A range of copper(I) alkynyl ladder polymers have been prepared via a simple single step microwave reaction at 100 °C for 2 minutes, using copper hydroxyacetate (Cu2(OH)3Ac.H2O) as the copper source, all with yields in excess of 80 %. A variety of functional groups were chosen ranging from a simple aromatic phenol ring, substituted aromatic groups, groups with a long carbon chain, and an example of 2 alkynyl units in one chain. The polymeric structure of these materials has been elucidated by powder X-ray diffraction, the results of which confirm that by changing the R groups on the copper ladder chains the structure of the ladder itself is altered to accommodate the variety of sizes and shapes. This was further detailed using a series of methyl substituted phenyl rings as the R group (ortho, meta and para), which were further examined by solid state NMR, and Raman spectroscopy. The raman data confirmed that the copper copper distance in the ladder backbone varied based on the side group present. The NMR results suggest that not only are there variations to copper backbone, but also there are different possible positions for the aromatic group to stack in based on the substitution on the aromatic ring. All data collected indicates the crystallinity of the polymer is strongly affected by the choice of alkyne. The range of ladder polymers has been used to catalyse a series of dipolar cycloaddition reactions of terminal alkynes and organic azides, with the aim to obtain additional mechanistic information on the alkyne-azide click reactions. These reactions were carried out using a simple microwave method requiring an excess of alkyne (1.5 eq) to azide (1 eq), using 10 mol% of the ladder polymer as catalyst for 10 minutes at 100 °C. These conditions were then modified slightly to allow for on water catalysis of the click reactions using copper(I) alkynyl ladder polymers. Triazole products were obtained in excellent yields ranging from approximately 60 -95%. Using similar conditions it was also possible to introduce an iodo group to the triazole product when starting with iodoacetylene rather than a terminal alkyne, with only slightly reduced yields of 50-70%. Flow chemistry was briefly tested and was shown to be a viable option for the synthesis of 1,2,3-traizoles using copper(I) alkynyl ladder polymer catalysts. The support material copper on carbon was investigated for comparison with the copper(I) alkynyl ladder polymers. The support material was found to actually be a composition of copper hydroxynitrate, a layered material capable of forming copper(I) ladder polymers, and carbon. A series of these materials were made using different supports using the same method as carbon, and all resulted in a mixture of copper hydroxynitrate and support material. An impurity was discovered in specific carbon batches (depending on the carbon preparation method) and was identified as libethenite (copper hydroxyphosphate). A series of click reactions were carried out using these copper hydroxynitrate/carbon mixtures and excellent yields of 80-90% were obtained, the impurity libethenite was also tested but found to not catalyse the click reaction.

No description available.

The isoprenoid biosynthetic pathway (IBP) plays an important role in cellular metabolism. Currently there are drugs, including lovastatin and the nitrogenous bisphosphonates risedronate and zoledronate, that are used clinically to lower cholesterol levels and treat bone disease, respectively. These drugs work by inhibition of the upstream enzymes, HMG-CoA reductase and farnesyl diphosphate synthase (FDPS), respectively. The enzyme FDPS catalyzes the formation of farnesyl pyrophosphate (FPP), an important intermediate that represents a branch point in the pathway. The post-translational modification known as protein prenylation is mediated by the three prenyltransferase enzymes. Even though compounds like lovastatin, risedronate, and zoledronate indirectly disrupt protein prenylation, they also impair processes downstream from the point of inhibition. Therefore a direct approach would be desirable where downstream enzymes are targeted so that the rest of the cellular processes can continue to function. One such downstream enzyme is geranylgeranyl transferase II (GGTase II). This enzyme and it catalyzes the transfer of two hydrophobic geranylgeranyl chains from geranylgeranyl pyrophosphate (GGPP) to Rab proteins, which are essential for intracellular membrane trafficking. Inhibition of GGTase II may be a good therapeutic target for diseases such as multiple myeloma characterized by an over secretion of proteins. A known GGTase II inhibitor is the carboxy phosphonate 3-PEHPC, however millimolar concentrations are necessary to observe cellular effects with this compound. In an effort to develop more potent inhibitors of this enzyme, a family of isoprenoid triazole bisphosphonates was initially prepared by click chemistry, first as a mixture of olefin isomers due to an allylic azide rearrangement. These compounds were tested by our collaborators to