Thesis advisor: Jianmin Gao / With the rapid evolution of antibiotic resistance, the need for more effective antibiotics is imminent. Bacterial membranes are an appealing target due to their accessibility and relatively conserved structures. Membrane targeting antibiotics, especially cationic antimicrobial peptides (CAMPs) such as host defense peptides, have been increasingly explored as novel antibiotics and tunable innate antimicrobials. The latter could be achieved by treatment with an antibiotic adjuvant: a compound that would increase the potency of host CAMPs without killing the bacteria on its own. Boosting the host’s own immune system with an adjuvant is beneficial over using antibiotics and would theoretically avoid triggering bacterial resistance. One mechanism of bacterial resistance is increasing the cationic charge of the membrane. As CAMPs are electrostatically attracted to anionic bacterial membranes, making the membrane more cationic decreases that attraction, rendering CAMPs less effective. To target this resistance mechanism chemically, two antibiotic adjuvant strategies were explored as co-treatments with various CAMPs: membrane targeting peptides used to bind and block surface amines, and small molecules used to either acetylate surface amines or convert a cationic membrane phospholipid to an anionic phospholipid. Co-treatment of the Staphylococcus aureus (S. aureus) membrane targeting peptide KAM-CT and various CAMPs increased S. aureus susceptibility to those CAMPs. Bacterial surface acetylation using sulfo-NHS-acetate followed by CAMP treatment caused up to 10 times increased CAMP potency. Hydrazine and hydroxylamine were shown to cleave the lysine moiety from the lysyl-phosphatidylglycerol (Lys-PG) phospholipid to generate phosphatidylglycerol (PG) in liposome models. S. aureus was treated with a hydroxylamine-CAMP conjugate, but it showed decreased antibiotic activity compared to the CAMP alone. To better understand what was happening in the bacteria, a novel Lys-PG quantification protocol was created by fluorophore labeling Lys-PG and quantifying the labeled Lys-PG via normal phase high-performance liquid chromatography (NP-HPLC). Cyclic peptides, such as KAM-CT, represent complex yet synthetically attainable moieties that could be used as novel antibiotics adjuvants. Expanding the repertoire of reversible covalent chemistries, especially those applied to peptide cyclization, is desirable due to the high potency and selectivity of such interactions. Herein, we also describe a novel reversible covalent chemistry between 2-formylphenylboronic acid (FPBA) and 2,3-diaminopropionic acid (Dap): the imidazolidino boronate (IzB) conjugate. It was found to be potent (Kd = 100 μM) and quickly reversible (t1 = ~6 sec) under physiological conditions. IzB formation was successfully employed as a peptide cyclization strategy as there was little interference from biologically relevant small molecules, except cysteine. Cysteine interference was utilized to create “smart” peptides that can linearize upon increasing cysteine concentrations via thiazolidino boronate (TzB) formation with the FPBA moiety in the peptide. Such “smart” peptides could be used as pH-responsive peptides or cysteine sensors able to report on the cysteine concentration in complex media. / Thesis (MS) — Boston College, 2017. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Predicting and quantifying solvent effects on non-covalent interactions is often very challenging, as they are influenced and modulated by multiple factors. In this thesis, a series of molecular torsion balances is used as a tool to tackle the complexities of noncovalent interactions in solution. Chapter 1 presents an up-to-date literature review on solvent effects on non-covalent interactions, with a particular focus on solvent effects on conformational equilibria and molecular torsion balances. Chapter 2 demonstrates the use of molecular torsion balances and a simple explicit solvation computational model to show that the electrostatic potential of the substituted aromatic rings is largely dependent on the explicit solvation of the substituent. The contribution of both bond polarisation and through-space field effects is also covered. Chapter 3 provides a literature review on the deuterium isotope effects on non-covalent interactions, presenting a range of contradictory findings. Molecular torsion balances are used here as a probe of H/D isotope effects on the conformational equilibria, solvent isotope effects and the solvophobic effect in aqueous mixtures. The balances are studied from thermodynamic and kinetic viewpoints, through which both intra- and intermolecular interactions are examined. It is shown here that H/D isotope effects on the presented system are either non-existent or negligibly small. Chapter 4 presents the use of molecular torsion balances to investigate carbonylcarbonyl interactions, taking into account steric and solvent effects. This is compared experimentally and computationally against two existing theories rationalising these interactions. In Chapter 5, a background of metal-ligand interactions is outlined, along the most widely utilised theories rationalising them. The electronic effects of Pt complexation by a pyridyl-substituted molecular torsion balance is analysed both experimentally and computationally, and the arising discrepancies are addressed. The applicability limits of the previously presented simple solvation models are determined using systems displaying extreme electronic effects.

