Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2005. / Vita. / Includes bibliographical references. / The success of cisplatin as an anticancer drug is attributed to the ability of the platinum compound to damage DNA and subsequently induce apoptosis. Details of the cellular processing of cisplatin-damaged DNA can provide invaluable insight into the rational design of cisplatin analogues or combination therapies. Chapter I provides a survey of recent developments in the understanding of the mechanism of cisplatin action and summarizes relevant platinum-based anticancer compounds. Chapter 2 describes a series of estrogen-tethered platinum(IV) complexes (BEPn, n=l -5) that were synthesized, evaluated for their ability to upregulate HMGB1 and screened for cytotoxicity against human breast cancer cell lines. All BEPn complexes induced the overexpression of HMGB I in ER(+) MCF-7 cells. BEP3 was nearly twice as cytotoxic in ER(+) MC'F-7 cells than in ER(-) HCC-1937 cells. This result suggests the possibility of using compounds in this class specifically to target ER(+) malignancies, such as breast and ovarian cancers. In addition, the series of BEPn compounds provide an example of a useful strategy in the development of platinum-containing anticancer agents, namely, using mechanistic insights to aid in the rational design of new complexes. / (cont.) The strategy of exploiting estrogen-induced HMGBI upregulation to sensitize ER(+) cells to platinum was further pursued in work described in chapters 3 and 4. Chapter 3 reports the synthesis and characterization of a series of platinum(IV)-estrogen conjugates derived from carboplatin. Although these BECPn complexes were moderately cytotoxic in ER(+) MCF-7 human breast cancer cells, no differential cytotoxicity was observed as compared to ER(-) HCC- 1937 cells. However, these compounds represent the first example of a biomolecule-tethered platinum(IV) complex that reduces to yield carboplatin in cells. The platinum estrogen conjugate described in chapter 4 was designed not only to induce upregulation of HMGB I but also to enter ER(+) cells selectively. Unlike the BEP and BECP compounds, BEEP was designed to maintain affinity for the estrogen receptor and by tethering platinum to estradiol through the 17c-position of the steroid ring. Compounds with affinity for the estrogen receptor, which is overexpressed in breast and ovarian cancers, are selectively taken up into ER(+) cells. Unexpectedly, BEEP had very low affinity for the estrogen receptor and was therefore equally cytotoxic in ER(+) and ER(-) human breast cancer cell lines. / (cont.) A common feature of many cancers is overexpression of the folate receptor, which is responsible for the uptake of folic acid. Therefore targeting the folic receptor is an attractive method for achieving selective uptake in cancer cells. Chapter 5 describes the synthesis and biological activity of a folic acid-tethered platinum(lV) compound, which demonstrates the validity of this premise. The nuclear protein HMGBI has recently been discovered to function as an extracellular signaling agent. Because of oxygen deprivation, the core of a solid tumor dies by necrosis and passively releases HMGB I into the extracellular environment. This characteristic of solid tumors leads to the hypothesis that extracellular HMGB I is taken up by surrounding viable tumor tissue and mediates cisplatin sensitivity. The final chapter investigates the capability of exogenously administered HMGB to modulate the cytotoxicity of cisplatin and trans-DDP in human cancer cells. The Appendix sections provide detailed experimental protocols for several useful laboratory methods. In Appendix A, a procedure for isolation of nuclei from cisplatin-treated cells is presented. / (cont.) The nuclei were subsequently used by our collaborators to examine the post- translational modifications of histones induced by cisplatin exposure. A protocol for isolation of protein extracts from formalin-fixed paraffin-embedded tissue is described in Appendix B. In addition, the extracts were probed by western blot analysis to examine the expression levels of HMGB1 in clinical testicular seminoma samples. Appendix C provides a solid-phase synthetic methodology for the preparation of peptide-conjugated platinum(IV) compounds. / by Katie R. Barnes. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1996. / Includes bibliographical references. / by Joel Stephen Freundlich. