Chemistry Commons^™

The Malonate Template: The Key To Unlocking Novel Amino Acids, Thomas Owens

Dissertations

The “Malonate Template” provides access to various amino acids, all from a common intermediate. Herein, demonstrates the use of the malonate template to establish a synthetic route to both 2-thiohistidine and 2-thio-3-N-methyl-histidine from a benzyl methyl malonate derived intermediate. Furthermore, efforts exploiting the applicability of the malonate template for the of both 2-thiohistidine and 2-thio-3-N-methyl-histidine as a suitable alternative to methods previously described by Erdelmeier are described.

The method presented incorporates modifications to the biomimetic pathway described by Erdelmeier for the synthesis of 2-thiohisidine. By exploiting the biomimetic formation of 2-thiohisitidne’s mechanism via mass spectrometry, we …

Elucidating The Mechanisms Of Collagenase H From Hathewaya (Clostridium) Histolytica In Collagen Degradation And Developing A Cross-Linked Platform For Efficient Capture And Release Of Adeno-Associated Virus Serotype 2 (Aav2), Adjoa Otubea Bonsu

Graduate Theses and Dissertations

In biological systems, Hathewaya (Clostridium) histolytica secretes collagenases that degrade structural collagen in host tissues and cause tissue necrosis. Despite their detrimental effects, these enzymes have significant therapeutic potential by effectively digesting various collagen subtypes to treat connective tissue disorders. The bacterium produces two homologous collagenases, ColG and ColH, with a catalytic module crucial for hydrolyzing collagen and binding domains, including collagen-binding domains (CBDs) and polycystic kidney disease-like domains (PKDs), for substrate interaction.

Although the crystal structure of the catalytic module of collagenase G (ColG) has been determined, shedding light on its chew-and-digest mechanism, the structure of collagenase H (ColH) …

Development Of Dual-Scan Nuclear Magnetic Resonance (Nmr) Pulse Programs For Spin-Lattice Relaxation Measurements, Zachary Mayes

Doctoral Dissertations

This research develops and refines the Split Inversion Pulse and Recovery (SIP R) methodology for spin-lattice relaxation (T₁) measurements in NMR spectroscopy. SIP R introduces a two-scan difference technique using a split inversion pulse sequence, where the 180° pulse is split into two 90° pulses phase-shifted with respect to each other. This approach simplifies data fitting, requiring only two parameters to extract T₁ values, compared to the traditional inversion-recovery method, which needs three. The SIP-R-DS and SIP-R-S adaptations extend this framework by incorporating selective NMR resonance excitations, enhancing its applicability to cross-polarization experiments and enabling unobstructed NOE measurements. These adaptations …

Technological Development Of In-Cell Nmr: Microfluidic, Metabolomic, And Fluxomic Approaches, Nicholas Sciolino

Electronic Theses & Dissertations (2024 - present)

In the fields of structural biology, metabolomics, and fluxomics, there is a driving, technique-based concern when it comes to high-resolution spectrometry and its marriage to biological and physiological relevance. Sample preparation often involves cellular perturbation, lysate separation schemes, combinations with non-biological reagents, and timeline slack. Conceptually, the farther we get from the cell, the greater the potential disparity between what exists in vivo and our in vitro manipulations. This is particularly true when seeking to collect data on transfected targets of interest, and on sensitive metabolic equilibria that occur on the order of minutes. The question remains: if we are …

Potential Metabolite Biomarkers Of Multiple Sclerosis From Multiple Biofluids, Fatema Bhinderwala, Heidi E. Roth, Mary Filipi, Samantha Jack, Robert Powers

Robert Powers Publications

Multiple sclerosis (MS) is a chronic and progressive neurological disorder without a cure, but early intervention can slow disease progression and improve the quality of life for MS patients. Obtaining an accurate diagnosis for MS is an arduous and error-prone task that requires a combination of a detailed medical history, a comprehensive neurological exam, clinical tests such as magnetic resonance imaging, and the exclusion of other possible diseases. A simple and definitive biofluid test for MS does not exist but is highly desirable. To address this need, we have employed NMR-based metabolomics to identify potentially unique metabolite biomarkers of MS …

