Ligand Design to Acquire Specificity to Intended G-Quadruplex Structures

A G-quadruplex is a nucleic acid secondary structure that is adopted by guanine-rich sequences, and is considered to be relevant in various pharmacological and biological contexts. G-Quadruplexes have also attracted great attention in the field of DNA nanotechnology because of their extremely high thermal stability and the availability of many defined structures. To date, a large repertory of DNA/RNA G-quadruplex-interactive ligands has been developed by numerous laboratories. Several relevant reviews have also been published that have helped researchers to grasp the full scope of G-quadruplex research from its outset to the present. This review focuses on the G-quadruplex ligands that allow targeting of specific G-quadruplexes. Moreover, unique ligands, successful methodologies, and future perspectives in relation to specific G-quadruplex recognition are also addressed.     

Optimizing Charge Switching in Membrane Lytic Peptides for Endosomal Release of Biomacromolecules

Endocytic pathways are practical routes for the intracellular delivery of biomacromolecules. Along with this, effective strategies for endosomal cargo release into the cytosol are desired to achieve successful delivery. Focusing on compositional differences between the cell and endosomal membranes and the pH decrease within endosomes, we designed the lipid-sensitive and pH-responsive endosome-lytic peptide HAad. This peptide contains aminoadipic acid (Aad) residues, which serve as a safety catch for preferential permeabilization of endosomal membranes over cell membranes, and His-to-Ala substitutions enhance the endosomolytic activity. The ability of HAad to destabilize endosomal membranes was supported by model studies using large unilamellar vesicles (LUVs) and by increased intracellular delivery of biomacromolecules (including antibodies) into live cells. Cerebral ventricle injection of Cre recombinase with HAad led to Cre/loxP recombination in a mouse model, thus demonstrating potential applicability of HAad in vivo.     

Synthesis,Structures, and Properties of Highly Strained Cyclophenylene–Ethynylenes with Axial and Helical Chirality

Single and double cyclophenylene–ethynylenes (CPEs) with axial and helical chirality have been synthesized by the Sonogashira cross-coupling of di- and tetraethynyl biphenyls with a U-shaped prearomatic diiodoparaphenylene followed by reductive aromatization. X-ray crystallographic analyses and DFT calculations revealed that the CPEs possess highly twisted bent structures. Bend angles on the edge of the paraphenylene units were close to the value of [5]cycloparaphenylene (CPP)—the smallest CPP to date. The double and single CPEs possessed stable chirality despite flexible biphenyl structures because of the high strain in the diethynyl–paraphenylene moiety. In both the single and double CPEs, orbital interactions along the biphenyl axis were observed by DFT calculations in LUMO and LUMO+2 of the single CPE and LUMO+1 of the double CPE, which likely cause lowering of these orbital energies. Concerning chiroptical properties: boosting of the g_abs value was observed in the biphenyl-based double CPE, as well as the binaphthyl-based single CPE, compared to the biphenyl-based single CPE.     

Enantioselective Synthesis of Polycyclic Aromatic Hydrocarbon (PAH)-Based Planar Chiral Bent Cyclophanes by Rhodium-Catalyzed [2+2+2] Cycloaddition

The enantioselective synthesis of polycyclic aromatic hydrocarbon (PAH)-based planar chiral cyclophanes was achieved for the first time by the rhodium-catalyzed intramolecular regio- and enantioselective [2+2+2] cycloaddition of tethered diyne-benzofulvenes followed by stepwise oxidative transformations. The thus synthesized planar chiral bent cyclophanes, that possess bent p-terphenyl- and 9-fluorenone-cores, were converted to 9-fluorenol-based ones with excellent ee values of >99 % by diastereoselective 1,2-reduction. These 9-fluorenol-based cyclophanes exhibited high fluorescence quantum yields, which were significantly higher than that of an acyclic reference molecule (78–82 % vs. 48 %). The bending effect on the chiroptical property was also examined, which revealed that the anisotropy factors (g_abs values) for electronic circular dichroism (ECD) of these 9-fluorenol-based planar chiral bent cyclophanes increase as the tether length becomes shorter.     

Development of variable‐magnification X‐ray Bragg optics

A novel X‐ray Bragg optics is proposed for variable‐magnification of an X‐ray beam. This X‐ray Bragg optics is composed of two magnifiers in a crossed arrangement, and the magnification factor, M, is controlled through the azimuth angle of each magnifier. The basic properties of the X‐ray optics such as the magnification factor, image transformation matrix and intrinsic acceptance angle are described based on the dynamical theory of X‐ray diffraction. The feasibility of the variable‐magnification X‐ray Bragg optics was verified at the vertical‐wiggler beamline BL‐14B of the Photon Factory. For X‐ray Bragg magnifiers, Si(220) crystals with an asymmetric angle of 14° were used. The magnification factor was calculated to be tunable between 0.1 and 10.0 at a wavelength of 0.112 nm. At various magnification factors (M≥ 1.0), X‐ray images of a nylon mesh were observed with an air‐cooled X‐ray CCD camera. Image deformation caused by the optics could be corrected by using a 2 × 2 transformation matrix and bilinear interpolation method. Not only absorption‐contrast but also edge‐contrast due to Fresnel diffraction was observed in the magnified images.     

