Small-Molecule-Based Self-Assembled Ligands for G-Quadruplex DNA Surface Recognition.

Most drugs are small molecules because of their attractive pharmacokinetics, manageable development and manufacturing, and effective binding into the concave crevices of bio-macromolecules. Despite these features, they often fall short when it comes to effectively recognizing the surfaces of bio-macromolecules. One way to overcome the challenge of biomolecular surface recognition is to develop small molecules that become self-assembled ligands (SALs) prior to binding. Herein, we report SALs made from 8-aryl-2'-deoxyguanosine derivatives forming precise hydrophilic supramolecular G-quadruplexes (SGQs) with excellent size, shape, and charge complementarity to G-quadruplex DNA (QDNA). We show that only those compounds forming SGQs act as SALs, which in turn differentially stabilize QDNAs from selected oncogene promoters and the human telomeric regions. Fluorescence resonance energy-transfer melting assays are consistent with spectroscopic, calorimetric, and light scattering studies, showing the formation of a "sandwichlike" complex QDNA·SGQ·QDNA. These results open the door for the advent of SALs that recognize QDNAs and potentially the surfaces of other bio-macromolecules such as proteins.

Structural Studies of Supramolecular G-Quadruplexes Formed from 8-Aryl-2'-deoxyguanosine Derivatives.

Self-assembly is a powerful tool for the construction of complex nanostructures. Despite advances in the field, the development of precise self-assembled structures remains a challenge. We have shown that, in the presence of suitably sized cations like K(+), 8-aryl-2'-deoxyguanosine (8ArG) derivatives self-assemble into sets of coaxially stacked planar tetramers, which we term supramolecular G-quadruplexes (SGQs). Previously, we reported that, when the 8-aryl group is a phenyl ring with a meta-carbonyl group, the resulting supramolecule is a hexadecamer, which is remarkably robust as illustrated by its isostructural assembly in both organic and aqueous environments. We report here a detailed three-dimensional structure of the SGQs formed by lipophilic, and hydrophilic, 8ArG derivatives with either 8-(meta-acetylphenyl), 8-(para-acetylphenyl), or 8-(meta-ethoxycarbonylphenyl) groups. The chirality and close contacts between the subunits impose different levels of steric and electrostatic constraints on opposite sides of the tetrads, which determine their preferred relative orientation. The balance between attractive noncovalent interactions juxtaposed with repulsive steric and electrostatic interactions explains the high cooperativity, fidelity, and stability of these SGQs. These structural studies, together with titration experiments and molecular dynamics simulations, provide insight into the mechanism of formation of these SGQs.

Development of rationally designed DNA N6 adenine methyltransferase inhibitors.

A series of bisubstrate inhibitors for DNA N6 adenine methyltransferase (Dam) have been synthesized by linking an amine analogue of S-adenosylmethionine to an aryl moiety designed to probe the binding pocket of the DNA adenine base. An initial structure-activity relationship study has identified substituents that increase inhibitor potency to the ∼10 µM range and improve selectivity against the human cytosine methyltransferase Dnmt1.

Walking a supramolecular tightrope: a self-assembled dodecamer from an 8-aryl-2'-deoxyguanosine derivative.

Controlling the properties of self-assembled supramolecules via intrinsic parameters (i.e., structural information in the subunits) enables the reliable construction of assemblies of well-defined size and composition. Here we show that an optimum balance between repulsive (e.g., steric) and attractive (e.g., pi-pi, dipole-dipole) noncovalent interactions between subunits of a lipophilic 8-(3-pyridyl)-2'-deoxyguanosine derivative enables the high fidelity formation of a stable and discrete self-assembled dodecamer. In contrast, the isosteric 8-phenyl-2'-deoxyguanosine derivative assembles into an octamer because it cannot engage in additional dipole-dipole interactions. Adding dodecamers to a supramolecular construction toolbox, already containing octamers and hexadecamers made from other 8-aryl-2'-deoxyguanosine derivatives, should enable the preparation of a wide variety of self-assembled nanostructures where the size and the number of functional elements can be precisely fine-tuned for specific applications.

Isostructural self-assembly of 2'-deoxyguanosine derivatives in aqueous and organic media.

We report the self-assembly of a hydrophilic 8-(m-acetylphenyl)-2'-deoxyguanosine (mAG) derivative into a discrete and thermally stable hexadecameric supramolecule in aqueous media. We demonstrate that this hexadecamer is isostructural to the one formed by a related lipophilic derivative in organic media. This mAG moiety represents a rare example of a small-molecule recognition motif that is capable of assembling isostructurally and with high fidelity in both organic and aqueous media.

Synthesis of 8-Heteroaryl-2'-deoxyguanosine Derivatives.

We describe the synthesis of 8-heteroaromatic-2'-deoxyguanosine analogues using Suzuki-Miyaura or Stille conditions. Unprotected and protected 8-bromo-2'-deoxyguanosine was coupled with commercially available heteroarylboronic acids or the trialkyltin derivatives of 2-pyridylbromides either with or without microwave irradiation in good yields.

The impact of 8-aryl-and 8-heteroaryl-2'-deoxyguanosine derivatives on G-quadruplex formation.

Guanine and G-rich oligonucleotides are known to self-assemble in the presence of a variety of cations to form higher ordered structures known as Gquadruplexes. We have synthesized a library of 8-aryl/heteroaryl-2'-deoxyguanosine derivatives (8ArGs) that are also able to self-assemble into quadruplex structures. We demonstrate that the properties of such quadruplexes can be modulated by the nature of the groups attached to the guanine base. These supramolecules are potentially useful in the development of self-assembled nanodevices.