determine the compounds’ activity as GGTase II inhibitors. Because some triazole bisphosphonates showed good activity as a mixture of isomers, a family of isoprenoid triazole bisphosphonates as single olefin isomers now has been prepared through the use of epoxy azides to avoid the azide rearrangement. The biological activity of these compounds has been studied and some of these triazole bisphosphonates were found to be potent and selective inhibitors of geranylgeranyl diphosphate synthase (GGDPS). While the enzyme GGDPS is upstream of the geranylgeranyltransferases, it is still downstream of the pathway’s primary branch point and provides GGPP for Rab geranylgeranylation. Two other families of triazole bisphosphonate analogues, homo- and bishomoisoprenoid triazole bisphosphonates, also have been prepared and tested by our collaborators to explore the compounds’ activity as GGDPS inhibitors, as well as the structure-activity-relationship. Previous research has shown digeranyl bisphosphonate (DGBP) and the bisphosphonate ether C-prenyl-O-geranyl bisphosphonate to be inhibitors of GGDPS. Two C-alkyl-C-homoalkyl DGBP analogues have been synthesized in order to study further the binding of these compounds to GGDPS, and dialkylated triazole bisphosphonates have been prepared to explore the effect of a triazole moiety on the analogue’s ability to inhibit GGDPS. The activity uncovered through these studies encourages further research on inhibitors of GGDPS.

Pt(II) based anticancer drugs—cisplatin, carboplatin, and oxaliplatin—are widely used in the treatment of a variety of cancers. Unfortunately, the clinical efficacy of these drugs is currently hindered by the development of undesirable side effects and resistance during treatment. The molecular mechanisms underlying these effects are still unclear. For decades, research has focused on DNA as the main cellular target of Pt(II) compounds. However, there is increasing interest in proteins as alternative targets of Pt(II) and contributors to cytotoxic and resistance mechanisms of cisplatin. In this work, I utilize Pt(II) compounds that have been functionalized to participate in the azide-alkyne cycloaddition ‘click’ reaction to study protein targets of platinum reagents. First, I describe the use of an azide-modified Pt(II) compound to fluorescently label and isolate Pt(II)-bound bovine serum albumin in vitro. Additionally, we discover that Pt(II) compounds form monofunctional adducts on BSA that can crosslink to DNA oligonucleotides. I then use the click-functionalized Pt(II) compound, azidoplatin, to enrich for Pt(II)-bound proteins in Saccharomyces cerevisiae using a biotin-streptavidin pull-down. I identified 152 proteins that are significantly enriched in AzPt-treated samples by LC-MS/MS analysis. A subset of these proteins are involved in proteostasis and ER stress, which I confirm is induced in both AzPt- and cisplatin-treated yeast. Of interest was the identification of the ER protein folding chaperone protein disulfide isomerase (PDI), which I observe is inhibited by Pt(II) binding in vitro. Finally, I investigate PDI activity in human cancer cell lines HeLa and MDA-MB-468 following treatment with Pt(II) compounds. Extracts from platinum-treated MDA-MB-468 cells show significant PDI inhibition at low concentrations of Pt(II), and these cells appear to have constitutive activation of the unfolded protein response. PDI activity in extracts from platinum-treated HeLa cells is inhibited only at high concentrations of Pt(II), and HeLa cells do not show significant XBP1 mRNA splicing during Pt(II) treatment. Additionally, MDA-MB-468 cells are nearly three times as sensitive to Pt(II) compounds than HeLa cells. From these data, I hypothesize that basal ER stress increases sensitivity to PDI inhibition by Pt(II) binding and that this interaction enhances Pt(II)-induced cell death. / 10000-01-01

The immobilization of surface-modified polyamidoamine (PAMAM) dendrimers on the cell surface introduces a novel approach for efficient and specific cellular uptake of therapeutic-carrying nanoparticles. This cell surface-nanoparticle hybridization event takes place via bioorthogonal copper-free click chemistry between a dibenzocyclooctyne (DBCO) group on the dendrimer surface and azide-capped glycans expressed on the cell membrane through metabolic incorporation of azido sugars. This particular cell-nanoparticle hybridization method can be exploited to deliver a variety of therapeutic, genetic or fluorescent payloads directly into cells. Here, this method was employed to deliver plasmid DNA, siRNA and the hydrophobic anticancer drug Camptothecin (CPT) to enhance transfection and therapeutic efficacy. Native, acetylated, and PEGylated generation 4 (G4) PAMAM dendrimers were conjugated with DBCO. When introduced to azide expressing NIH3T3 fibroblasts and HN12 cancer cells, successful surface hybridization was achieved. The physiochemical properties of PAMAM dendrimers allowed for successful hydrophobic drug encapsulation and electrostatic nucleic acid condensation.