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2010. / Cataloged from PDF version of thesis. Vita. / Includes bibliographical references. / Plant alkaloid biosynthesis produces many natural products with medicinal value. For example, vinblastine and vincristine from Catharanthus roseus monoterpene indole alkaloid biosynthesis, and camptothecin derivatives from Ophiorrhiza pumila quinoline alkaloid biosynthesis, are anticancer agents currently used in the clinic. Strictosidine synthase is a key enzyme in the biosynthesis of these medicinal natural products, but its narrow substrate scope limits precursor-directed biosynthesis of alkaloid analogs in plant cell cultures. I describe two new assays to monitor strictosidine synthase activity, which enable the rapid screening of enzyme mutant libraries to identify two strictosidine synthase variants that accept new substrates. A transgenic plant cell culture that contains one of these mutants generated "unnatural" monoterpene indole alkaloids in C. roseus. I also describe the characterization of 0. pumila strictosidine synthase, which has considerably broader substrate specificity than the homologous enzyme from C. roseus. This alternative catalyst is a candidate enzyme for construction of transgenic cell cultures, and potentially useful as a biocatalyst, since it catalyzes the asymmetric Pictet- Spengler reaction to form tetrahydro-p-carboline pharmacophores. I used computer modeling to propose a model for how strictosidine synthase achieves its high stereoselectivity; this model may be used to engineer a Pictet-Spenglerase that forms the alternative stereoisomer. / (cont.) Such a stereocomplementary catalyst would be useful in biocatalysis, giving the synthetic organic chemist access to both stereoisomers in high enantiomeric purity. Finally, I describe the total synthesis of stereoisomer mixtures of indole alkaloid precursors, and use these mixtures to determine the stereoselectivity of strictosidine synthase and two subsequent enzymes in monoterpene indole alkaloid biosynthesis. The combination of chemical synthesis and the recruitment of enzymes from unrelated biosynthetic pathways could generate diverse alkaloid libraries, containing different stereoisomers, for bioactivity evaluation. / by Peter Bernhardt. / Ph.D.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1999. / Vita. / Includes bibliographical references. / by David S. Rovnyak. / Ph.D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2015. / Vita. Cataloged from PDF version of thesis. / Includes bibliographical references. / Chemical sensors that identify and monitor volatile organic compounds (VOCs) have an important role in assessing public security, food and water quality, industrial environment, and health. The fabrication of carbon-based sensors by printing, dip coating, drop casting, or drawing has advantages of being simple and low-cost without the need for highly specialized facilities. We have investigated the fabrication of sensors both by drop casting and drawing. Single-walled carbon nanotubes (SWCNT) electronic and spectroscopic properties for sensory applications are described. SWCNTs have unique properties wherein their conductance can be altered by environmental effects. These carbon nanomaterials can be easily integrated into a chemiresitive device to detect various analytes. In our studies using the drop cast method, we noncovalently functionalized SWCNT with a trifunctional selector that has three important properties: it noncovalently functionalizes SWCNTs with cofacial n-n interactions, it binds to cyclohexanone (a target analyte for explosive detection) via hydrogen bond, and it improves the overall robustness of SWCNT-based chemiresistors (e.g., humidity and heat). In our other studies, we fabricated sensors by drawing. Abrasion is a safe, simple, solvent-free, and low cost method for deposition of carbon-based materials onto a substrate. We successfully demonstrated fabrication on a wide variety of substrates (e.g., weighing paper, polymethyl methacrylate, silicon, and adhesive tape) of fully-drawn chemical sensors on a chip that can detect in real time parts-per-million (ppm) quantities of various vapors using SWCNTs as sensing materials and graphite as electrodes. This fabrication methodology does not require specialized facilities (e.g., clean room, thermal evaporator) and can be performed entirely on a desktop (with appropriate ventilation and safety precautions for handling nanomaterials). We also extended the abrasion method to detect anions such as fluoride (use to manufacture nuclear weapons) and cyanide (chemical warfare agent). These sensor are highly sensitive detecting the United State Environmental Protection Agency (EPA) maximum contaminant level (MCL) of fluoride and cyanide selectively. / by Kelvin Mitchell Frazier. / Ph. D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Solid-state nuclear magnetic resonance (SSNMR) has been frequently used to elucidate the structure and dynamics of membrane proteins and fibrils that are difficult to characterize by Xray crystallography or solution NMR. This thesis