DNA serves as a major target for mainstream drugs used in the treatment of cancer, but current DNA-targeted drugs have significant issues due to their poor selectivity giving rise to adverse effects. Recent research on targeting DNA has focused on DNA interactive compounds with novel mechanisms of action and new cancer-related DNA molecular targets. An understanding of molecular level details of small molecule interactions with their DNA targets is critical for understanding the molecular mechanisms of action and for structure-based rational drug design. This dissertation presents two studies focused on gaining a structural understanding of DNA-targeted small molecules, one with a novel mechanism of action and the second with a cancer-specific DNA molecular target. XR5944 is potent anticancer drug and a novel mechanism of action, DNA bis-intercalation with a major groove binding. It is able to recognize and bind the estrogen response element (ERE) sequence via the major groove to inhibit estrogen receptor-α activity. This mechanism of action may be useful for overcoming drug resistance to currently available antiestrogen treatments for breast cancer, all of which target the hormone-receptor complex. We determined the nuclear magnetic resonance solution structure of the 2:1 complex of XR5944 with the naturally occurring TFF1-ERE, which exhibits important and unexpected features. In the determined structure, each bis-intercalating XR5944 molecule is strongly bound at one of its intercalating site, but weakly at the other. Our results show the sites of intercalation within a native promoter sequence appear to be context and sequence dependent. The binding of one drug molecule influences the binding site of the second. The structure underscores the fact that the DNA binding of a bis-intercalator is directional and differs from the simple addition of two single intercalation sites. Our results provide insights toward future structure-based rational drug design of DNA bis-intercalators to modulate ERα-induced transcriptional activity, as well as for designing bis-intercalators with major groove binding modes in general. Human telomeric DNA G-quadruplex secondary structures have emerged as an attractive molecular target for anticancer drugs. G-quadruplex formation in human telomeres inhibits telomerase, which plays a key role in maintaining the malignant phenotype by stabilizing telomere length and integrity. Under physiologically relevant conditions, human telomeric DNA sequences form two equilibrating G-quadruplex structures, with the hybrid-2 structure being the predominant in an extended sequence Thus, the hybrid-2 human telomeric G-quadruplex is considered to be a potential target for anticancer drugs targeting telomere biology and telomerase. We discovered that epiberberine, a naturally occurring isoquinoline alkaloid, can specifically bind the hybrid-2 telomeric G-quadruplex and induce the conversion of hybrid-1 telomeric G-quadruplex to the hybrid-2 structure. We determined the structure of the hybrid-2 G-quadruplex in complex with epiberberine by NMR in K⁺ solution. This NMR solution structure shows an unexpected, large, drug-induced conformational change in the flanking and loop regions, creating a very well-defined “induced intercalated quasi-triad pocket” with an extensive capping structure. Our result demonstrates the importance of ligand shape as well as the G-quadruplex folding topology and flanking and loop sequences in small molecule targeting the intramolecular hybrid-2 human telomeric G-quadruplex. Our result also indicates that asymmetric compounds containing a crescent-shaped moiety are more likely to bind in a specific manner to an intramolecular G-quadruplex.

An increasing interest in non-canonical nucleic acid structures has drawn the attention of the scientific community during the last few decades. One such structure, the G-quadruplex, has been the focus of an increasing number of scientists as G-quadruplexes are believed to play a role in biological processes such as telomere integrity and gene expression. Their existence in vivo is largely unproven but they have stimulated a lot of research into small molecules that interact with them. The development of a new class of such molecules is described in this thesis. A member of this family showed to be very selective in stabilising one particular G-quadruplex. The further development of another family of G-quadruplex interacting small molecules is also presented in this thesis and some of their effects in cellulo were assessed. Based on the scaffold of this family, an affinity probe was developed, which can mediate the isolation of its nucleic acid targets from human cells. This is the first example of the use of a small molecule with an affinity tag that has been used to isolate a nucleic acid target in a structure specific manner from human cells.