Non-covalent interactions are fundamental to molecular recognition processes that underpin the structure and function of chemical and biological systems. Their study is often difficult due to the interplay of multiple interactions and solvent effects common in complex systems. Herein, chapter one provides some general background on the area before presenting a literature review of key, contemporary developments on the use of folding molecules for the quantification of non-covalent interactions. Chapter two investigates the magnitude and extent of energetic cooperativity in H-bond chains. Utilising supramolecular complexes and synthetic molecular torsion balances, direct measurements of energetic cooperativity are presented in an experimental system in which the geometry and number of H-bonds in a chain were systematically controlled. Strikingly, it was found that adding a second H-bond donor to form a chain can almost double the strength of the terminal H-bond, while further extension had very little effect. Computations provide insights into this strong, short-range cooperative effect in a range of H-bonding contexts. Chapters three and four build on the concepts and molecular models discussed in chapter two. Chapter three discusses the effects of interplay and competition between strong H-bond acceptors such as formyl groups and the weaker organofluorine H-bond acceptor. There has been some debate in recent literature about the latter’s ability to accept H-bonds, the work presented shows that although organofluorine is a weak H-bond acceptor, it can have a significant modulating effect on stronger interactions when in direct competition. Chapter four investigates deuterium isotope effects on conformational equilibria governed by non-covalent interactions. The results show that any deuterium isotope effect which exists is less than the margins of experimental error. Finally, chapter five discusses a molecular torsion balance designed to investigate halogen∙∙∙arene interactions. The interaction energies were investigated in a range of solvents and mixtures in order to dissect out the dispersive and solvophobic components of folding. Overall, these interactions were found to be weak. Nonetheless, a model was used to dissect trends in solvophobic and electronic contributions to the binding using multiple linear regression based upon the cohesive energy density and polarisabilities of the solvents.

Unconventional non-covalent interactions such as halogen, chalcogen, and tetrel bonds are gaining interest in several domains including but not limited to drug design, as well as novel catalyst design. Non-covalent interactions are known as weak forces of interactions when they are considered on an individual basis, but on a molecular basis, these effects become important such that their prevalence can be seen in the construction of large biomolecules like proteins, DNA and RNA. In this work, the fundamental aspects of these interactions are looked upon using ab initio and Density Functional Theory (DFT). An essential aspect of chalcogen bonds involving Sulfur as donor atom with nitrogen, oxygen and π-system as electron sources was examined. These bonds are strong with binding energy that varies from a minimum of 3 kcal/mol in some π-system to 19 kcal/mol in primary amine systems. Decomposition of the total interaction energy reveals that the induction energy constitutes more than half of the total interaction energy. The shortness and strength of some of the chalcogen bond interactions suggest these interactions may in some cases be described as weak covalent bonds. A comparative study of π-hole tetrel bonding with σ-hole halogen bonds in complexes of XCN (X = F, Cl, Br, I) and ammonia shows that the π-hole geometry if favored for X = F, and the σ-hole structure is preferred for the heavier halogens. Also, the potential use of these non-covalent interactions in organic catalysis was explored. The energy barrier of the Aza-Diels-Alder reaction is substantially lowered by the introduction of an imidazolium catalyst with either a Hydrogen or halogen (X) atom in the 2-position.

Diabetes is a debilitating disease affecting millions of people worldwide. The transplantation of insulin-producing, pancreatic islet cells has been an extensively explored approach for the treatment of Type 1 Diabetes. However, the need for a multi-donor source, the strong host immune responses, and a life-long immunosuppressive therapy regimen limits the widespread applicability of islet transplantation. Encapsulation of islet cells within a semi-permeable biomaterial as a means to mask transplanted cells from the host has been shown to be a viable option for the protection of islets upon transplantation. Recent advancements, incorporating additional knowledge of biomaterials, have revitalized the field of islet encapsulation. This thesis work focused on both micro- and nano-scale encapsulation techniques. Initially, a novel, covalently linked alginate-poly(ethylene glycol) (PEG), termed XAlginate-PEG, microcapsule was evaluated, and was shown to exhibit superior stability over traditional ionically bound alginate microcapsules. The XAlginate-PEG capsules exhibited a 5-fold decrease in osmotic swelling than traditional alginate microcapsules, and remained completely intact upon chelation of ionic interactions. In addition, in vitro study of the novel polymer matrix showed high compatibility with mouse insulinoma cell lines, rat and human islets. Furthermore, no disruption in islet function was observed upon encapsulation. The second study of this thesis work focused on the nano-scale encapsulation of islets with a single layer PEG coating. A PEG polymer was grafted directly on the collagen matrix of the islet capsule to form a stable amide bond. PEGylation of the islet cells was shown to camouflage inflammatory agents, such as tissue factor (TF), present on the surface of the islet, while maintaining islet morphology and function. In summary, PEG dampened coagulation cascade activation, and concealed activated factor X (afX) generation under pro-inflammatory culture conditions. The present findings contribute to the field of cellular encapsulation, both in the fabrication of novel encapsulation techniques and the evaluation of nano-scale coatings. The future potential of this research includes the attenuation of immune responses to transplanted cells, elimination of continuous immunosuppression, and provide flexibility in cell source. Furthermore, the platforms evaluated in this thesis are generalized for all cell types, thereby permitting translation of techniques to alternative cellular therapies.

