Bifunctional small molecule-oligonucleotide hybrid as microRNA inhibitor.

miRNAs are key regulators of various biological processes. Dysregulation of miRNA is linked to many diseases. Development of miRNA inhibitor has implication in disease therapy and study of miRNA function. The biogenesis pathway of miRNA involves the processing of pre-miRNA into mature miRNA by Dicer enzyme. We previously reported a proximity enabled approach that employs bifunctional small molecules to regulate miRNA maturation through inhibiting the enzymatic activity of Dicer. By conjugating to an RNA targeting unit, an RNase inhibitor could be delivered to the cleavage site of specific pre-miRNA to deactivate the complexed Dicer enzyme. Herein, we expanded this bifunctional strategy by showing that antisense oligonucleotides (ASOs), including morpholinos and γPNAs, could be readily used as the RNA recognition unit to generate bifunctional small molecule-oligonucleotide hybrids as miRNA inhibitors. A systematic comparison revealed that the potency of these hybrids is mainly determined by the RNA binding of the targeting ASO molecules. Since the lengths of the ASO molecules used in this approach were much shorter than commonly used anti-miRNA ASOs, this may provide benefits to the specificity and cellular delivery of these hybrids. We expect that this approach could be complementary to traditional ASO and small molecule based miRNA inhibition and contribute to the study of miRNA.

Regulating miRNA-21 Biogenesis By Bifunctional Small Molecules.

We report a new strategy to regulate microRNAs (miRNAs) biogenesis by using bifunctional small molecules that consist of a pre-miRNA binding unit connected by a linker to a Dicer inhibiting unit. In this effort, fluorescence polarization-based screening was used to identify neomycin as a pre-miR-21 binding ligand. Although neomycin cannot inhibit miR-21 maturation, linking it to the RNase inhibitor 1 forms the bifunctional conjugate 7A, which inhibits the production of miR-21. We expect that this strategy will be applicable to design other molecules for miRNA regulation.

Synthesis of bifunctional molecules containing [12]aneN3 and coumarin moieties as effective DNA condensation agents and new non-viral gene vectors.

A series of bifunctional molecules with different combinations of macrocyclic polyamine [12]aneN3 and coumarin moieties, 4a/b and 5a/b, were synthesized by a two-step copper(I)-mediated alkyne­azide click reactions between 1,3,5-tris(azidomethyl)benzene and Boc-protected N-propynyl-[12]aneN3/7-propynyloxycoumarins. Agarose gel electrophoresis experiments indicated that bifunctional molecules 4b and 5b effectively induced complete plasmid DNA condensation at concentrations up to 40 µM. It was found that the structural variation had a major impact on the condensation behavior of these compounds. The electrostatic interaction involving the [12]aneN3 moiety can be compensated by the binding contribution of the coumarin units during the DNA condensation process. These two types of interaction showed different effects on the reversibility of DNA condensation. Results from studies using dynamic laser scattering, atomic force microscopy, and EB replacement assay further supported the above conclusion. Cytotoxicity assays on bifunctional compounds 4a/b and 5a/b indicated their low cytotoxicity. Results from cellular uptake and cell transfection experiments proved that bifunctional compounds 4b and 5b successfully served as non-viral gene vectors. Furthermore, methyl substituents attached to the coumarin unit (4b and 5b) greatly enhanced their DNA condensation capability and gene transfection. These bifunctional molecules, with the advantages of lower cytotoxicity, good water solubility, and potential structural modification, will have great potential for the development of new non-viral gene delivery agents.

Light control of cellular processes by using photocaged abscisic acid.

Abscisic acid (ABA) was chemically modified with a photocaging group to promote photo-induced protein dimerization. This photocontrolled chemically induced dimerization (CID) method based on caged ABA enables dose-dependent light regulation of cellular processes, including transcription, protein translocation, signal transduction, and cytoskeletal remodeling, without the need to perform extensive protein engineering. Caged ABA can be easily modified to respond to different wavelengths of light. Consequently, this strategy should be applicable to the design of light-regulated protein dimerization systems and potentially be used orthogonally with other light-controlled CID systems.

