The Thiophene “Sigma‐Hole” as a Concept for Preorganized, Specific Recognition of G⋅C Base Pairs in the DNA Minor Groove

Abstract

In spite of its importance in cell function, targeting DNA is under-represented in the design of small molecules. A barrier to progress in this area is the lack of a variety of modules that recognize G•C base pairs (bp) in DNA sequences. To overcome this barrier an entirely new design concept for modules that can bind to mixed GC and AT sequences of DNA is reported. Because of their successes in biological applications, minor-groove-binding heterocyclic cations were selected as the platform for design. Binding to AT sequences requires H-bond donors while recognition of the G-NH2 requires an acceptor. The concept that we report here uses preorganized N-methylbenzimidazole (N-MeBI) thiophene modules for selective binding with mixed bp DNA sequences. The interaction between the thiophene sigma-hole (positive electrostatic potential) and electron donor nitrogen of N-MeBI preorganizes the conformation for accepting an H-bond from G-NH2. The compound-DNA interactions were evaluated with a powerful array of biophysical methods and the results show that N-MeBI-thiophene monomer compounds can strongly and selectively recognize single G•C bp sequences. Replacing the thiophene with other moieties significantly reduces binding affinity and specificity, as predicted by the design concept. These results show that the use of molecular features, such as sigma-hole, can lead to new approaches for small molecules in biomolecular interactions.

Small Sequence‐Sensitive Compounds for Specific Recognition of the G⋅C Base Pair in DNA Minor Groove

“…Our goal was to prepare entirely new types of compounds without the amide group that could bind to mixed A⋅T and G⋅C bps containing sequences but would also have varied chemical and structural properties that would allow them to specifically bind to target sequences and effectively target a variety of different cell types. The initial research in the area has produced quite different compounds that are undergoing additional development to increase affinity and selectivity for the target sequence type with a single G⋅C flanked by A⋅T bps . Among them, the N‐MeBI‐thiophene containing compounds were found to be effectively modified to improve their binding affinity and specificity …”

“…Incorporating the N‐MeBI thiophene unit into a heterocyclic cation base structure, as in Figure , resulted in DB2429 which can recognize a target G⋅C bp in an AT sequence . Exploration of the importance of the N‐MeBI‐thiophene module to binding and specificity shows that both the N‐MeBI and thiophene are essential for the strong, specific interactions with the target sequence.…”

“…Replacing the thiophene or N‐MeBI with other similar structures decreased the binding affinity and specificity. Compounds with the N‐MeBI replaced by benzimidazole (BI), for example, bind much more strongly to pure AT DNA sequences than to any sequence with a G⋅C bp . For the design of strong binders in DNA minor groove, compounds should have, for example, the appropriate curvature to fit the convex shape of the minor groove …”

A modular design for minor groove binding and recognition of mixed base pair sequences of DNA

“…11 Using this approach a thiophene- N -methylbenzimidazole (thiophene- N -MeBI) compound (DB2429, Figure 1A) was designed according to the “σ-hole” preorganizing principle for macromolecular targeting. 17 This effect is based on the presence of low-lying C–S σ* orbitals on the thiophene S that possess positive electrostatic potential for interaction with electron donating atoms such as the unsubstituted N in N -MeBI. 18,19 Such rational control of the conformation of small molecules is a key concept of optimized molecular design for targeting macromolecules and can lead to significantly improved binding affinity and specificity that is independent of compound–DNA contacts.…”

“…Compounds with furan or pyridine in place of the thiophene in DB2429 bind with less affinity and selectivity in support of the role of σ-hole interactions with the thiophene. 17 …”