Size-Specific Ligands for RNA Hairpin Loops

RNA binding properties of novel gene silencing pyrrole-imidazole polyamides

Pyrrole-imidazole (PI) polyamides are a novel group of gene-silencing compounds, which bind to a minor groove of double stranded (ds)DNA in a sequence-specific manner. To explore the RNA binding properties of PI polyamides targeting rat transforming growth factor-β1 (TGF-β1 Polyamide) and influenza A virus (PA polyamide), we designed dsRNAs with an identical sequence to the target DNA and analyzed RNA binding properties of the polyamide. Biacore assay showed fast binding of TGF-β1 Polyamide to the dsRNA, whereas mismatch polyamide did not bind to the dsRNA. Dissociation equilibrium constant (KD) value was 6.7×10(-7) of the target dsRNA. These results indicate that PI polyamide could bind to RNA with a 2 log lower binding affinity than its DNA-binding affinity. We designed a PI polyamide targeting the panhandle stem region of influenza A virus. KD value of the PI polyamide to dsRNA targeting influenza A virus was 4.6×10(-7). Gel-shift assay showed that TGF-β1 and PA polyamides bound to the appropriate dsDNA, whereas these PI polyamides did not show obvious gel-shift with the appropriate dsRNA. Structural modeling suggests that PI polyamide binds to the appropriate B-form dsDNA in the minor groove, whereas it does not fit in the minor groove to dsRNA. Thus PI polyamides have a lower binding affinity with target dsRNA than they do with dsDNA. The distinct binding properties of PI polyamides to dsRNA and dsDNA may be associated with differences of secondary structure and chemical binding properties between target RNA and DNA.

Preparation, preliminary screening of new types of steroid conjugates and their activities on steroid receptors

There were synthesized new types of ribbon type steroidal dimers derived from three types of steroidal skeletons (cholic acid, etienic acid, estrone) using Cu(I) catalyzed 1, 3-dipolar cycloaddition reaction. Steroid parts of the molecular "ribbons" are linked by heterocyclic moiety, namely by 2,6-bis((1H-1,2,3-triazol-1-yl)-methyl)pyridine. Compounds synthesized possess different cytotoxic and hormone receptor modulating activities.

Cross-linked DNA: site-selective "click" ligation in duplexes with bis-azides and stability changes caused by internal cross-links

Heterodimeric interstrand cross-linked DNA was constructed by the "bis-click" reaction carried out on preformed oligonucleotide duplexes with the bis-azide 1. For this, alkynylated 8-aza-7-deazapurine or corresponding 5-substituted pyrimidine nucleosides were synthesized. Cross-linking resulted in chemoselective formation of heterodimeric duplexes while homodimers were suppressed. For product identification, heterodimeric DNA was prepared by the "stepwise click" reaction, while noncomplementary homodimers were accessible by "bis-click" chemistry, unequivocally. Studies on duplex melting of complementary cross-linked duplexes (heterodimers) revealed significantly increased Tm values compared to the non-cross-linked congeners. The stability of this cross-linked DNA depends on the linker length and the site of modification. Cross-linked homodimers hybridized with single-stranded complementary oligonucleotides show much lower stability.

Identification of small molecule inhibitors of the HIV-1 nucleocapsid-stem-loop 3 RNA complex

Stem-loop 3 RNA (SL3) in ψ-RNA is a highly conserved motif in different strains of HIV-1 and serves as a principle determinant for viral packaging. Viral encapsulation is critical for viral replication, and disruption of the nucleocapsid-ψ-RNA complex interferes with viral replication. We have used SL3 RNA as a target for identification of small molecule inhibitors of the interactions of nucleocapsid protein (NCp7) and ψ-RNA. We report the use of computational and high-throughput screening approaches to identify 16 compounds that bind SL3 RNA with micromolar affinities. Among the identified ligands, two molecules, compounds 7 and 17, bind with higher affinity to SL3 RNA than to double- and single-stranded RNAs. Four of the 16 SL3 RNA ligands inhibit interactions between SL3 RNA and NCp7 with micromolar inhibition constants. In general, the identified SL3 ligands have simple molecular structures and low molecular weights and are, therefore, possible lead compounds for the development of ligands that target the elements of ψ-RNA of HIV-1 with high affinity and specificity.

Synthesis of phidianidines A and B

Reaction of a substituted indole-3-acetyl chloride with N-5-azidopentyl-N'-hydroxyguanidine generated a substituted 3-(5-azidopentylamino)-5-((indol-3-yl)methyl)-1,2,4-oxadiazole. Reduction of the azide with zinc and ammonium formate afforded the amine, which was elaborated to the guanidine, completing short and efficient syntheses of the cytotoxic natural products phidianidines A and B in 19% overall yield by a convergent route that will make analogues readily available for biological evaluation. Initial screening in the NCI 60 cell line at 10(-5) M indicated that the bromine on the indole is necessary for activity and that the amine precursor to phidianidine A is more potent than phidianidine A.