Chemical transformations that join two molecular components together rapidly while remaining highly efficient and selective are valued for their elegant simplicity and effectiveness in a myriad of applications. By applying the principles of ‘click’ chemistry to biology, information about molecular interactions in vivo can therefore be gained from minimally perturbing bioorthogonal coupling reactions. Developing bioorthogonal ‘click’ reactions – reactions that do not cross-react with biological components – provides new ways to accurately study biological systems at the molecular level. This thesis describes the development of such tools. Strain-promoted alkyne-nitrone cycloadditions (SPANC) represent rapid, efficient, selective, and tunable conjugation strategies that are applicable to biomolecular labelling experiments. Herein, SPANC reactions with bicyclo[6.1.0]nonyne are examined using physical organic methods to determine the stereoelectronic factors governing SPANC reactivity. Second-order rate constants (k2) of up to 1.49 M-1s-1 were measured and the resulting cycloadditions are applied to the design and synthesis of nitrone-based molecular probes. The first example of SPANC-mediated metabolic labelling in live-cell bacteria is reported, establishing SPANC as an efficient and bioorthogonal metabolic labelling strategy for cellular labelling.

No description available.

Latently-reactive conjugated polymer-coated single-walled carbon nanotubes / Single-walled carbon nanotubes (SWNTs) are intensely investigated nanomaterials that exhibit intriguing physical and optoelectronic properties. Although SWNTs are highly regarded in terms of their potential societal impact, commercialization of SWNT applications has been dampened by the difficulty in SWNT processability and purification. Current commercially viable carbon nanotube syntheses produce complex mixtures of metallic and semiconducting SWNTs, as well as amorphous carbon and metal catalyst particles. Furthermore, the ability to decorate carbon nanotube surfaces to modulate their properties is non-trivial, especially if concurrent preservation of optoelectronic properties is desired. To date, the issues of SWNT solubilization, sorting, and functionalization have been approached in a piecemeal fashion. Conjugated polymers, which are macromolecules that possess extended π-systems, have the potential to address all of these issues simultaneously. In my Thesis, I explore conjugated polymer structures to investigate (i) factors that influence dispersion selectivity, and (ii) the decoration of polymer-SWNT complexes by incorporating reactive moieties into the polymer structure. The work presented in this Thesis begins by examining the ability of conjugated polymers to sort SWNTs. To date, the selective dispersion of metallic SWNTs is unrealized. In Chapter 2, I examine the effect of the electronic nature of the conjugated backbone on the selective dispersion of SWNTs by preparing SWNT dispersions pre- and post-methylation of a pyridine-containing conjugated polymer. In doing so, I prepare a series of polymers with identical degrees of polymerization and dispersity (to minimize extraneous selectivity factors) and find that electron rich π-systems disperse only semiconducting SWNTs, while electron poor π-systems disperse relatively more metallic SWNTs. In Chapter 3, I challenge the conventional wisdom that complete backbone conjugation is required to selectively disperse semiconducting SWNTs by introducing non-conjugated linkers into the polymer backbone and demonstrating that nanotube sorting is still possible. I next examine conjugated polymers as tools that can simultaneously sort SWNTs and impart reactivity to the polymer-SWNT complex, while preserving SWNT optoelectronic properties. In Chapter 4, I incorporate azides into polyfluorene side chains and perform solution-phase Strain-Promoted Azide-Alkyne Cycloaddition (SPAAC). I show that the polymer-SWNT complex can be rapidly decorated with strained cyclooctyne derivatives, and that only pre-clicked