This thesis describes the host-guest chemistry between cucurbit[7]uril (CB[7]) and various guests that contain isoquinoline groups, including tacrine, papaverine, N-methyl papaverinium, N-methyl laudanosinium, 6,7-dimethoxy-1,2,3,4,-tetrahydroisoquinoline, N, N-dimethyl-6,7-dimethoxy-1,2,3,4-tetrahydroisoquinolinium, α,α'-bis(isoquinolinium)-p-xylene and a series of 1,n-bis(isoquinolinium) alkane dications (Isq(CH2)nIsq2+, where n = 2, 4-6, 8-10 and 12). The stoichiometries and strengths of the host-guest interactions were studied using UV-visible and 1H NMR spectroscopy and high-resolution electrospray ionization mass spectrometry. A focus of this thesis is an investigation of the effects of varying the chemical structure within a series of isoquinoline-based guest on the strength of the binding affinity . The 1H NMR spectra indicates that CB[7] prefers the saturated ring of tacrine as opposed to the aromatic ring, resulting in a binding constant of (2.7 ± 0.25) x 104 M-1. The N-methylations of papaverine and 6,7-dimethoxy-1,2,3,4,-tetrahydroisoquinoline increased their respective binding constants from those of the protonated forms and changed the nature of the interaction of the guest with CB[7]. . With the series of 1,n-bis(isoquinolinium)-alkane dications, the mode of binding to CB[7] depends on the number of carbons in the polymethylene chain that bridges the two isoquinolinium groups. When the bridge is less than six carbons, CB[7] binds sequentially on the isoquinolinium groups to form 1:1 and 2:1 host-guest complexes. If the polymethylene chain length is between six and ten carbons, or is replaced with a p-xylyl group, the first CB[7] will bind over the central bridge, resulting in both of the polar portals forming ion-dipole interactions with both positively charged nitrogens. A second CB[7] binds to a terminal isoquinolinium group, which forces the original bound CB[7] to relocate to the other isoquinolinium group. When the polymethylene bridges contains twelve carbons, two CB[7] binds sequentially to the isoquinolinium groups, as observed with the shortest polymethylene bridges. With this series of guest, the binding constant is the largest when the bridge is two carbons long. This is due to the two isoquinolinium groups being in close proximity to each other, allowing CB[7] to interact with both nitrogens while still binding around the isoquinoline group. / Thesis (Master, Chemistry) -- Queen's University, 2011-09-30 10:02:47.285

archives@tulane.edu / A recent development in the field of DNA nanotechnology is the use of synthetic moieties that are tethered to DNA to construct functional nanostructures for a wide range of applications. Due to the unique properties such as molecular recognition, self-assembly, biocompatibility and water solubility, a large number of these modified DNA-based structures were developed for application in biomedical fields. One intriguing goal of the studies is to regulate protein activities with the DNA-based nano-switches. Conceptually mimicking an allosteric protein, a well-designed DNA-based switch can recognize a biomarker from the biological environment, and then undergo a major conformational change, leading to a switch between ON and OFF states for protein activity modulation. This dissertation starts with a background on DNA Supramolecular Chemistry and also provides examples of the current mechanisms and strategies to control protein activities using DNA-based structures. The use of host-guest chemistry in conjugation with DNA systems is also discussed in this first chapter. Then, the development of two novel DNA-based transducers are described in the following chapters. The first transducer is based on a cucurbit[7]uril-DNA conjugate, which is capable of responding to an ATP input to release a carbonic anhydrase II (CA-II) inhibitor for protein activity regulation. The third chapter details an aptamer V7t1/DNA-small molecule chimera duplex that targets the CA-IX protein after recognizing a vascular endothelial growth factor (VEGF) trigger, thus raising the possibility of rewiring the HIF-1α signaling pathway. / 1 / Xiao Zhou