Cross-linked DNA: propargylated ribonucleosides as "click" ligation sites for bifunctional azides

2'-O or 3'-O-propargylated adenosines and ribothymidines were used as click targets for cross-linking of oligonucleotides with aliphatic and aromatic azides. The cross-link generates a sugar modification at the 2'-O-ligation site. Inexpensive ribonucleosides were used as starting materials. Cross-linking of oligonucleotides was performed at internal or terminal positions. Hybridization of homodimers with two complementary single strands resulted in stable ligated DNA duplexes.

Construction and assembly of branched Y-shaped DNA: "click" chemistry performed on dendronized 8-aza-7-deazaguanine oligonucleotides

Branched DNA was synthesized from tripropargylated oligonucleotides by the Huisgen-Meldal-Sharpless cycloaddition using "stepwise and double click" chemistry. Dendronized oligonucleotides decorated with 7-tripropargylamine side chains carrying two terminal triple bonds were further functionalized with bis-azides to give derivatives with two terminal azido groups. Then, the branched side chains with two azido groups or two triple bonds were combined with DNA-fragments providing the corresponding clickable function. Both concepts afforded branched (Y-shaped) three-armed DNA. Annealing of branched DNA with complementary oligonucleotides yielded supramolecular assemblies. The concept of "stepwise and double click" chemistry combined with selective hybridization represents a flexible tool to generate DNA nanostructures useful for various purposes in DNA diagnostics, delivery, and material science applications.

Antimicrobial studies of unsymmetrical bis-1,2,3-triazoles

Aryl azides were treated with allenylmagnesium bromide to generate 1,5-disubstituted butynyl 1,2,3-triazoles in a domino fashion, which upon Cu(I) catalyzed 1,3-dipolar cycloaddition with aryl azides afforded novel bis-1,2,3-triazoles in quantitative yields. The final products were analyzed for their antimicrobial activities against a panel of bacterial and fungal strains which revealed the products to be potent antimicrobials.

Development of a bivalent dopamine D₂ receptor agonist

Bivalent D₂ agonists may function as useful molecular probes for the discovery of novel neurological therapeutics. On the basis of our recently developed bivalent dopamine D₂ receptor antagonists of type 1, the bivalent agonist 2 was synthesized when a spacer built from 22 atoms was employed. Compared to the monovalent control compound 6 containing a capped spacer, the bis-aminoindane derivative 2 revealed substantial steepening of the competition curve, indicating a bivalent binding mode. Dimer-specific Hill slopes were not a result of varying functional properties because both the dopaminergic 2 and the monovalent control agent 6 proved to be D₂ agonists substantially inhibiting cAMP accumulation and inducing D₂ receptor internalization. Investigation of the heterobivalent ligands 8 and 9, containing an agonist and a phenylpiperazine-based antagonist pharmacophore, revealed moderate steepening of the displacement curves and antagonist to very weak partial agonist properties.

A convenient route to diversely substituted icosahedral closomer nanoscaffolds

The design and synthesis of icosahedral polyhedral borane closomer motifs based upon carbonate and carbamate anchoring groups for biomedical applications are described. Dodecacarbamate closomers containing easily accessible groups of interest at their linker termini were synthesized via activation of the B-OH vertices as aryl carbonates and their subsequent reaction with primary amines. Novel dodecacarbonate closomers were successfully synthesized for the first time by reacting [closo-B(12)(OH)(12)](2-) with an excess of respective aryl chloroformates, utilizing relatively short reaction times, mild conditions and simple purification strategies, all of which had previously presented difficulties in closomer chemistry. This methodology for the 12-fold degenerate synthesis of carbonate and carbamate closomers will greatly facilitate further exploration of closomers as monodisperse nanomolecular delivery platforms.

Iron(III) chloride as an efficient catalyst for stereoselective synthesis of glycosyl azides and a cocatalyst with Cu(0) for the subsequent click chemistry

A highly efficient and mild method for azido glycosylation of glycosyl β-peracetates to 1,2-trans glycosyl azides was developed by using inexpensive FeCl(3) as the catalyst. In addition, we demonstrated, for the first time, that FeCl(3) in combination with copper powder can promote 1,3-dipolar cycloaddition (click chemistry) of azido glycosides with terminal alkynes. Good to excellent yields were obtained with exclusive formation of a single isomer in both glycosyl azidation and subsequent cycloaddition processes.