Hepatitis C virus (HCV) is remarkably capable of efficiently hijacking host cell pathways including lipid metabolism in the liver in order to create pro-viral environments for pathogenesis. It is becoming increasingly clear that identifying small molecule inhibitors that target host factors exploited by the virus will expand available HCV treatment options. As such, a thorough understanding of host-virus interactions is critical to the development of alternative therapeutic strategies. Hepatic lipid droplets (LDs) are recruited by HCV to play essential roles in the viral lifecycle. The intracellular location of LDs is modified upon interacting with viral structural core protein. This enables formation of platforms that support viral particle assembly. Because these interactions are non-static, capturing its dynamic processes in order to better understand viral assembly can be achieved with label-free molecular imaging enhanced with live-cell capabilities. Chemical biology approaches that includes CARS microscopy employed in a multi-modal imaging system was used to probe interactions between HCV and host LDs. By successfully tracking LD trajectories, we identified core protein’s ability to alter LD speed and control for LD directionality. Using protein expression model systems that allowed for simultaneous tracking of core protein and LDs, our data revealed that mutations in the core protein region that vary in hydrophobicity and LD binding strengths, are factors that control for differential modulation of LD kinetics. Furthermore, we measured bidirectional LD travels runs and velocities, and observed critical properties by which core protein induces LD migration towards regions of viral particle assembly. Given that many steps in the HCV lifecycle are directly linked to host lipid metabolism, it is not surprising that disrupting lipid biosynthetic pathways would negatively affect viral replication. From this outlook, we explored small molecule inhibitors that targeted several lipid metabolic pathways to study its antiviral properties. Using fluorescent probes covalently labeled to viral RNA, we captured the visualization of disrupted replication complexes upon antagonizing nuclear hormone receptors that are linked to regulating lipid homeostasis. Correspondingly, biochemistry and molecular imaging techniques were also employed to identify novel antiviral mechanisms of small molecule inhibitors that target additional HCV-dependent lipid metabolic pathways.

As one of the most promising solar cell technologies, organic solar cells have unique superiorities distinct from inorganic counterparts, such as semitransparency, flexibility and solution-processability, as well as tunable photophysical properties, which originate from the structural verstailities of organic semiconductors. A major breakthrough in OSCs was the exploration of novel non-fullerene electron acceptor (NFAs): In comparison with traditional fullerene derivative acceptors, NFA possesses several advantages, such as low synthesis cost, tunable absorption range and adjustable energetic level, which effectively provides a wide light-harvesting window with low energetic loss. In recent decades, fused-ring electron acceptors (FREAs) have obtained an irreplaceable status in the development of OSCs. However, there are still initial drawbacks to FREA-based devices including: 1: the degree of molecular packing and the corresponding impact on device performance, which has not been studied in depth; 2: the feasibility of approaches for controlling the bulk heterojunction morphology of the film, which also has not been systemic researched; 3: the presence of bulk (geminate and non-geminate) and surface recombination which significantly affects the efficiency and stability of working devices. In this thesis, I took the above three issues as my main doctoral research subjects. In the first part of the thesis, I shine light onto the strength of π-conjugated backbones in FREA molecular structures, which strongly affect the intramolecular interaction. Herein, two FREA with different conjugated framework (IDT core vs IDTT core) are synthesized and employed as electron acceptors in OSCs. A significantly enhanced power conversion efficiency of 11.2% is obtained from IDTTIC-based devices in comparison with that of IDTIC-based devices (5.6%). After considering the electron-donating part in FREA molecules, I also study the effect of the terminal unit, which has a strong relationship with the intramolecular charge transfer effect and intermolecular interactions. Solvent additives are another powerful strategy to further improve the photovoltaic efficiency. 1-chloronaphthalene (CN) was found to be useful in the PTB7-Th:IEICO-4F system, which show a PCE improvement from 9.5% to 12.8%. Furthermore, by utilizing a small molecule donor, BIT-4F-T, as a third component, an optimum PCE of 14.0% is achieved in the devices based on PTB7-Th:IEICO-4F.