This thesis describes the use of electrospray mass spectrometry, 1H NMR, and UV-visible spectroscopy, along with molecular modeling studies, to characterize the host-guest complexes that are formed between the cucurbit[7]uril (CB[7]) host molecule and a series of cationic alkylammonium (benzethonium), biguanidinium (metformin, phenformin, chlorhexidine and alexidine), amidinium (berenil, pentamidine, and 4-hydroxy- and 4-aminobenzamidines), and flavylium (4’- and 6-methoxyflavylium and 6,4’-dimethoxyflavylium) guests in aqueous solution. The stoichiometries and binding strengths of the CB[7] host-guest complexes with these series of drug and dye molecules were determined, and have been rationalized in terms of the specific ion-dipole interactions and hydrophobic effects involved. The potential uses of CB[7] as a slow-release drug delivery agent and molecular stabilizing agent are indicated from kinetic and spectroscopic studies on the reactivities of the host-guest complexes. CB[7] forms 1:1 and 2:1 host-guest complexes with the benzethonium cation by sequential binding to the hydrophilic benzyldimethylammonium group and the hydrophobic 2,4,4-trimethylpentyl group, respectively. The binding strength at the former site is consistent with data for other CB[7]-benzylammonium guests, while the strength of binding of the neutral hydrophobic group results from efficient packing within the inner CB[7] cavity. Each of the biguanidinium guests was shown to form strong 1:1 host-guest complexes with CB[7]. Metformin proved to be small enough to form 1:2 host-guest complexes at low concentrations of CB[7], while chlorhexidine and alexidine were shown to be large enough to form sequential 2:1 and 3:1 host-guest complexes with CB[7]. UV-visible pH titrations showed that CB[7] binds more strongly to mono-protonated metformin than the di-protonated form of this guest. Both pentamidine and berenil formed tightly bound complexes with CB[7], indicating that this host could potentially act as carrier for these drug molecules. CB[7] catalyzes the acid decomposition of berenil and each of the decomposition products, 4-hydroxy- and 4-aminobenzamidinium, bind to CB[7] with increases in their pKa values in the presence of CB[7]. The three flavylium dyes, with cationic oxonium centers, were shown to complex strongly with CB[7], resulting in a stabilization of the flavylium cation, with respect to the ring-opened 2-hydroxychalcones in neutral solutions. / Thesis (Master, Chemistry) -- Queen's University, 2012-09-15 00:02:15.516

Supramolecular systems comprised of non-covalent interactions are reversible in nature. This intrinsic reversibility of these systems is essential in achieving several functions, making it crucial to understand the dynamics of supramolecular systems. However, studies on the dynamics of supramolecular systems have always lagged behind structural and thermodynamic characterization of innumerable supramolecular systems developed. The first objective of this work was to understand the dynamics leading to a shift in the acidity constant (pKa) for 2-aminoanthracenium cation (AH+) upon binding with cucurbit[7]uril (CB[7]) host molecule. The adiabatic deprotonation of free AH+ in water was found to be inhibited in the complex with CB[7]. Different spectral characteristics for the protonated and deprotonated form of the guest molecule were used to understand the mechanism of this pKa shift associated with the binding to CB[7]. The results suggested that the pKa shift upon binding with CB[7] is a result of the slowing down of the deprotonation step in the complex, whereas the association rate constant did not change very much. The second objective of this work was to understand the role of cations on the binding dynamics of the N-phenyl-2-naphthyl amine (Ph-A-Np) binding to CB[7]. Ph-A-Np has two binding sites, which can lead to 1:1 and 2:1 host-guest complexes. The results indicate a switch in the binding mechanism for Ph-A-Np at low and high concentration regimes of sodium ions. Sodium ion was found to reduce the binding affinity of the naphthyl group to CB[7] whereas the complex formed by the phenyl group with CB[7] bound to one sodium ion was found to be stabilized. The final objective of this work was to study how structural changes to a guest molecule can affect the binding dynamics for the formation of a 2:1 “capsule” like complex with octa acid (OA). The dissociation for the OA capsule with pyrene (Py) as the encapsulated guest was shown to happen in 2.7 s previously. Two pyrene derivatives, 1-methylpyrene (MePy) and 1-pyrenemethanol (PyMeOH) were chosen as guest molecules to study the effect of these substituents on pyrene on the capsule dissociation dynamics. The results show that the residence time for the guests in the OA capsule depends on the substituents. For PyMeOH and MePy a shorter and longer residence time respectively in the capsule was observed when compared to Py. / Graduate / 2019-09-30