polymer enables for sorting of semiconducting SWNTs. The sorted SWNT population can then be made water soluble post-SPAAC, enabling for the study of SWNT emission in solvents with very different polarity. In Chapter 5, I examine the reactivity of azide-containing polymer-SWNT thin films and show that thin film properties can be drastically altered. Interfacial chemistry enables for the spatially-resolved patterning of a Janus polymer-SWNT thin film containing both hydrophilic and hydrophobic regions. In Chapter 6, I devise a system to perform aqueous solution-phase chemistry on the polymer-SWNT complex. The water soluble polymer-SWNT complex allows for functionalization of the hydrophobic SWNT scaffold with polar and charged molecules. Clicking an acidochromic switch onto the polymer-SWNT surface enables for control over the SWNT emission properties. Lastly, in Chapter 7 I develop a conjugated polymer whose backbone can be functionalized using visible light. The visible-light mediated photoclick coupling of a conjugated polymer backbone enables for rapid polymer modification and is the first example of spatially-resolved conjugated polymer backbone functionalization. / Thesis / Doctor of Philosophy (PhD) / Carbon nanotubes are cylindrical shells of carbon that possess fascinating physical, optical, and electrical properties. Commercial syntheses of carbon nanotubes produce complex mixtures of impure material, and raw carbon nanotube samples further suffer from insolubility. A grand challenge preventing commercialization of carbon nanotube applications is simultaneously solubilizing, sorting, and functionalizing carbon nanotube structures while avoiding damage to the nanotube properties. To date, these issues have been tackled in a piecemeal fashion. In my Thesis, I explore conjugated polymer coatings as a solution to address these problems all at once. I investigate how modifying conjugated polymer structure can (i) influence carbon nanotube purification and (ii) produce latently-reactive polymer-nanotube complexes that can be used to decorate carbon nanotubes without damaging nanotube properties.

Thesis advisor: Amir H. Hoveyda / Chapter One: Development of a New Catalytic Click Reaction Involving Nitriles and Allenes (CuPDF)Catalytic click reactions, although small in number, have made a profound impact on chemistry research, including the fields of drug discovery, biological chemistry, and materials science. What is much needed are additional catalytic reactions that bring about the union of commonly occurring and robust functional groups, are mutually orthogonal to those that exist and offer a function other than connecting two fragments. We have developed a catalytic click process that connects a nitrile and a monosubstituted allene in the presence of commercially available B2(pin)2 and a readily accessible Cu(I) complex. The modification stage involves alkene isomerization by base and condensation with a hydrazine and both processes are performed in situ. The resulting linkages contain a robust diazaborinine that is fluorescent. We demonstrate that the click process, which we have named copper(I)-catalyzed phenoxydiazaborinine formation (CuPDF) is mutually orthogonal to copper(I)-catalyzed azide–alkyne cycloaddition (CuAAC) as well as sulfur-fluorine exchange (SuFEx). These click reactions can therefore be used for efficient synthesis of sequence-defined oligomers that may contain modifiable linkages and peptide-drug conjugates. For applications in aqueous media, we have also developed, copper(I)- and palladium-catalyzed quinoline formation (Cu/PdQNF). These latter processes generate fluorescent connectors as well. Chapter Two: Development of a Catalytic Click Reaction Involving Ketones and Allenes (CuAKA) We have developed another click reaction, this time bringing about the union of a ketone and, similar to CuPDF, a monosubstituted allene and B2(pin)2. We label this click reaction copper(I)-catalyzed allene–ketone addition or CuAKA. As a consequence of shared reactants, identifying catalysts