Discovery of novel triple helical DNA intercalators by an integrated virtual and actual screening platform

Virtual Screening is an increasingly attractive way to discover new small molecules with potential medicinal value. We introduce a novel strategy that integrates use of the molecular docking software Surflex with experimental validation by the method of competition dialysis. This integrated approach was used to identify ligands that selectively bind to the triplex DNA poly(dA)-[poly(dT)]2. A library containing ∼2 million ligands was virtually screened to identify compounds with chemical and structural similarity to a known triplex intercalator, the napthylquinoline MHQ-12. Further molecular docking studies using compounds with high structural similarity resulted in two compounds that were then demonstrated by competition dialysis to have a superior affinity and selectivity for the triplex nucleic acid than MHQ-12. One of the compounds has a different chemical backbone than MHQ-12, which demonstrates the ability of this strategy to ‘scaffold hop’ and to identify small molecules with novel binding properties. Biophysical characterization of these compounds by circular dichroism and thermal denaturation studies confirmed their binding mode and selectivity. These studies provide a proof-of-principle for our integrated screening strategy, and suggest that this platform may be extended to discover new compounds that target therapeutically relevant nucleic acid morphologies

Biologically Relevant Heterocyclic Compounds

Heterocyclic chemistry is a rapidly growing branch of organic chemistry. [...

Noncovalent labeling of biomolecules with red and near-infrared dyes”, Molecules 2004

Abstract: Biopolymers such as proteins and nucleic acids can be labeled with a fluorescent marker to allow for their detection. Covalent labeling is achieved by the reaction of an appropriately functionalized dye marker with a reactive group on a biomolecule. The recent trend, however, is the use of noncovalent labeling that results from strong hydrophobic and/or ionic interactions between the marker and biomolecule of interest. The main advantage of noncovalent labeling is that it affects the functional activity of the biomolecule to a lesser extent. The applications of luminescent cyanine and squarylium dyes are reviewed

Effect of a Triplex-Binding Ligand on Parallel and Antiparallel DNA Triple Helices Using Short Unmodified and Acridine-Linked Oligonucleotides

We have used DNase I footprinting to investigate the effect of a triplex-binding ligand on the formation of intermolecular DNA triple helices at target sites that have been cloned into longer DNA fragments. In the presence of a triplex-binding ligand (N-[2-(dimethylamino)ethyl]-2-(2-naphthyl)quinolin-4-ylamine), the concentrations of T5C5 and C5T5 required to generate DNase I footprints at the target sites A6G6·C6T6 and G6A6·T6C6, respectively, are reduced by at least 100-fold. Complexes with the acridinelinked oligonucleotides Acr-T5C5 and Acr-C5T5 are stabilized to a much lesser extent and produce footprints at concentrations similar to those of the unmodified oligonucleotides in the presence of the ligand. The stabilizing effects of acridine modification or the addition of a triplex-binding ligand are not additive. The position and length of the footprints produced by Acr-T5C5 and T5C5 at the target sequence A6G6·C6T6 are unaffected by the ligand. In contrast, footprints at the target site G6A6·T6C6 appear 3–4 bases shorter in the presence of the ligand, when viewed from the pyrimidine strand, and 1–2 bases longer on the purine strand. These results are explained by suggesting that the compound binds at T·AT triplets and prevents the transmission of any DNA structural changes into the flanking duplex. The compound has a smaller stabilizing effect on short antiparallel triplexes consisting of G·GC and T·AT triplets. Binding of Acr-G5T5 to A6G6·C6T6 is enhanced slightly by the compound, which increases the apparent footprinting site, probably by preventing fraying at the 3′-end of the third strand. The compound does not promote the binding of G5T5 to A6G6·C6T6, or that of Acr-T5G5 and T5G5 to G6A6·T6C6.</p

The search for structure-specific nucleic acid-interactive drugs: effects of compound structure on RNA versus DNA interaction strength. Biochemistry

ABSTRACT: The R N A genomes of a number of pathogenic R N A viruses, such as HIV-1, have extensive folded conformations with imperfect A-form duplexes that are essential for virus function and could serve as targets for structure-specific antiviral drugs. As an initial step in the discovery of such drugs, the interactions with R N A of a wide variety of compounds, which are known to bind to DNA in the minor groove, by classical or by threading intercalation, have been evaluated by thermal melting and viscometric analyses. The corresponding sequence R N A and DNA polymers, poly(A)-poly(U) and poly(dA)-poly(dT), were used as test systems for analysis of R N A binding strength and selectivity. Compounds that bind exclusively in the minor groove in AT sequences of DNA (e.g., netropsin, distamycin, and a zinc porphyrin derivative) do not have significant interactions with RNA. Compounds that bind in the minor groove in AT sequences of DNA but have other favorable interactions in G C sequences of D N A (e.q., Hoechst 33258, DAPI, and other aromatic diamidines) can have very strong R N A interactions. A group of classical intercalators and a group of intercalators with unfused aromatic ring systems contain compounds that intercalate and have strong interactions with RNA. At this time, no clear pattern of molecular structure that favors R N A over DNA interactions for intercalators has emerged. Compounds that bind to DNA by threading intercalation generally bind to R N A by the same mode, but none of the threading intercalators tested to date have shown selective interactions with RNA. RNA viruses are responsible for a number of serious human diseases, and attempts to design drugs against these viruses are proceeding along several lines Our experimental approach to the design of structurespecific RNA-interactive antiviral agents involves three steps: (i) discovery of compounds that bind strongly and specifically to RNA duplexes; (ii) modification of the RNAinteractive compounds of (i) to improve their ability to interact with RNA duplexes in general and with specific RNA conformations in particular; and (iii) continued development of the agents such that they will have improved specificity for RNA conformational units, such as those that exist in TAR This work was supported by NIH Grant AI-27196. * Author to whom correspondence should be addressed. 0006-2960/93/0432-4098%04.0Q/Q or RRE. As part of this process, we have investigated the interaction with corresponding RNA and DNA duplexes of a number of very different compounds that are known to have very different interactions with DNA. The goals are to define a library of molecular structures and substituents that provide specific interactions in RNA complexes and to begin to understand how RNA conformations are selectively recognized by small molecules. Our aim at this stage is to increase the fundamental data base regarding RNA interactions. Thermal melting (Tm) methods have been used for the comparisons (cf. Compound Groups. For comparison purposes, the compounds have been grouped according to their known DNA interaction modes. All compounds are cations, and their structures, arranged by group, are shown i