Supramolecular systems, which are formed by the noncovalent intermolecular interactions between molecules, are highly dynamic. The high reversibility of supramolecular systems leads to some functional features that cannot be achieved by the single chemical component. The kinetic information for the supramolecular systems can not be inferred from thermodynamic studies or structural studies. Furthermore, the information provided by the dynamic study can be employed to infer or explain the results from the thermodynamic study and the structural study. The first objective of this work was to study the dynamics and the binding mechanism of cucurbit[7]uril with a charged guest molecule (2-naphthyl-1-ethylammonium cation, NpAmH+). In general, the binding affinity of cucurbit[7]uril to the positively charged guests are very high compared with other host systems such as cyclodextrins and bile salt aggregates. In this work, the complexation of cucurbit[7]uril and NpAmH+ was studied from a kinetic point of view. Results showed that the high binding affinity of cucurbit[7]uril to NpAmH+ was due to the high association rate constant and the low dissociation rate constant for the complexation of cucurbit[7]uril and NpAmH+. Moreover, the competition between co-cations and NpAmH+ for the binding sites of cucurbituril molecules retarded the complexation process for cucurbit[7]uril binding to NpAmH+ and decreased the overall equilibrium constant for the formation of cucurbit[7]uril-NpAmH+ complex. The second objective of this work was to study the chiral recognition observed for the formation of 2:2 complexes between β-cyclodextrin and 2-naphthyl-1-ethanol (NpOH). The binding of β-cyclodextrin and NpOH leads to the formation of two 1:1 complexes and three 2:2 complexes. The binding dynamics of NpOH with β-cyclodextrin in the 1:1 complex is fast and occurs within microseconds. A much slower dynamics was observed for the formation of the 2:2 complex. Results showed that more 2:2 complex were formed for (R)-NpOH than for (S)-NpOH, which is due to the difference of the dissociation rate constant of the 2:2 complex for both NpOH enantiomers. The dissociation rate constant of the 2:2 complex for (R)-NpOH is 46.8% lower than that for (S)-NpOH while the association rate constant of the 2:2 complex are similar for both NpOH enantiomers. The third objective of this work was to study the dynamics and the binding mechanism of octa acid with pyrene. As known from the work of other researchers, the accessibility of small molecules (e.g. I- or O2) to pyrene bound to octa acid is largely limited by the octa acid capsule. In this study, a two-step successive process was observed for the complexation of octa acid and pyrene. The first step, which was related to the formation of octa acid-pyrene 1:1 complex, was sufficiently fast to be viewed as a pre-equilibrium process. The second step, which was related to the formation of octa acid-pyrene 2:1 complex, was slow on the millisecond – second time scale. The high binding affinity of octa acid to pyrene was observed, which is due to the low dissociation rate constant for the octa acid-pyrene 2:1 complex. / Graduate