A Multi-Omics Investigation Into The Mechanism Of Action Of An Anti-Tubercular Fatty Acid Analog, Isin T. Sakallioglu, Amith S. Maroli, Aline De Lima Leite, Darrell D. Marshall, Boone W. Evans, Denise K. Zinniel, Patrick H. Dussault, Raul G. Barletta, Robert Powers

Patrick Dussault Publications

The mechanism of action (MoA) of a clickable fatty acid analogue 8-(2-Cyclobuten-1-yl)octanoic acid (DA-CB) has been investigated for the first time. Proteomics, metabolomics, and lipidomics were combined with a network analysis to investigate the MoA of DA-CB against Mycobacterium smegmatis (Msm). The metabolomics results showed that DA-CB has a general MoA related to that of ethionamide, a mycolic acid inhibitor that targets enoyl-ACP reductase (InhA), but DA-CB likely inhibits a step downstream from InhA. Our combined multi-omics approach showed that DA-CB appears to disrupt the pathway leading to the biosynthesis of mycolic acids, an essential mycobacterial fatty acid …

Leveraging The Hmbc To Facilitate Metabolite Identification, Fatema Bhinderwala, Thao Vu, Thomas G. Smith, Julian Kosacki, Darrell D. Marshall, Yuhang Xu, Martha D. Morton, Robert Powers

Department of Chemistry: Faculty Publications

The accuracy and ease of metabolite assignments from a complex mixture are expected to be facilitated by employing a multi-spectral approach. The 2D ¹H-¹³C HSQC and 2D ¹H-¹H-TOCSY are the experiments commonly used for metabolite assignments. The 2D ¹H-¹³C HSQC-TOCSY and 2D ¹H-¹³C HMBC are routinely used by natural products chemists but have seen minimal usage in metabolomics despite the unique information, the nearly complete ¹H-¹H and ¹H-¹³C and spin systems provided by these experiments that may improve the accuracy and reliability …

Efficient Sabre-Sheath Hyperpolarization Of Pyruvate And Other Alpha-Ketocarboxylates And Ultra-High-Qualityfactor Wireless Masing Magnetic Resonance Sensing Of Hyperpolarized Contrast Media, Isaiah Olabisi Adelabu

Wayne State University Dissertations

Over the years, there has been research geared towards mitigating disease conditions such as cancers and tumors by molecular sensing of their aberrant metabolism in humans and animal models of diseases. Some of these biomolecules of interest are pyruvate, α-ketoglutarate, and ketoisocaproate, that play a central role in eukaryotic and human metabolic pathways. Nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) have become predominant in investigating and imaging cancers and tumors for early detection and treatment. Although conventional NMR spectroscopy is limited by low sensitivity, we overcame this barrier through the use of hyperpolarization techniques. NMR hyperpolarization improves …

Illuminating Function And Enabling Inhibition At The Protein-Membrane Interface Of Glutathione Peroxidase 4., Courtney L. Labrecque

Theses and Dissertations

Membrane proteins act as gateways to cells and are responsible not only for signaling, lipid transport, and cellular homeostasis, but they are also integral in disease pathologies. One class of membrane proteins, peripheral membrane proteins (PMPs), reside in aqueous compartments of the cell until they are recruited to the membrane to perform their function. Glutathione peroxidase 4 (GPx4) is a PMP enzyme responsible for engaging the membrane and reducing lipid hydroperoxides, thereby preventing cellular death via ferroptosis. Due to its central function surrounding ferroptosis, GPx4 is an interesting drug target that has recently gained interest for inflammatory diseases as well …

Autoregulatory Mechanism Of Enzyme Activity By The Nuclear Localization Signal Of Lysine-Specific Demethylase 1, Dulmi Senanayaka, Danyun Zeng, Sahar Alishiri, William J. Martin, Khadijah I. Moore, Roshni Patel, Zigmund Luka, Alexander Hirschi, Nicholas J. Reiter