Layer-by-layer (LbL) assembly based on ionic interactions has proven to be a versatile route for surface modification and construction of ultrathin nanocomposites. Covalent LbL assembly based on facile ‘click’ covalent bond formation is an effective alternative, especially for the applications where a more robust ultrathin films or nanocomposites is desired. The subject of this dissertation focuses on the design of three different covalent LbL assemblies and their applications on conductive thin films, superhydrophobic surfaces, and solute responsive surfaces, respectively. Surface modification of PE substrates using covalent LbL assembly with PEI and Gantrez is a successful route to prepare a surface graft. The procedure is relative easy, fast and reproducible. Grafting multiple layers of PEI/Gantrez to the PE powder surface provided excellent coverage and promoted stable LbL film growth and excellent adhesion. This carbon black (CB) coated powder was compression molded into films, and their conductivity was measured, which revealed a percolation threshold below 0.01 wt % CB for the PEI-grafted system. Electrical conductivity of 0.2 S/cm was achieved with only 6 wt % CB, which is exceptional for a CB-filled PE film. Direct amination of MWNTs with PEI is a convenient and simple method leading to highly functionalized product that contains 6-8 % by weight PEI. Superhydrophobic PE films can be formed either from ionic LbL self-assembly of MWNT-NH-PEIs and poly(acrylic acid) or from covalent LbL self-assembly of MWNTNH- PEIs and Gantrez when the final graft is acrylated with octadecanoic acid. While the ionically assembled nanocomposite graft is labile under acid, the covalently assembled graft is more chemically robust. Responsive surfaces with significant, reversible, reproducible wettability changes can be prepared by covalent LbL grafting using PNIPAM-c-PNASI and aminated silica nanoparticles. A 65º ΔΘ value was observed with water vs. 1.4 M Na2SO4. The prepared film shows a high surface roughness of ~300 nm, which contributes to the large solute responsive ΔΘ values. The surfaces are reconfigurable in different solute conditions and that the changes in water contact angle are likely due to combination of change in surface roughness along with swell and intercalation of the solute ions into the PNIPAM surface.

Nanoparticles (such as, carbon nanotubes, carbon black, clay etc.) have one or more dimensions of the order of 100 nm or less. Owing to very high van der Waals force of attraction, these nanoparticles exist in a highly aggregated state. It is often required to break these aggregates to truly experience the “nanosize” effect for any required end use. There are several strategies proposed for dispersing/exfoliating nanoparticles but limited progress has been made towards controlling their dispersion state. The ability to tailor nanoparticle dispersion state in liquid and solid media can ultimately provide a powerful method for tailoring the properties of solution processed nanoparticle-filled polymer composites. This dissertation reports the use of a variety of stimuli-responsive polymers to control the dispersion state of single-walled carbon nanotubes. Stimuli-responsive polymers exhibit conformational transitions as a function of applied stimulus (like pH, temp, chemical etc.). These variations in conformations of the polymer can be used tailor nanotube dispersion state in water and solid composites.The use of pH and temperature responsive polymers to stabilize/disperse single walled carbon nanotubes (SWNTs) in water is presented. Non-covalent functionalization of SWNTs using pH and temperature responsive polymer show tailored dispersion state as a function of pH and temperature, respectively. Carbon nanotube microstructure in these aqueous suspensions was characterized using several techniques (cryo-TEM, viscosity measurements, uv-vis spectroscopy, zeta potential measurements and settling behavior). Furthermore, nanotube dispersion state in aqueous suspensions is preserved to a large extent in the composites formed by drying these suspensions as evidenced by SEM images and electrical conductivity measurements. Based on the results obtained a mechanism is proposed to explain the tailored dispersion of SWNTs as a functions of applied external stimulus (i.e., pH, temperature). Such stimuli-controlled dispersion of carbon nanotubes could have a variety of applications in nanoelectronics, sensing, and drug and gene delivery systems. Furthermore, this dissertation also contains a published study focused on controlling the dispersion state of carbon black (CB) in epoxy composites using clay.