<p>Molecular recognition is arguably the most elementary physical process essential for life that arises at the molecular scale. Molecular recognition drives events across virtually all length scales, from the folding of proteins and binding of ligands, to the organization of membranes and the function of muscles. Understanding such events at the molecular level is massively complicated by the unique medium in which life occurs: water. In contrast to recognition in non-aqueous solvents, which are driven largely by attractive interactions between binding partners, binding reactions in water are driven in large measure by the properties of the medium itself. Aqueous binding involves the loss of solute-solvent interactions (desolvation) and the concomitant formation of solute-solute interactions. Despite decades of research, aqueous binding remains poorly understood, a deficit that profoundly limits our ability to design effective pharmaceuticals and new enzymes. Particularly problematic is understanding the energetic consequences of aqueous desolvation, an area the Toone and Beratan groups have considered for many years.</p><p> In this dissertation, we embark on a quest to shed new light on aqueous desolvation from two perspectives. In one component of this research, we improve current computational tools to study aqueous desolvation, employing quantum mechanics (QM), molecular dynamics (MD) and Monte Carlo (MC) simulations to better understand the behavior of water near molecular surfaces. In the other, we use a synthetic host, cucurbit[7]uril (CB[7]), in conjunction with a de novo series of ligands to study the structure and thermodynamics of aqueous desolvation in the context of ligand binding with atomic precision, a feat hitherto impossible. A simple and rigid macrocycle, CB[7] alleviates the drawbacks of protein systems for the study of aqueous ligand binding, that arise from conformational heterogeneity and prohibitive computational costs to model.</p><p> </p><p> We first constructed a novel host-guest system that facilitates internalization of the trimethylammonium (methonium) group from bulk water to the hydrophobic cavity of CB[7] with precise (atomic-scale) control over the position of the ligand with respect to the cavity. The process of internalization was investigated energetically using isothermal titration microcalorimetry and structurally by nuclear magnetic resonance (NMR) spectroscopy. We show that the transfer of methonium from bulk water to the CB[7] cavity is accompanied by an unfavorable desolvation enthalpy of just 0.49±0.27 kcal*mol-1, a value significantly less endothermic than those values suggested from previous gas-phase model studies. Our results offer a rationale for the wide distribution of methonium in biology and demonstrate important limitations to computational estimates of binding affinities based on simple solvent-accessible surface area approaches.</p><p> To better understand our experimental results, we developed a two-dimensional lattice model of water based on random cluster structures that successfully reproduces the temperature-density anomaly of water with minimum computational cost. Using reported well-characterized ligands of CB[7], we probed water structure within the CB[7] cavity and identified an energetically perturbed cluster of water. We offer both experimental and computational evidence that this unstable water cluster provides a significant portion of the driving force for encapsulation of hydrophobic guests.</p><p> The studies reported herein shed important light on the thermodynamic and structural nature of aqueous desolvation, and bring our previous understanding of the hydrophobic effect based on ordered water and buried surface area into question. Our approach provides new tools to quantify the thermodynamics of functional group desolvation in the context of ligand binding, which will be of tremendous value for future research on ligand/drug design.</p> / Dissertation

[Formulae and special characters can only be approximated here. Please see the pdf version of the Abstract for an accurate reproduction.] Several inert platinum complexes were synthesised: [(en)Pt([special character]-dpzm)2Pt(en)]4+, [{Pt(dien)}2[special character]-dpzm]4+, [{Pt(dien)}2[special character]-H2N-(CH2)6-NH2]4+, cis-[(NH3)2Pt([special character]--dpzm)2Pt(NH3)2]4+, trans-[Pt(NH3)2([special character]-dpzm)2]2+. Three active complexes, all with chloro ligands, were also synthesised: trans-[{Pt(NH3)Cl2}2[special character]-dpzm)], trans-[{Pt(NH3)2Cl}2[special character]-dpzm]2+ (di-Pt) and trans-[trans-{Pt(NH3)2Cl}2{trans-[Pt(NH3)2([special character]-dpzm)2]}]4+ (tri-Pt). 