Chemistry Faculty Research and Publications

The N-terminal region of the human lysine-specific demethylase 1 (LSD1) has no predicted structural elements, contains a nuclear localization signal (NLS), undergoes multiple posttranslational modifications (PTMs), and acts as a protein-protein interaction hub. This intrinsically disordered region (IDR) extends from core LSD1 structure, resides atop the catalytic active site, and is known to be dispensable for catalysis. Here, we show differential nucleosome binding between the full-length and an N terminus deleted LSD1 and identify that a conserved NLS and PTM containing element of the N terminus contains an alpha helical structure, and that this conserved element impacts demethylation. Enzyme assays …

Investigating The Magnetic And Electronic Properties Of Cobalt(Ii) Heteroscorpionate Isomers, Jamie Dawn Freeman

Theses and Dissertations

Cobalt(II) scorpionates possess distinct electronic and magnetic properties in comparison to other first-row transition metal complexes in this ligand class. One unique property is their significantly downfield paramagnetically shifted 11B NMR signals. The utilization of a heteroscorpionate ligand Tp’ introduces asymmetry to metal scorpionates, producing cis and trans isomers. cis- and trans-Co(Tp’)2 were synthesized and separated by column chromatography. 11B NMR data show cobalt(II) homoscorpionates resonances in a narrow 20 ppm shift range around 270 ppm while cis- and trans-Co(Tp’)2 differ with signals at 230 ppm and 140 ppm, respectively. Paramagnetic NMR studies indicate both isomers maintain the same spin …

Studies Toward A Total Synthesis Of The Pyrrole-Imidazole Alkaloid Palau'amine And Computationally Assisted Stereochemical Elucidation, Brandon Fulton

Chemistry & Biochemistry Dissertations - Archive

This thesis documents progress toward a total synthesis of the marine natural product palau'amine, a stereochemically dense hexacyclic pyrrole-imidazole alkaloid with pharmaceutically relevant anticancer, antifungal, and antibacterial activity. Also described herein are several miscellaneous synthesis projects and the application of computational NMR as an aid for solving structure elucidation problems. Chapter 1 is a continuation of our lab’s prior work utilizing vinylimidazoles in cycloaddition reactions to gain rapid access to scaffolds resembling dimeric pyrrole-imidazole alkaloids such as ageliferin or palau’amine. Mechanistic aspects of these cycloadditions for both inter- and intramolecular cases were probed via time-course NMR experiments and computational studies, …

Computational Study About Noncovalent Bonding Systems Involving Halogen, Chalcogen And Pnicogen Bonds, Jia Lu

All Graduate Theses and Dissertations, Fall 2023 to Present

First terms used in this thesis are introduced and defined as follows. In the periodic table, the elements in the 17^th column are named halogen including fluorine (F), chlorine (Cl), bromine (Br) and iodine (I). The elements in the 16^th column are named chalcogen including oxygen (O), sulfur (S), selenium (Se) and tellurium (Te). The elements in the 15^th column are named pnicogen including nitrogen (N), phosphorus (P), arsenic (As) and antimony (Sb).

After hydrogen bonds (B-H⋅⋅⋅B) are well studied and understood by scientists and researchers, halogen bonds (R-X⋅⋅⋅B) have drawn attention due to the similarities in …

Scandium Triflate-Catalyzed Aromatic Aldehydic C-H Activation, Nicholas Griffin

Honors Projects

Herein described is a scandium triflate-catalyzed C-H activation of commercially available aromatic aldehydes achieved in low yields. The reaction occured in a one-pot synthesis over a two-hour duration and required minimal purification. Inclusion of a fluorine-tagged phenol allowed for reaction monitoring via ¹⁹FNMR.

Elucidating The Structure And Regulatory Interactions Of The Hotair Non-Coding Rna And The Bacterial Rnase P. Holoenzyme, Ainur Abzhanova

Dissertations (1934 -)

RNA structures and RNA-protein interactions are studied as potential drug targets, biomarkers in cancer, and can be administered as vaccines. The cancer associated HOTAIR (HOX transcript antisense RNA) exists in higher vertebrates and interacts with chromatin remodeling enzymes. We examined the thermodynamic folding properties and structural propensity of the exonic regions of HOTAIR using biophysical methods and NMR spectroscopy. Different exons of HOTAIR contain variable degrees of structural heterogeneity. We identify one exonic region, exon 4, that adopts a stable and compact fold under low magnesium concentrations. Close agreement of NMR spectroscopy and chemical probing confirm conserved base pair interactions …