In the last decade, organic photovoltaics (OPVs) have been attracting much attention for their low cost, and feasibility of mass production in large-area modules. Reported power conversion efficiencies (PCE) of organic solar cells have reached more than 10%. These promising PCEs can be realized by uncovering important principles: (1) rational molecular design, (2) matching of the material energy level, (3) favorable morphology of donor-acceptor (D/A) network, (4) higher carrier mobilities, and (5) suppression of charge recombination within the bulk heterojunction (BHJ). Though these key properties are frequently stated, the relationships between these principles remain unclear, which motivates us to fill these gaps. In the beginning, we show that changing the sequence of donor and acceptor units of the benzodithiophene-core (BDT) SM donors critically impacts molecular packing and charge transport in BHJ solar cells. Moreover, we find out that by adding small amount of the external solvent additive, the domain size of the SMFQ1 become relatively smaller, resulting in the FF enhancement of ~70% and thus pushing PCE to >6.5%. To further improve the device performance, we utilize another technique of device optimization: Solvent Vapor Annealing (SVA). Compared with solvent additive, the SVA creates a solvent-saturated environment for SMs to re-arrange and crystalize, leading to PCE of >8%, with nearly-free bimolecular recombination. When the systems are shifted from fullerene acceptors to nonfullerene acceptors, using solvent additives in indacenodithiophene-core (IDT) systems significantly reduces the domain size from >500nm to <50nm and also allows the SM donors to orderly packed, rising the PCE from <1% to 4.5%. Furthermore in a similar IDT-based system, it shows unexpectedly high VOC and low energy loss, and high PCE > 6% can be reached by employing the dimethyl disulfide (DMDS) as the SVA solvent to re-organize the morphology from excessive mixing to ordered phase-separated D/A network. Lastly, taking advantage of the distinct and complementary absorption of fullerene and nonfullerene acceptors, we show that the SM ternary system successfully realizes the high PCE of 11%, good air stability, and scalable property.

Indiana University-Purdue University Indianapolis (IUPUI) / The human aldehyde dehydrogenase (ALDH) superfamily consists of 19 isoenzymes that are critical for normal physiology as well as the removal of toxic aldehydes. Members of the ALDH1/2 family have vital roles in cell signaling during early development, ethanol metabolism, and the removal of aldehydes derived from oxidative stress. We sought to develop selective compounds toward ALDH2 to help determine its individual contribution to biological function, as many of the ALDH1/2 family possess overlapping substrate preferences. A high-throughput screen of over 100,000 compounds uncovered a class of aromatic lactones which inhibit the ALDH1/2 enzyme family. The lactones were then characterized using a combination of enzyme kinetics, X-ray crystallography, and cell culture experiments. We found that many of the lactones are over ten times more potent toward ALDH2 than daidzin, a previously described ALDH2 inhibitor. Our ability to produce many more ALDH isoenzymes allowed us to determine that daidzin is not as selective as previously believed, inhibiting ALDH2, ALDH1B1, and ALDH1A2 with equal potency. This inhibition pattern was seen with several of the aromatic lactones as well. Structural studies show that many of the lactones bind between key aromatic residues in the ALDH1/2 enzyme substrate-binding sites. One lactone in particular mimics the position of an aldehyde substrate and alters the position of the catalytic cysteine to interfere with the productive binding of NAD+ for enzyme catalysis. Further characterization of related compounds led to the realization that the mechanism of inhibition, potency, and selectivity differs amongst the lactones based off the substituents on the aromatic scaffold and its precise binding location. Two of these compounds were found to be selective for one of the ALDH1/2 family members, BUC22, selective for ALDH1A1, and BUC27, selective for ALDH2. BUC22 demonstrates ten-fold selectivity for ALDH1A1 over ALDH1A2 and does not inhibit the remaining ALDH1/2 enzymes. Additionally, treatment with BUC22 led to decreased growth of triple-negative breast cancer cells in culture. BUC27 inhibits ALDH2 with the same potency as daidzin. Both BUC22 and BUC27 could be further developed to use as chemical tools to better understand the functional roles of ALDH1A1 and ALDH2 in biological systems.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第20396号 / 工博第4333号 / 新制||工||1671(附属図書館) / 京都大学大学院工学研究科物質エネルギー化学専攻 / (主査)教授 村田 靖次郎, 教授 辻 康之, 教授 中村 正治 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