Controlling ion-sensing specificity of N-amidothioureas: from anion-selective sensors to highly Zn(2+)-selective sensors by tuning electronic effects.

N-Amidothioureas bearing nitro groups showed different sensitivities to various anions, while those with methoxy moieties exhibited the sensitive and selective fluorescence turn-on property for Zn(2+) in aqueous solution and in cells. N-Amidothioureas can therefore be adjusted from anion-selective sensors to Zn(2+)-selective sensors by varying the electronic effects of their substituents.

Syntheses of [12]aneN3-oligopeptide conjugates as effective DNA condensation agents.

With the aim to develop effective and low toxicity DNA condensation agents, a series of oligopeptide derived macrocyclic polyamine [12]aneN(3) conjugates 7a-h·3HCl have been designed and synthesized through multi-step amidation reactions. Structure-property study through gel electrophoresis proved that the conjugates containing high hydrophobic ending amino acids exhibited effective condensation ability at concentration of 150-250 µM, which was further confirmed by dynamic light scattering and atomic force microscopy experiments. EB displacement assay, ionic salt effect, and structure-property relationship in gel electrophoresis indicated that DNA condensation resulted from both the electrostatic interaction of [12]aneN(3) unit and hydrogen-bonding/hydrophobic multi-interaction of oligopeptide moiety in the conjugates with DNA. The reversible condensation process and their low cytotoxicity suggest that the new condensing agents are potential for the development of non-viral vectors.

Effective and reversible DNA condensation induced by bifunctional molecules containing macrocyclic polyamines and naphthyl moieties.

A series of bifunctional molecules containing macrocyclic polyamines [12]aneN(3) and naphthyl moieties 1-3(a, b) have been designed and synthesized through efficient N-alkylation and copper-mediated alkyne-azide click reactions. Experiments on gel electrophoresis, dynamic light scattering and atomic force microscopy confirmed that 2b and 3b with two [12]aneN(3) units efficiently induced the DNA condensation at the concentration of 120 µM in less than 5 min. The condensation mechanism was studied by EB displacement fluorescence spectra, viscosity titration, and ionic strength effects. The condensation process was found to be reversible, and the presence of both naphthyl and [12]aneN(3) units in the molecules was proved to be necessary for the effective DNA condensation inductions. Cytotoxicity assay showed that the presence of triazole moieties can result in lower toxicity.

Synthesis of mono- and di-[12]aneN3 ligands and study on the catalytic cleavage of RNA model 2-hydroxypropyl-p-nitrophenyl phosphate with their metal complexes.

A series of mono- and di-[12]aneN(3) ligands 1-6, which contain different substituents on the coordinating backbone, different linkers between two [12]aneN(3) units and different N-methylation on the [12]aneN(3) units, have been synthesized and fully characterized. The catalytic activities of their metal complexes on the cleavage of RNA model phosphate 2-hydroxypropyl-p-nitrophenyl phosphate (HPNPP) varied with the structures of the ligands and metal ions. Click reactions afforded an efficient method to prepare a series of [12]aneN(3) ligands, however, the incorporation of triazole moieties reduced the catalytic activities due to their coordination with metal ions and the strong inhibition from the triflate counter ion. Dinuclear zinc(II) complexes containing an m-xylyl bridge showed higher catalytic activities with synergistic effects up to 700-fold. Copper(II) complexes with the ligands without triazole moieties proved to be highly reactive and showed strong cooperativity between the two copper(II) ions. In terms of k(2), dinuclear complexes Zn(2)-3b, Zn(2)-3d, Zn(2)-4b, and Cu(2)-4b afforded activities of 7.9 × 10(5), 3.9 × 10(4), 9.0 × 10(4), and 8.1 × 10(4)-fold higher than that of methoxide. The ortho arrangement of the two [12]aneN(3) units and the presence of 5- or 2-positioned substituents in the benzene ring as well as N-methylation of [12]aneN(3) units greatly reduced the catalytic activities due to the steric effects. These results clearly indicate that the structures of the linker between two [12]aneN(3) units play very important role in their catalytic synergistic effects.