Stepwise "click" chemistry for the template independent construction of a broad variety of cross-linked oligonucleotides: influence of linker length, position, and linking number on DNA duplex stability

Cross-linked DNA was constructed by a "stepwise click" reaction using a bis-azide. The reaction is performed in the absence of a template, and a monofunctionalized oligonucleotide bearing an azido-function is formed as intermediate. For this, an excess of the bis-azide has to be used compared to the alkynylated oligonucleotide. The cross-linking can be carried out with any alkynylated DNA having a terminal triple bond at any position of the oligonucleotide, independent of chain length or sequence with identical or nonidentical chains. Short and long linkers with terminal triple bonds were introduced in the 7-position of 8-aza-7-deaza-2'-deoxyguanosine (1 or 2), and the outcome of the "stepwise" click and the "bis-click" reaction was compared. The cross-linked DNAs form cross-linked duplexes when hybridized with single-stranded complementary oligonucleotides. The stability of these cross-linked duplexes is as high as respective individual duplexes when they were ligated at terminal positions with linkers of sufficient length. The stability decreases when the linkers are incorporated at central positions. The highest duplex stability was reached when two complementary cross-linked oligonucleotides were hybridized.

Bivalent dopamine D2 receptor ligands: synthesis and binding properties

Dopamine D(2) receptor homodimers might be of particular importance in the pathophysiology of schizophrenia and, thus, serve as promising target proteins for the discovery of atypical antipsychotics. A highly attractive approach to investigate and control GPCR dimerization may be provided by the exploration and characterization of bivalent ligands, which can act as molecular probes simultaneously binding two adjacent binding sites of a dimer. The synthesis of bivalent dopamine D(2) receptor ligands of type 1 is presented, incorporating the privileged structure of 1,4-disubstituted aromatic piperidines/piperazines (1,4-DAPs) and triazolyl-linked spacer elements. Radioligand binding studies provided diagnostic insights when Hill slopes close to two for bivalent ligands with particular spacer lengths and a comparative analysis with respective monovalent control ligands and unsymmetrically substituted analogues indicated a bivalent binding mode with a simultaneous occupancy of two neighboring binding sites.

Nanometer-sized reactor--a porphyrin-based model system for anion species

Although many cagelike molecules can create a catalytic environment for promoting chemical reactions, the construction of receptors that can host anionic species and sensitize their reaction is novel. Here we report the photochemically induced dimerization of the anion radicals of TCNQ (7,7,8,8-tetracyano-para-quinodimethane) in organic solvent under aerobic conditions when they are encapsulated inside a cationic photoactive receptor. There is clear evidence for a rate increase of over two orders of magnitude, photosensitization of the host, and demonstrated turnover of the catalyst.

Cross-linked DNA generated by "bis-click" reactions with bis-functional azides: site independent ligation of oligonucleotides via nucleobase alkynyl chains

Template-free cross-linking of single-stranded DNA bearing octadiynyl side chains at the 7-position of 8-aza-7-deazapurine moieties with bisfunctional azides is reported employing a Cu(I)-catalyzed azide-alkyne "bis-click" reaction. Bis-adducts were formed when the bis-azide:oligonucleotide ratio was 1:1; monofunctionalization occurred when the ratio was 15:1. Four-stranded DNA consisting of two cross-linked duplexes was obtained after hydridization. Cross-linked duplexes are as stable as individual duplexes when ligation was introduced at terminal positions; ligation at a central position led to a slight duplex destabilization.

Small molecule ligands for bulged RNA secondary structures

A class of wedge-shaped small molecules has been designed, synthesized, and shown to bind bulged RNA secondary structures. These minimally cationic ligands exhibit good affinity and selectivity for certain RNA bulges as demonstrated in a fluorescent intercalator displacement assay.

Strategies for the design of RNA-binding small molecules

Bacterial ribosomal RNA is the target of clinically important antibiotics, while biologically important RNAs in viral and eukaryotic genomes present a range of potential drug targets. The physicochemical properties of RNA present difficulties for medicinal chemistry, particularly when oral availability is needed. Peptidic ligands and analysis of their RNA-binding properties are providing insight into RNA recognition. RNA-binding ligands include far more chemical classes than just aminoglycosides. Chemical functionalities from known RNA-binding small molecules are being exploited in fragment- and ligand-based projects. While targeting of RNA for drug design is very challenging, continuing advances in our understanding of the principles of RNA–ligand interaction will be necessary to realize the full potential of this class of targets.