No description available.

Highly cross-linked monoliths prepared from single cross-linking monomers were found to increase surface area and stability. Therefore, seven cross-linking monomers, i.e., 1,3-butanediol dimethacrylate (1,3-BDDMA), 1,4-butanediol dimethacrylate (1,4-BDDMA), neopentyl glycol dimethacrylate (NPGDMA), 1,5-pentanediol dimethacrylate (1,5-PDDMA), 1,6-hexanediol dimethacrylate (1,6-HDDMA), 1,10-decanediol dimethacrylate (1,10-DDDMA), and 1,12-dodecanediol dimethacrylate (1,12-DoDDMA), were used to synthesize highly cross-linked monolithic columns in 75-µm i.d. capillaries by one-step UV-initiated polymerization using dodecanol and methanol as porogens for reversed-phase liquid chromatography (RPLC) of small molecules. Selection of porogen type and concentration was investigated in detail. Isocratic elution of alkylbenzenes at a flow rate of 300 nL/min was conducted for all of the monoliths. Gradient elution of alkylbenzenes and alkylparabens provided high resolution separations. Several of the monoliths demonstrated column efficiencies in excess of 50,000 plates/m. Monoliths with longer alkyl-bridging chains showed very little shrinking or swelling in solvents of different polarities. In addition, highly cross-linked monolithic capillary columns poly(1,6-HDDMA), poly(cyclohexanediol dimethacrylate) [poly(CHDDMA)] and poly(1,4-phenylene diacrylate) [poly(PHDA)], were synthesized and compared for RPLC of small molecules. Isocratic elution of alkylbenzenes was performed using 1,6-HDDMA and CHDDMA monolithic columns. Gradient elution of alkylbenzenes using all three monolithic columns showed good separations. Monolithic columns formed from 1,6-HDDMA, which had a linear alkyl-bridging chain structure, exhibited the highest column efficiencies (86,000 plates/m). Optimized columns showed high permeability and high run-to-run and column-to-column reproducibilities. Monoliths prepared from controlled/living polymerization was demonstrated exhibiting narrower molecular weight distribution and more homogeneous cross-linked structures due to the reversible character of this polymerization method. Thus, monolithic columns were developed from three cross-linking monomers, i.e., 1, 12-DoDDMA, trimethylolpropane trimethacrylate (TMPTMA) and pentaerythritol tetraacrylate (PETA) using organotellurium-mediated living radical polymerization (TERP) in 150-µm i.d. capillaries for RPLC of small molecules. Selection of the polymerization conditions for the 1,12-DoDDMA monolirh was investigated in detail. Isocratic elution of alkylbenzenes was achieved with good efficiency (47,700 to 64,200 plates/m for uracil) using all monolithic columns prepared using TERP.

Design and development of novel one-step reactions that produce nitrogen-containing scaffolds is an invaluable area of chemistry due to the abundance of these moieties in natural products and biologically active molecules. Discovering novel methods using uncommon substrates and rare earth metals to access these significant scaffolds present a challenge. Over the course of my doctoral studies, I have designed, developed and optimized novel reactions by using rarely known substrates and rare earth metals that have afforded important nitrogen-containing scaffolds. The products obtained allow access to otherwise long-to-synthesize molecules and expeditious construction of biologically active molecules.