Development of pyrrole-imidazole polyamide for specific regulation of human aurora kinase-A and -B gene expression

Pyrrole-imidazole polyamide (PIP) is a nuclease-resistant novel compound that inhibits gene expression through binding to the minor groove of DNA. Human aurora kinase-A (AURKA) and -B (AURKB) are important regulators in mitosis during the cell cycle. In this study, two specific PIPs (PIP-A and PIP-B) targeting AURKA and AURKB promoter regions were designed and synthesized, and their biological effects were investigated by several in vitro assays. PIP-A and PIP-B significantly inhibited the promoter activities, mRNA expression, and protein levels of AURKA and AURKB, respectively, in a concentration-dependent manner. Moreover, 1:1 combination treatment with both PIPs demonstrated prominent antiproliferative synergy (CI value [ED(50)] = 0.256) to HeLa cells as a result of inducing apoptosis-mediated severe catastrophe of cell-cycle progression. The novel synthesized PIP-A and PIP-B are potent and specific gene-silencing agents for AURKA and AURKB.     

Discrimination of hairpin polyamides with an alpha-substituted-gamma-aminobutyric acid as a 5'-TG-3' reader in DNA minor groove

Pyrrole-imidazole (Py-Im) polyamides containing stereospecifically alpha-amino- or alpha-hydroxyl-substituted gamma-aminobutyric acid as a 5'-TG-3' recognition element were synthesized by machine-assisted Fmoc solid-phase synthesis. Their binding properties to predetermined DNA sequences containing a core binding site of 5'-TGCNCA-3'/3'-ACGN'GT-5' (N.N' = A.T, T.A, G.C, and C.G) were then systematically studied by surface plasmon resonance (SPR). SPR results revealed that the pairing of stereospecifically alpha-amino-/alpha-hydroxyl-substituted gamma-aminobutyric acids, (R or S)-alpha,gamma-diaminobutyric acid (gammaRN or gammaSN) and (R or S)-alpha-hydroxyl-gamma-aminobutyric acid (gammaRO or gammaSO), side-by-side with beta-alanine (beta) in such polyamides significantly influenced the DNA binding affinity and recognition specificity of hairpin polyamides in the DNA minor groove compared with beta/beta, beta/gamma, and gamma/beta pairings. More importantly, the polyamide Ac-Im-gammaSO-ImPy-gamma-ImPybetaPy-beta-Dp (beta/gammaSO) favorably binds to a hairpin DNA containing a core binding site of 5'-TGCNCA-3'/3'-ACGN'GT-5' (N.N' = A.T) with dissociation equilibrium constant (K(D)) of 1.9 x 10(-)(7) M over N.N' = T.A with K(D) = 3.7 x 10(-)(6) M, with a 19-fold specificity. By contrast, Ac-Im-gammaSN-ImPy-gamma-ImPybetaPy-beta-Dp (beta/gammaSN) binds to the above sequence with N.N' = A.T with K(D) = 8.7 x 10(-)(7) M over N.N' = T.A with K(D) = 8.4 x 10(-)(6) M, with a 9.6-fold specificity. The results also show that the stereochemistry of the alpha-substituent, as well as the alpha-substituent itself may greatly alter binding affinity and recognition selectivity of hairpin polyamides to different DNA sequences. Further, we carried out molecular modeling studies on the binding by an energy minimization method, suggesting that alpha-hydroxyl is very close to N3 of the 3'-terminal G to induce the formation of hydrogen bonding between hydroxyl and N3 in the recognition event of the polyamide Ac-Im-gammaSO-ImPy-gamma-ImPybetaPy-beta-Dp (beta/gammaSO) to 5'-TGCNCA-3'/3'-ACGN'GT-5' (N.N' = A.T). Therefore, SPR assays and molecular modeling studies collectively suggest that the (S)-alpha-hydroxyl-gamma-aminobutyric acid (gammaSO) may act as a 5'-TG-3' recognition unit.     

C-H to N substitution dramatically alters the sequence-specific DNA alkylation, cytotoxicity, and expression of human cancer cell lines

We designed and synthesized sequence-specific alkylating conjugates 1 and 2, which selectively alkylate matched sequences at nanomolar concentrations. Conjugates 1 and 2 differ only in that the C-H is substituted by an N in the second ring, which precisely recognizes and effectively alkylates DNA according to the recognition rule of Py-Im polyamides. We investigated sequence-specific DNA alkylation, cytotoxicity in 39 human cancer cell lines, and the effect on expression levels in cancer cell lines by Py-Im conjugates 1 and 2. The COMPARE analysis of the mean graphs showed that conjugates 1 and 2 did not correlate well with each other (r = 0.65) despite having a common DNA alkylating mechanism (purine N3 alkylation). Array-based gene expression analysis demonstrated that there are several oppositely regulated genes. The results suggest the intriguing possibility that DNA alkylating agents recognizing longer base-pair sequences may provide a promising approach for developing new types of antigene agents.