Dynamics Of Diffusion, Evaporation, And Retention Of Organic Solvents In Paints By Unilateral Nmr And Hr-Mas Nmr Spectroscopy, Valeria Di Tullio, Roberta Pigliapochi, Nicholas Zumbulyadis, Silvia A. Centeno, Jaclyn Catalano, Molly Wagner, Cecil Dybowski

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

Transport of organic solvents in polymeric matrices plays a central role in many processes of interest to the coatings industry. Previous studies have focused on individual processes taking place in the solvent-paint system. In the present study, we report results on the molecular dynamics in a solvent/paint system during the entire sequence of absorption, diffusion, swelling, and evaporation processes, obtained non-invasively, in situ, and in real time using unilateral NMR relaxometry. The associated chemical structures were investigated using HR-MAS NMR spectroscopy. Four distinct ranges of molecular motion in the solvent/paint film were identified based on proton NMR transverse relaxation time …

Advances In Structure Elucidation Of Small Molecules And Peptides By Nuclear Magnetic Resonance Spectroscopy And Mass Spectrometry, Ryan D. Cohen

Seton Hall University Dissertations and Theses (ETDs)

This dissertation reports on improvements in nuclear magnetic resonance (NMR) and mass spectrometry (MS) structure determination methods of organic compounds, with particular focus on challenging cyclic peptides. A recent and important innovation in NMR spectroscopy is the combination of theoretical property predictions, such as chemical shifts, using density functional theory (DFT) to aid in challenging NMR structure assignments, such as determination of regio- and stereo-configurations. In the first part of this thesis, a comprehensive benchmark study of DFT chemical shift prediction methods was performed using experimental NMR data collected from 50 well curated compounds, which was referred to as the …

Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel

Honors Scholar Theses

Among structural biology techniques, Nuclear Magnetic Resonance (NMR) provides a holistic view of structure that is close to protein structure in situ. Namely, NMR imaging allows for the solution state of the protein to be observed, derived from Nuclear Overhauser Effect restraints (NOEs). NOEs are a distance range in which hydrogen pairs are observed to stay within range of, and therefore experimental data which computational models can be compared against. To that end, we investigated the effects of adding the NOE restraints as distance restraints in Molecular Dynamics (MD) simulations on the 24 residue HP24stab derived villin headpiece subdomain to …

The Reversible Low-Temperature Instability Of Human Dj-1 Oxidative States, Tessa Andrews, Javier Seravallic, Robert Powers

Robert Powers Publications

DJ-1 is a homodimeric protein that is centrally involved in various human diseases including Parkinson disease (PD). DJ-1 protects against oxidative damage and mitochondrial dysfunction through a homeostatic control of reactive oxygen species (ROS). DJ-1 pathology results from a loss of function, where ROS readily oxidizes a highly conserved and functionally essential cysteine (C106). The over-oxidation of DJ-1 C106 leads to a dynamically destabilized and biologically inactivated protein. An analysis of the structural stability of DJ-1 as a function of oxidative state and temperature may provide further insights into the role the protein plays in PD progression. NMR spectroscopy, circular …

Tenvr: Matlab-Based Toolbox For Environmental Research, Aleksandar I. Goranov, Rachel L. Sleighter, Dobromir A. Yordanov, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

With the advancements in science and technology, datasets become larger and more multivariate, which warrants the need for programming tools for fast data processing and multivariate statistical analysis. Here, the MATLAB-based Toolbox for Environmental Research "TEnvR" (pronounced "ten-ver") is introduced. This novel toolbox includes 44 open-source codes for automated data analysis from a multitude of techniques, such as ultraviolet-visible, fluorescence, and nuclear magnetic resonance spectroscopies, as well as from ultrahigh resolution mass spectrometry. Provided are codes for processing data (e.g., spectral corrections, formula assignment), visualization of figures, calculation of metrics, multivariate statistics, and automated work-up of large datasets. TEnvR allows …