focuses on the structure determination and the proton conduction mechanism of the full-length matrix protein 2 (M2) of influenza A virus. The M2 membrane protein can be separated into three domains: an N-terminal ectodomain (1-2 1), an cc-helical transmembrane domain (TM) (22-46) connected to an amphipathic helix (AH) and a Cterminal cytoplasmic tail (63-97). The TM domain of M2 is responsible for proton conduction ant the ectodomain has been the target for vaccine development. The cytoplasmic tail has been implicated in M2 interaction with other viral proteins from mutagenesis studies. Given the importance of both N- and C-termini, it is essential to determine the structure and the dynamics of M2FL. Furthermore, we are interested in how the cytoplasmic tail affects proton conduction and the interaction of the anti-viral drug amantadine with M2 in the presence of the C-terminus. Using uniformly ¹³C, ¹⁵N-labeled M2FL, our water-selected 2D ¹³C-¹³C correlation experiment indicated that N- and C- termini are on the surface of the lipid bilayer moreover combining with chemical shift prediction, we determined that these two domains are mostly disordered. Deleting the ectodomain of M2FL (M2(21-97)) proved that a small [beta]-strand is located at the N-terminus only in the DMPC-bound state. The M2 conformation is found to be cholesterol-dependent since [beta]-strand is not found in cholesterol-rich membranes. M2(21-97) shows cationic histidine at higher pH, in contrast to M2TM, indicating that the cytoplasmic tail shifts the His37 pKa equilibria. Quantification of the ¹⁵N intensities revealed two pKa's as opposed to of four in M2TM suggesting cooperative proton binding. A possible explanation is that the large number of positively charged residues in the cytoplasmic tail facilitates proton conduction. The cytoplasmic tail was also found to restore drug-binding as amantadine no longer binds to M2(21-61) a in virus-mimetic membrane. These results have extended our understanding of the influence of the cytoplasmic domain on the structure and proton conduction of M2. / by Shu-Yu Liao. / Ph. D.

Thesis (Ph. D. in Biological Chemistry)--Massachusetts Institute of Technology, Dept. of Chemistry, 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Major impediments to the full utility of current and potential drugs include issues of resistance and delivery. To address these challenges, in this thesis two directions of research were pursued: (1) the use of multivalent polymeric inhibitors to overcome drug resistance in human and avian influenza and (2) low-viscosity, high-concentration protein suspensions for therapeutic antibody, in particular monoclonal antibody (MAb), delivery. (1) Influenza resistance to small molecule neuraminidase (NA) inhibitors is spreading. Little emphasis, however, has been placed on alternative formulations of inhibitors. We investigated the design of multivalent antivirals, wherein small molecule ligands of viral proteins are conjugated via a linker to a linear polymeric backbone. Unexpectedly, we found that a poly-L-glutamine bearing pendant zanamivir (ZA) groups is at least as potent as those containing both ZA and sialic acid (SA). By examining the structure-activity relationship of such monofunctional conjugates, we show that the most potent one has 10% ZA attached to a neutral, high molecular weight backbone through a short alkyl linker. Importantly, we also demonstrate that such a polymer conjugate entirely compensates for weakened binding in and has 2,000-fold enhanced anti-viral potency against, ZA-resistant strains. We further evaluated this optimized inhibitor in vivo and observed that it is an effective therapeutic of established infection in ferrets and reduces viral titers up to 190-fold when used as a combined prophylactic/therapeutic in mice. Additionally, we see no evidence that the conjugate stimulates an immune response in mice upon repeat administration. (2) Typically, high doses of MAb therapeutics are required for clinical effect. Ideally, these MAbs would be delivered by subcutaneous injection of a small liquid volume. Such highly concentrated MAb solutions, however, are far more viscous than the 50 centipose (cP) permitted by the FDA. We evaluated approaches to reduce formulation viscosity by forming protein suspensions. Aqueous suspensions induced by poly(ethylene glycol), precipitating salts, or ethanol actually increased viscosity. However, non-aqueous suspensions of amorphous antibody powders in organic solvents that have s 1 hydrogen atom available for hydrogen-bonding, exhibited up to a 38-fold decrease in viscosity. / by Alisha K. Weight. / Ph.D.in Biological Chemistry

