bond When one helical turn comprises many repeating units,13 the torsion is minimal The torsions are larger for highly curved helices with only a few units per turn (Figure 1.4) By tuning parameters of helical cavity, the applications of these helical oligoamides have been extended Usually, helices with a large hole or those with few units per turn permit easy access

to objects with a high aspect ratio at minimal synthetic efforts.18 On the other hand, helices with a large diameter can be exploited as a cylindrical channel that may be applied for molecule recognition, catalysis and transport.19

a) b)

Figure 1.5 A typical structure of aromatic oligoamide -Cl- complex.20a

Those helical aromatic foldamers have been demonstrated to display a number of interesting supramolecular properties, especially host-guest chemistry.20a One noticeable example is the helices formed by oligoamides of 2,6 pyridinediarboxylic acid and 2,6-diaminopyridine that contain a polar hollow which may bind water molecules (Figure 1.3c).14b What’s more, helically folded oligomers possessing a hollow cavity is able to provide confined environments suitable for recognizing chiral guests due to their inherent chirality Based on this concept, the encapsulation of tartaric acid in a helically folded aromatic oligoamide was presented.20b Very high affinities, guest selectivities and diasteroselectivies have been observed that bode well for extensions of this approach to larger and more complex guests Finally, crescent oligoamides have also been found to act as hosts for substituted guanidinium ions21 or dialkylammonium25d with high specificity and affinity

Figure 1.6 Solid state structure of L-tartaric Acid-binding M-1 helix (a) CPK and (b) stick

representations of the M-1 helix (c) Top view of the central part of the M-1 helix, showing tartaric acid

H-bonded to N2-pyr-pyz-pyr-N2

Therefore, oligoamides with helical conformation are fascinating considering their nonplanar structures Such molecules should be inherently chiral, resulting in amazing optical and electronic properties In addition, supramolecular helices could be formed

by the columnar stacks caused by π-π interaction However, until now, the consistent columnar packing of these shape-persistent crescent and helical oligoamides has rarely been studied

1.2.3 Circular Aromatic Oligoamides

As mentioned in 1.2.2, one of the most important applications of hollow cavities contained within the aromatic oligoamides is their potential to bind corresponding guest molecules Based on this intention, circular oligoamides, as a kind of macrocycles, were designed Shape-persistent circular oligoamides are structures with rigid, noncollapsible backbones and lumens of various sizes These structures are very interesting because of their unique properties that differ from their linear analogues However, examples of these molecules are rare, mainly attributed to the difficulty in their preparation and lack of the suitable building blocks Some of reported examples are elaborated below

Gong’s group pioneered the work of H-bonding enforced macrocycles by synthesizing a new class of shape-persistent, cyclic hexa(armides) from the one-step macrocyclization involving monomeric diamine and diacid chloride.23 Macrocycles 1

contain a large (8Å across), noncollapsible hydrophilic cavity defined by six

introverted amide oxygen atoms The face-to-face stacking of 1 may align the

macrocycles into nanotubes containing a large channel (or nanopore) (Figure 1.7) As expected, this class of macrocycle was demonstrated to form transmembrane channel with very large conductance and a model of the transport pore was prompted as

Figure 1.7b.24

Figure 1.7 Circular aromatic oligoamides from Gong’s group (a) Chemical structures of shape

persistent macrocyles 1, (b) with their large aromatic surfaces, 1 assemble anisotropically into a tubular

structure that acts as a transmembrane channel or pore in the hydrophobic environment of a lipid bilayer

Li’s group also demonsrated that hydrogen bonding-induced aryl amide foldamer could function as new synthetic receptors for binding neutral and ionic species or as preorganized scaffolds for assembling well-defined architectures.25 Furthermore, they prepared a new rigidified macrocycle that complex fullerene or coronene in chloroform viah intromolecular π-stacking interactions, as in Figure 1.8.25i

Figure 1.8 Stacking interaction between C60 and macrocycle from Li’s group

In addition to the application in molecular recognition and ion transportation, macrocycle based on aromatic oligoamides was also found to bind to DNA G-quadruplex through intermolecular hydrogen bonding and/or л-л stacking