Rational and modular design of potent ligands targeting the RNA that causes myotonic dystrophy 2

Most ligands targeting RNA are identified through screening a therapeutic target for binding members of a ligand library. A potential alternative way to construct RNA binders is through rational design using information about the RNA motifs ligands prefer to bind. Herein, we describe such an approach to design modularly assembled ligands targeting the RNA that causes myotonic dystrophy type 2 (DM2), a currently untreatable disease. A previous study identified that 6'-N-5-hexynoate kanamycin A (1) prefers to bind 2x2 nucleotide, pyrimidine-rich RNA internal loops. Multiple copies of such loops are found in the RNA hairpin that causes DM2. The 1 ligand was then modularly displayed on a peptoid scaffold with varied number and spacing to target several internal loops simultaneously. Modularly assembled ligands were tested for binding to a series of RNAs and for inhibiting the formation of the toxic DM2 RNA-muscleblind protein (MBNL-1) interaction. The most potent ligand displays three 1 modules, each separated by four spacing submonomers, and inhibits the formation of the RNA-protein complex with an IC(50) of 25 nM. This ligand has higher affinity and is more specific for binding the DM2 RNA than MBNL-1. It binds the DM2 RNA at least 30 times more tightly than related RNAs and 15-fold more tightly than MBNL-1. A related control peptoid displaying 6'-N-5-hexynoate neamine (2) is >100-fold less potent at inhibiting the RNA-protein interaction and binds to DM2 RNA >125-fold more weakly. Uptake studies into a mouse myoblast cell line also show that the most potent ligand is cell permeable.

Small molecule microarrays of RNA-focused peptoids help identify inhibitors of a pathogenic group I intron

Peptoids that inhibit the group I intron RNA from Candida albicans, an opportunistic pathogen that kills immunocompromised hosts, have been identified using microarrays. The arrayed peptoid library was constructed using submonomers with moieties similar to ones found in small molecules known to bind RNA. Library members that passed quality control analysis were spotted onto a microarray and screened for binding to the C. albicans group I intron ribozyme. Each ligand binder identified from microarray-based screening inhibited self-splicing in the presence of 1 mM nucleotide concentration of bulk yeast tRNA with IC(50)'s between 150 and 2200 microM. The binding signals and the corresponding IC(50)'s were used to identify features in the peptoids that predispose them for RNA binding. After statistical analysis of the peptoids' structures that bind, a second generation of inhibitors was constructed using these important features; all second generation inhibitors have improved potencies with IC(50)'s of <100 microM. The most potent inhibitor is composed of one phenylguanidine and three tryptamine submonomers and has an IC(50) of 31 microM. This compound is 6-fold more potent than pentamidine, a clinically used drug that inhibits self-splicing. These results show that (i) modulators of RNA function can be identified by designing RNA-focused chemical libraries and screening them via microarray; (ii) statistical analysis of ligand binders can identify features in leads that predispose them for binding to their targets; and (iii) features can then be programmed into second generation inhibitors to design ligands with improved potencies.

Synthesis and biological evaluation of multivalent carbohydrate ligands obtained by click assembly of pseudo-rotaxanes

Multivalent carbohydrate ligands have been prepared by assembling alpha-cyclodextrin-based pseudo-rotaxanes through "click chemistry". The inclusion complex formed by a lactosyl-alpha-CD conjugate and a decane axle carrying a lactosyl stopper at one extremity and an azido group at the other end was dimerized by bis-propargyl spacers of different lengths to provide oligorotaxanes having adjustable threading ratios. For the first time, saccharidic ligands have been introduced on rotaxanes both as a biological recognition element and as a capping group. The supramolecular species have been isolated and characterized by mass spectrometry as well as by 1D and DOSY NMR experiments. Their ability to inhibit the binding of Arachis hypogaea agglutinin to asialofetuin, assayed by enzyme linked lectin assays (ELLA), was shown to be valency-dependent.

Inhibition of dicing of guanosine-rich shRNAs by quadruplex-binding compounds

RNA interference is triggered by small hairpin precursors that are processed by the endonuclease dicer to yield active species such as siRNAs and miRNAs. To regulate the RNAi-mediated suppression of gene expression, we imagined a strategy that relies on the sequence-specific inhibition of shRNA precursor processing by immediate RNA-small molecule interactions. Here, we present a first step in this direction by augmenting shRNAs with guanosine-rich sequences that are prone to fold into four-stranded structures. The addition of small molecules that selectively bind to such quadruplex sequences should allow for the specific inhibition of dicing of shRNAs that contain suitable G-rich elements. In an attempt to find compounds that protect against dicer processing, we have examined the effects of quadruplex-binding compounds on the dicer processing of shRNAs containing G-quadruplexes. Although a variety of small molecules that are known to bind to quadruplexes inhibited in vitro dicing of shRNAs, only two substance classes, namely certain porphyrazines and bisquinolinium compounds, showed selective inhibition of G-rich shRNAs compared to control sequences lacking guanine-rich elements. The G-rich shRNAs displayed a potent knockdown of gene expression in mammalian cell culture, but the effect was not influenced by addition of the respective quadruplex-binding compounds.