The nucleolus of eukaryotic cells contain a number of the intron-coding small nucleolar RNAs (snoRNAs), which functions are related to covalent modification of pre-rRNAs. The snoRNA that from long, phylogenetically conserved sequence complementarity to 28S, 18S, 5.8S and 5S rRNAs are designated as 28S, 18S, 5.8S and 5S snoRNAs, respectively. In the present study, studying on human 5S snoRNAs had been carried out. The human genome encoding candidate 5S snoRNAs were searched using database mining. The transcripts of 5S snoRNA genes were identified by RT-PCR analyses and DNA sequencing. No appreciable diversities of 5S snoRNA genes were observed as evidenced by single strand conformation polymorphism (SSCP) and high resolution agarose gel. Moreover, sequence conservation of 5S snoRNAs reflects a requirement for maintaining their secondary structure on exerting their function. The results of RT-PCR analyses revealed a tissue-specific transcription of 5S snoRNAs. A 5S snoRNA designated as N117 was identified to be highly expressed in normal brain. On the contrary, its expression markly decreased in brain tumor (meningioma). This seems to be associated with the expression of host gene, which encodes a protein similar to synapsin III protein. Consequently, this may implicate that the use of snoRNA as a potential index for the transcription of its host gene.

A series of studies from our lab have investigated the threading polyintercalator approach to sequence specific DNA binding using a 1,4,5,8-naphthalene tetracarboxylic diimide (NDI) intercalating unit connected by flexible peptide linkers. Herein is a report of the sequence specificity, as well as a detailed kinetic analysis, of a threading NDI tetraintercalator. DNase I footprinting using two ~500 base pair DNA fragments containing one designed binding site for the tetraintercalator confirmed highly sequence specific binding. Kinetic analyses include 1H NMR, gel mobility-shift assays, and stopped-flow UV measurements to reveal a polyintercalation binding mode that demonstrates significant similarities between association rate profiles and rate constants for the tetraintercalator binding to its preferred versus a random oligonucleotide sequence. Sequence specificity was found to derive almost entirely from large differences in dissociation rates from the preferred versus random oligonucleotide sequences. Interestingly, the dissociation rate constant of the tetraintercalator complex dissociating from its preferred binding site was extremely slow, corresponding to a 16 day half-life at a benchmark 100 mM [Na+]. This dissociation result for the tetraintercalator is one of the longest bound half-lives yet measured, and to the best of our knowledge, the longest for a DNA binding small molecule. Such a long-lived complex raises the possibility of using threading polyintercalators to disrupt biological processes for extended periods. Current focus is given to deciphering a mechanism for the molecular recognition of the tetraintercalator preferred binding site within a long sequence of DNA. Initial DNase I footprinting results on an approximate 500mer DNA sequence containing three sequential preferred binding sites reveal that the tetraintercalator likely locates its designed binding site by a macro- or microscopic dissociation/re-association type of mechanism. Cooperativity is a possible ally to binding, leaving future studies to distinguish the mechanism for molecular recognition in a manner that is capable of circumventing cooperative binding. Taken together, the threading polyintercalation binding mode presents an interesting topology to sequence specific DNA binding. Extraordinarily long dissociation rates from preferred binding sites offers many future possibilities to disrupt biological processes in vivo. / text

Presented in this dissertation are studies of protein dynamics and protein/protein interactions using solution phase hydrogen/deuterium exchange in combination with mass spectrometry (HXMS). In addition, gas phase fragmentation behaviors of deuterated peptides are investigated, with the purpose of increasing resolution of the HXMS. In the area of single protein dynamics, two protein systems are studied. Studies on the cytochrome c2 from Rhodobacter capsulatus indicate its domain stability to be similar to that of the horse heart cytochrome c. Further comparison of the exchange kinetics of the cytochrome c2 in its reduced and oxidized state reveals that the so-called hinge region is destabilized upon oxidation. We also applied a similar approach to investigate the conformational changes of photoactive yellow protein when it is transiently converted from the resting state to the signaling state. The central β-sheet of the protein is shown to be destabilized upon photoisomerization of the double bond in the chromophore. Another equally important question when it comes to understanding how proteins work is the interactions between proteins. To this end, two protein complexes are subjected to studies by solution phase hydrogen deuterium exchange and mass spectrometry. In the case of LexA/RecA interaction, both proteins show decreases in their extents of exchange upon complex formation. The potential binding site in LexA was further mapped to the same region that the protein uses to cleave itself upon interacting with RecA. In the sHSP/MDH system, hydrogen/deuterium exchange experiments revealed regions within sHSP-bound MDH that were significantly protected against exchange under heat denaturing condition, indicative of a partially unfolded state. Hydrogen/deuterium exchange therefore provides a way of probing low resolution protein structure within protein complexes that have a high level of heterogeneity. Finally, the feasibility of increasing resolution of HXMS by gas phase peptide fragmentation is investigated by using a peptide with three prolines near the C-terminus. Our data show that deuterium migration indeed occurs during the collision activated dissociation process. Caution is required when interpreting the MS/MS spectra as a way of pinpointing the exact deuterium distribution within peptides.