Extracellular Poly(Hydroxybutyrate) Bioplastic Production Using Surface Display Techniques, Kevin Beaver, Ashwini Dantanarayana, Willisa Liou, Markus Babst, Shelley D. Minteer

Chemistry Faculty Research & Creative Works

Poly(hydroxybutyrate) is a biocompatible, biodegradable polyester synthesized naturally in a variety of microbial species. A greener alternative to petroleum-based plastics and sought after for biomedical applications, poly(hydroxybutyrate) has failed to break through as a leading material in the plastic industry due to its high cost of production. Specifically, the extraction of this material from within bacterial cells requires lysis of cells, which takes time, uses harsh chemicals, and starts the process again with growing new living cells. Recently, surface display of enzymes on bacterial membranes has become an emerging technique for extracellular biocatalysis. In this work, a fusion protein lpp-ompA-phaC …

Hyperpolarized Nitrogen-15 Mri Contrast Agents For Hypoxia Sensing Via Reversible Exchange With Parahydrogen, Mohammad Shah Hafez Kabir

Wayne State University Dissertations

The detection of hypoxia in hypoxic-related diseases can provide crucial information for treatment planning and assessment of therapy response. Although Positron Emission Tomography (PET) was employed as a research tool for imaging of hypoxia detection, it has several limitations. Our motivation is to develop a hyperpolarized (HP) molecular probe for hypoxia sensing. My dissertation presents the utility of Signal Amplification By Reversible Exchange in SHield Enables Alignment Transfer to Heteronuclei (SABRE-SHEATH) to hyperpolarize a wide range of N-heterocyclic compounds, which can be employed as MRI contrast agents for hypoxia sensing and other molecular imaging applications.SABRE-SHEATH is a rapid, simple, cost-effective …

Enhancing The Conformational Stability Of The Cl-Par-4 Tumor Suppressor Via Site-Directed Mutagenesis, Samjhana Pandey, Krishna K. Raut, Antoine Baudin, Lamya Djemri, David S. Libich, Komala Ponniah, Steven M. Pascal

Chemistry & Biochemistry Faculty Publications

Intrinsically disordered proteins play important roles in cell signaling, and dysregulation of these proteins is associated with several diseases. Prostate apoptosis response-4 (Par-4), an approximately 40 kilodalton proapoptotic tumor suppressor, is a predominantly intrinsically disordered protein whose downregulation has been observed in various cancers. The caspase-cleaved fragment of Par-4 (cl-Par-4) is active and plays a role in tumor suppression by inhibiting cell survival pathways. Here, we employed site-directed mutagenesis to create a cl-Par-4 point mutant (D313K). The expressed and purified D313K protein was characterized using biophysical techniques, and the results were compared to that of the wild-type (WT). We have …

Synthesis And Characterization Of Polymer Grafted Nanoparticles, Eric Gerald Ruzicka

Theses and Dissertations

This dissertation focuses on the design, synthesis, and characterization of well controlled interfaces on nanoparticle surfaces. Reversible addition-fragmentation chain transfer (RAFT) polymerization was used to synthesize block copolymers and polymer grafted silica nanoparticles (PGNs) with precise control over molecular weight, graft density, and architectures.

In the first chapter, polymer molecular weights were determined through diffusion ordered spectroscopy NMR (DOSY NMR) as an alternative to size exclusion chromatography (SEC). Polymer standards of known molecular weight were analyzed through DOSY to obtain their respective diffusion coefficients. A calibration curve was generated correlating diffusion coefficients with polymer molecular weights. The reliability of the …

Conformation Of The U12-U6atac Snrna Complex Of The Minor Spliceosome And Binding By Ntc-Related Protein Rbm22, Joanna Ciavarella

Dissertations, Theses, and Capstone Projects

Splicing of precursor messenger (pre-m)RNA is a critical process in eukaryotes in which the non-coding regions, called introns, are removed and coding regions, or exons, are ligated to form a mature mRNA. This process is catalyzed by the spliceosome, a multi-mega Dalton ribonucleoprotein complex assembled from five small nuclear ribonucleoproteins (snRNP) in the form of small nuclear (sn)RNA-protein complexes (U1, U2, U4, U5 and U6) and >100 proteins. snRNA components catalyze the two transesterification reactions while proteins perform critical roles in assembly and rearrangement. U2 and U6 snRNAs are the only snRNAs directly implicated in catalyzing the splicing of pre-mRNA. …