that would allow CuAKA and CuPDF to be mutually orthogonal was at the center of our investigations. Our studies resulted in the identification of copper(I) complexes that can be used to perform a click reaction on a nitrile or a ketone. Furthermore, we found that mutual orthogonality can be achieved between CuAKA and CuAAC using an amino phosphine–Cu(I) catalyst. Computational and kinetics studies were performed that shed light on the origins of catalyst-controlled chemoselectivity. Importantly, similar to CuPDF, CuAKA can be performed in aqueous media. Chapter Three: Preparation of Multi-drug Conjugates with Mutually Orthogonal Click Reactions We show that with CuAAC, CuPDF and CuAKA, three mutually orthogonal click processes can be efficiently merged to assemble complex molecules efficiently with no protection/deprotection needed. With CuAKA, similar to CuAAC and CuPDF, being also orthogonal to SuFEx, a four-armed core molecule may be used in a similar fashion. A central finding in this part of study was the discovery that CuAKA, similar to CuAAC but unlike CuPDF, can be used to link molecules that contain acidic protons, such as phenol or a carboxylic acid moieties. Chapter Four: Controlled Rupture of CuAKA-Generated Linkages A distinct attribute of CuAKA is that it forms a linkage that is cleavable under mild aqueous oxidative conditions. We show that the tertiary hydroxy group accelerates the oxidation of the nearby C–B bond within the connector to generate a -hydroxy ketone that undergoes a retro-aldol reaction to effect rupture. We show that an aryl linker between the ketone and the carrier molecule, such a bile acid or a cell-penetrating peptide (CPP) may be used to achieve the steric and electronic parameters that are needed for optimal clicking and clipping rates. To demonstrate applicability, we used CuAKA was used for efficient linking of camptothecin, an anti-cancer agent with low selectivity, to a ketone attached to unprotected penetratin, a CPP. The ensuing release of the payload proceeded readily in a 68 mM aqueous solution of hydrogen peroxide at 37 °C with control experiments indicating that a proximal lysine residue accelerates the retro-aldol reaction. / Thesis (PhD) — Boston College, 2024. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Yes / We report a simple temperature-responsive bioconjugate system comprising superfolder green fluorescent protein (sfGFP) decorated with poly[(oligo ethylene glycol) methyl ether methacrylate] (PEGMA) polymers. We used amber suppression to site-specifically incorporate the non-canonical azide-functional amino acid p-azidophenylalanine (pAzF) into sfGFP at different positions. The azide moiety on modified sfGFP was then coupled using copper-catalyzed “click” chemistry with the alkyne terminus of a PEGMA synthesized by reversible addition–fragmentation chain transfer (RAFT) polymerization. The protein in the resulting bioconjugate was found to remain functionally active (i.e., fluorescent) after conjugation. Turbidity measurements revealed that the point of attachment of the polymer onto the protein scaffold has an impact on the thermoresponsive behavior of the resultant bioconjugate. Furthermore, small-angle X-ray scattering analysis showed the wrapping of the polymer around the protein in a temperature-dependent fashion. Our work demonstrates that standard genetic manipulation combined with an expanded genetic code provides an easy way to construct functional hybrid biomaterials where the location of the conjugation site on the protein plays an important role in determining material properties. We anticipate that our approach could be generalized for the synthesis of complex functional materials with precisely defined domain orientation, connectivity, and composition. / Engineering and Physical Sciences Research Council (EPSRC), University of Warwick, National Science Foundation (U.S.) (NSF), United States. Defense Advanced Research Projects Agency (DARPA), Seventh Framework Programme (European Commission) (FP7), European Research Council (ERC)