1H NMR established that multi-nuclear platinum complexes will preferentially associate in the DNA minor groove with a preference for A/T sequences, and with a binding constant [special character]-105 M-1, regardless of the charge, linking ligand, length or shape. Using [(en)Pt([special character]-dpzm)2Pt(en)]4+ and the oligonucleotide d(GC)5 it was determined that the metal complex binds G/C rich sequences also in the minor groove, but with a much reduced binding constant, 103 M-1. CD studies showed [(en)Pt([special character]-dpzm)2Pt(en)]4+ was able to induce a DNA conformation change from B-type to what appeared to be a partial Z-type. Transcription assays showed that even though the metal complex does not bind DNA covalently, it is still able to inhibit DNA transcription at particular sites. The complexes di-Pt, tri-Pt, [{Pt(dien)}2[special character]-dpzm]4+ and trans-[Pt(NH3)2([special character]-dpzm)2]2+ were tested for anti-cancer activity in the L1210 murine leukaemia cell line, and gave values of 3.8, 2.5, [special character]200 and 64 [special character]M respectively. In the cisplatin resistant line (L1210/DDP), trans-[Pt(NH3)2([special character]-dpzm)2]2+ showed an increase in activity with a drop to 32 [special character]M, while both di-Pt and tri-Pt showed decreases in activity to values of 8.8 and 3.6 [special character]M. In the human ovarian carcinoma 2008 cell line and its cisplatin resistant derivative C13[special character]5, both complexes showed good activity with values of 2.5 and 20.9 [special character]M respectively, but again both showed decreases in activity in the resistant line with values of 17.8 and 37.7 [special character]M respectively. To help explain the difference between activity of these complexes and the complexes BBR3464 and BBR3005, cell uptake and DNA interstrand cross-linking experiments were performed. The cell uptake studies showed that both di-Pt and tri-Pt are taken up by cells at very high levels, when administered at 100 [special character]M, thus indicating that the difference is unlikely to be due to large differences in cell uptake. The DNA interstrand cross-linking studies showed both complexes readily form interstrand adducts (50% interstrand cross-linking at 12 nM and 22 nM respectively, c.f cisplatin 3 [special character]M). These results suggest that the rigid nature of the dpzm linker may be affecting the DNA adducts formed, with more interstrand links being formed than BBR3464. Possibly, it is this that causes the large differences in cytotoxicity. The DNA binding of di-Pt and tri-Pt was examined with the nucleosides adenosine and guanosine and the dinucleotide d(GpG). Both complexes bound at the N7 of guanosine, but 2-fold slower than cisplatin. In addition, di-Pt bound at the N7 and either the N1 or N3 of adenosine, 7-fold slower than guanosine. Di-Pt forms a large variety of cross-links between two d(GpG) molecules, however it could not be established whether the 1,2-intrastrand adduct could be formed. Di-Pt, however, forms a 1,2-GG interstrand adduct with the oligonucleotide d(ATGCAT)2 resulting in a conformation change away from B-type DNA. The sugar pucker of the G3 nucleoside changes from 2[special character]-endo towards 3[special character]-endo, and the position of the nucleotide relative to the sugar changes from anti to syn. The ability of multi-nuclear platinum complexes to form covalent adducts in the DNA minor groove remains unclear. It appears that di-Pt can form up to 33% minor groove adducts with the oligonucleotide d(AT)5, but when added to the oligonucleotide d(GCCAAATTTCCG)2 no definite minor groove adducts are seen and the major adduct appears to be a 1,2-interstrand cross-link between the two A6's or between the G1 and G11. Finally, a study of the encapsulation of platinum complexes within cucurbit[7]uril (Q7) as a means of reducing drug toxicity was made. For complex A and di-Pt, encapsulation of the linker ligand occurred. The effect of Q7 on the rate of hydrolysis of di-Pt was at least a 3-fold reduction as compared to free di-Pt with guanosine. Studies with [{Pt(dien)}2[special character]-dpzm]4+/Q7 and the oligonucleotide d(CGCGAATTCGCG)2 showed that the metal complex could dissociate from the Q7 and associate with the oligonucleotide, where an equilibrium is achieved with 15 % of the metal complex bound to the oligonucleotide and 75 % encapsulated in Q7. Tests in the L1210 and L1210/DDP cancer cell lines showed that di-Pt/Q7 has almost the same activity compared to free di-Pt.

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