Meta-Analysis Reveals Both The Promises And The Challenges Of Clinical Metabolomics, Heidi E. Roth, Robert Powers

Department of Chemistry: Faculty Publications

Clinical metabolomics is a rapidly expanding field focused on identifying molecular biomarkers to aid in the efficient diagnosis and treatment of human diseases. Variations in study design, metabolomics methodologies, and investigator protocols raise serious concerns about the accuracy and reproducibility of these potential biomarkers. The explosive growth of the field has led to the recent availability of numerous replicate clinical studies, which permits an evaluation of the consistency of biomarkers identified across multiple metabolomics projects. Pancreatic ductal adenocarcinoma (PDAC) is the third-leading cause of cancer-related death and has the lowest five-year survival rate primarily due to the lack of an …

Determining The 3d Structure And Dynamics Of Mouse Notch1 Epidermal Growth Factor-Like Repeat 26 Using Nuclear Magnetic Resonance Spectroscopy, Kendra D. Jenkins

LSU Doctoral Dissertations

NOTCH is a transmembrane protein that transmits signals between cells in direct contact and alters gene expression. The signaling pathway is important because it is involved in cell fate determination. The NOTCH1 extracellular domain has 36 epidermal growth factor-like (EGF) repeats that are responsible for ligand binding. Mutations in the EGF-like repeats cause various neurological and developmental disorders. NOTCH1 signaling initiates when DSL ligands bind to EGF11-12, the minimum Ligand Binding Domain (LBD). The Abruptex region of the NOTCH1 protein (EGF24-29) is a highly glycosylated, flexible region with calcium binding sites that regulates NOTCH1 signaling and binding by interacting with …

The Synthesis Of Deuterated Isohumulones For Use As Internal Standards In Lc-Ms Stable Isotope Dilution Assays, Patrick Gleason, Bruce Hamper Dr.

Undergraduate Research Symposium

Humulones are compounds that are prevalent in the hops flowers (Humulus Lupulus) used in beer brewing. These compounds undergo isomerization during the brewing process, and the resulting isohumulones are considered to be the primary contributors to the bitter flavors present in beer. As such, quantifying their presence, and the relative presence of their homologs(n-, co-, ad-), is of great importance in the characterization of beer. In this effort, one of the homologs of humulone (co) was isolated before being subsequently isomerized and deuterated for the purpose of analyzing beer by stable isotope dilution assay mass spectrometry(SIDA-MS). The addition of this …

Bodipy-Based Light-Responsive Materials, Zhaoxiong Wan

Dissertations

The energy required for life on our planet is provided by light. In science, light is an important and powerful tool for measuring and modifying substances. For example, under the effect of illumination, light-responsive materials can change their physical and chemical properties. Photochemistry is a branch of research to study the effects of light irradiation on chemical structures and reactions. Some photochemical changes could lead to chemical bond dissociation (such as in photosynthesis) and structure isomerization (such as in the retina). Photochemistry has a strong relationship with human lives and it is essential in many ways. Among photophysics, fluorescence emission …

Determining The Structure And Activity Of A Pseudomonas Aeruginosa Protein, Ivyp2, Katherine Letsinger

Master of Science in Chemical Sciences Theses

Various biophysical methods were employed to structurally characterize and assess the activity of an important resistance factor (Ivyp2) from the multi-drug resistant Gram-negative bacterium Pseudomonas aeruginosa. This opportunistic pathogen accounts for approximately 10% of all hospital-acquired infections in the United States and contains a number of virulence factors that aid in its ability to infect and colonize immunocompromised individuals and those with cystic fibrosis. One of these factors – inhibitor of vertebrate lysozyme, or Ivy – neutralizes the lytic activity of lysozyme, an antimicrobial enzyme part of the innate immune system that hydrolyzes the linkages between bacterial cell wall subunits. …