Thesis: S.M., Massachusetts Institute of Technology, Department of Chemistry, 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Porous aromatic frameworks (PAFs) have recently emerged as a new class of materials with impressive stability and high surface area, which led to their applications in gas storage and small molecule recognition. Herein, the synthesis and functionalization of PAFs were described, and their potential use as selective oligomerization for fuel upgrading was investigated. However, functionalized PAFs showed undesired reactivity possibly due to low rate of substrate and product diffusion in and out of the framework. On the other hand, a novel C3-symmetric hydrogen bonding receptor was synthesized and investigated for its use as size- and regioselective catalyst. It was demonstrated that the receptor was able to distinguish substrates with different functional groups in binding experiments, and was able to improve SN2 reaction yield although with some significant limitations. / by Anont Tanaset. / S.M.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2008. / Vita. / Includes bibliographical references. / To study the nucleotide reduction system in Archaea, we have expressed the Archaeoglobus fulgidus gene encoding the adenosylcobalamin (AdoCbl) dependent ribonucleotide reductase (afuRNR) protein. Initial characterization of the recombinant afuRNR indicates that it reduces CDP to dCDP in an AdoCbl dependent manner. One astonishing finding is the capacity of afuRNR to reduce both diphosphate and triphosphate nucleosides to their respective deoxynucleosides. This is the first instance of a RNR displaying dual substrate selectivity. Our investigation of redox regulation focused on thioredoxin reductase (TrR) and thioredoxin (Tr). In addition to providing the reducing equivalents for many RNRs, TrRs are involved in maintaining the intracellular redox environment. This process typically involves the transfer of electrons from NADPH to Trs. Here the characterization of a putative TrR (Ta0984) and Tr (Ta0866) from Thermoplasma acidophilum are presented. To explore the apparent inability of taTrR to use NADPH or NADH as a reductant, we carried out a complete electrochemical characterization, which ruled out redox potential as the source of this non-reactivity. A 2.35 A resolution structure of taTrR, also presented here, shows that despite the overall structural similarity to the wellcharacterized TrR from E. coli, the "NADPH binding pocket" is not conserved. E. coli TrR residues implicated in NADPH binding, H175, R176, R177, and R181 have been substituted with E185, M186, Y187, and M191 in the ta protein. Thus, we have identified a Tr and TrR protein system from T. acidophilum for which the TrR shares overall structural and redox properties with other TrRs, but lacks the appropriate binding motif to use the standard NADPH reductant. Our discovery of a TrR that does not use NADPH provides a new twist in redox regulation.Further, four A. fulgidus genes encoding four Trs (afuTr 1, afuTr 2, afuTr 3, and afuTr 4) proteins have been identified and their proteins expressed. Electrochemical characterization via protein-film voltammetry shows that the afuTrs reduction potentials are -32 mV for afuTr 1, -301 mV for afuTr 2, -287 mV for afuTr 3, and -309 mV for afuTr 4. This set of reduction potentials found in this Archaeon represents the greatest range in a specific organism. / by Hector Hugo Hernandez. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2009. / Includes bibliographical references (p. 147-155). / In this thesis research, I implemented a terahertz generation scheme that enables high-field near-single-cycle terahertz (THz) pulse generation via optical rectification in a LiNbO3 (LN) crystal. I also developed a method for the non reconfigurable generation of high-intensity multiple-cycle THz fields aimed to more efficiently deliver THz energy to resonant samples. A novel free-space THz-pump/THz-probe setup enabled time-resolved measurement of ultrafast nonlinear electronic responses in doped bulk semiconductor samples. The ability to spectrally and temporally resolve the response of the semiconductor sample using a THz probe allowed us to uncover both the dynamics of impact ionization and interesting phonon-plasma interactions in indium antimonide (InSb) for the first time. Nonlinear vibrational responses in LN were ob-served first in a dual THz beam setup on an integrated LN waveguide platform with optical probing to reveal the generation of terahertz second harmonic signals and also in THz transmission measurements in cooled LN where THz intensity-dependent self-phase modulation and harmonic generation were observed. An outlook and preliminary results toward implementation and observation of high-field THz-driven responses in ferroelectric materials are given in the final chapter of this thesis. / by Ka-Lo Yeh. / Ph.D.