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School of Chemistry and Biochemistry
School of Chemistry and Biochemistry
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ItemExploration of copper-catalyzed Grignard cross-coupling between 3-halo-4-alkoxybenzoates and bromoisoprenoids(Georgia Institute of Technology, 2022-05) Lutin, David J.Allylic functionality, often taking the form of terpenes, is a mainstay of marine natural products. The aryl-allyl connection is particularly common, appearing in several product classes derived from Callophycus serratus, many of which exhibit promising initial biological activities. In pursuit of several total syntheses, which leverage a copper-catalyzed Grignard cross-coupling between a 3-halo-4-alkoxybenzoate and geranylgeranyl bromide, we explored the effects of alkoxybenzoate and halogen substitutions on the coupling. By scrutinizing the constraints and influences of these protecting groups on cross-coupling success, we lay out the potential for downstream deprotection chemistry. Here, we present the results of this investigation, along with a theoretical basis for the observations.
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ItemCCSP 2.0: An Open-Source Jupyter Tool for the Prediction of Ion Mobility Collison Cross Sections in Metabolomics(Georgia Institute of Technology, 2021-05) Watson, Chandler AveryTandem mass spectrometric methods revolutionized the chemical identification landscape, allowing serums and molecules to be separated in two or more dimensions. Ion Mobility Mass Spectrometry workflows combined with liquid or gas chromatographic separation have continued to progress chemical identification and further increase the amount and confidence of these identities. Such advancements have also given birth to a new molecular descriptor: the Collision Cross Section, sparking heavy interest in the analytical-computational chemistry to compile these values for known molecules. The main shortcoming has been predicting the CCS value for new molecules such as Poly-Fluorinated Alkyl Sub-stances. Preliminary prediction software has revealed that predicting CCS values for this molecular class is possible, but it can prove temporally, computationally, and financially expensive between different licenses and genetic algorithm. This work combines open-source Python modules (NumPy, Mordred, Pandas, etc.) to construct an alternative workflow that is completely free and capable of running on a mid-specification laptop within a half hour. Using the M-H and combined M+H and M-H datasets taken from the McClean CCS Compendium, median prediction errors of 2.07% and 1.84%, respectively, were found using Support Vector Regression within 5 minutes on a mid-spec laptop, satisfying the 2.50% benchmark. This overall success illustrates the power and versatility of this workflow to produce low errors with datasets as large as 1300+ molecules and as few as 37. This script can be distributed on file-sharing sites like GitHub where other users may customize the free source code to fit their experimental needs.
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ItemDiscovery of Monoclonal Antibodies for Diagnostics and Therapies Using Conjugate Virus-like Particle Vaccines(Georgia Institute of Technology, 2021-05) Schroeder, MichelleMonoclonal antibodies (mAbs) are highly specific antigen binding proteins that are used as biological reagents, therapeutics, and in rapid diagnostics. While mAbs have extensive potential applications, their means production for small molecules and conformationally specific peptides is difficult. Here, we use a method of mAb production in which we pair conjugate virus-like particle (VLP) vaccine with hybridoma technology to produce high-affinity mAbs against three classes of molecules 1) fentanyl derivatives, 2) SARS-CoV-2 peptides, and 3) α-amanitin and microcystin LR cyclic peptide toxins. We successfully produced broad and derivative-selective mAbs against eight fentanyl derivatives. We also showed early signs of success targeting neutralizing and mutant SARS-CoV-2 peptides with conformational specificity using a heterologous prime-boost strategy. Lastly, we produced high affinity mAbs for both α-amanitin and microcystin LR, two highly toxic cyclic peptides. The early success of mAb production against the variety of targets presented in this thesis shows the viability and exceptional versatility of conjugate VLP vaccines as a means to producing mAbs.
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ItemAnalysis and illustration of primary and secondary structures of ribosomal RNA and ribosomal proteins(Georgia Institute of Technology, 2020-08) Meade, Caeden DanielRiboVision is a collection of applications housed on servers at the Georgia Institute of Technology which serves to facilitate the development of publication-quality diagrams of ribosomal RNA (rRNA) and ribosomal protein (rProtein) structures (Petrov et. al, 2014). In particular, RiboVision seeks to promote analysis of key properties of rRNA and rProteins in primary, secondary, and tertiary structures. As key semantides (ubiquitous macromolecules which carry genetic equivalent to the information intrinsic to DNA molecules and may be used by comparison to inform phylogenetic relationships), comparison of the primary and secondary structures of 16S and 18S RNA allows for the phylogenetic comparison of prokaryotic species and eukaryotic species, respectively (Fuerst, 2001). Sequence alignments are housed on the RiboVision server and stored in a MySQL database. Over the next two semesters, major improvements will be made to the server resulting in the newest edition, RiboVision3, which will feature improvements over the preceding RiboVision2 including the integration of XRNA, a program responsible for the generation of rRNA secondary structures and their exportation of their data into common computer-file formats (CSV, SVG, PDF, etc.) and the PDB Topology Viewer, a program responsible for production of protein secondary structures and their exportation into SVG image files. The core functionality of XRNA - demonstration and editing tools of rRNA secondary structures needs to be iterated upon to allow for a more diverse set of purposes, including processing of high-quality hand-edited images into formats which are compatible with on-server management and conversion into formats native to web browsers.
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ItemSynthesis of Degradable Monomers for Ring-Opening Metathesis Polymerization(Georgia Institute of Technology, 2020-05) Crolais, Alex E.Ring opening metathesis polymerization (ROMP) is a type of olefin metathesis chain-growth polymerization that has shown great versatility in the field of polymer chemistry. Although it allows polymerization of monomers containing a variety of functional groups, how effective it is in polymerizing degradable monomers is largely unknown. In this report, we demonstrate a novel synthetic pathway to synthesize an acetal-containing degradable monomer that is compatible with ROMP and the Grubbs 3 (G3) catalyst. Polymers made from this monomer were characterized by GPC analysis and underwent degradation studies. Acetals generally undergo hydrolysis in mildly acid conditions and even in biologically relevant pH ranges, so this new monomer will have potential applications in drug delivery systems. The monomer also has the capacity to have its functional groups modified, changing its functionality which will be further studied.
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ItemEffects of Nuclear-Targeted Nanoparticles on the Cell Function in Human Oral Squamous Cell Carcinoma Cells During Cisplatin Treatment(Georgia Institute of Technology, 2020-05) Mann, Breanna E.This project focuses on evaluating the effects of nanoparticles on the cellular responses in human oral squamous cell carcinoma (HSC) cells during the administration of cisplatin. Cisplatin is an effective chemotherapeutic drug used to treat numerous forms of human cancer. It is, however, also highly susceptible to creating drug resistance in cancer cells. Restriction of the mobility of HSC cells reduces its ability to spread resistant cells throughout the body. In this study, we investigated the cellular mobility of HSC cells in the presence of a combination of cisplatin and nuclear-targeted gold nanocubes. The HSC cells were treated with cisplatin with and without nanocubes to study their effects on the mobility. Trends were assessed for changes in position and velocity over time. It was found that, the presence of nanoparticles alone restricts the displacement of the HSC cells. As an extension, the effects of nanoparticles on drug resistant HCS cells was studied. HSC cells were systematically treated with cisplatin to create cisplatin-resistant cell lines. The viability of these cell lines were then tested at different levels of drug resistance. Furthermore, the effect of nuclear-targeted nanoparticles on bypassing drug resistance in cisplatin-resistant HSC cells were evaluated. Trends amongst cell resistance and nanoparticle presence were assessed. Furthermore, the radius and surface charge were analyzed to understand characteristics that lead to optimal uptake. Additionally, the growth and changes in uptake experienced by cisplatin resistant cells were analyzed to gain insight into how these changes effected uptake of the nanoparticles.