Chemistry

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Access status: Open Access ,
From Metabolite Profiling To Biomolecule Quantification: Modern Mass Spectrometry Techniques Applied To Biological Research
(2025-07-23) Parasecolo, Leonardo; Ifa, Demian
Mass spectrometry (MS) is a versatile and powerful analytical technique that has revolutionized our ability to analyze complex biological systems. In this dissertation, we explore novel applications of various MS methodologies, including paper spray ionization (PSI), sandpaper spray ionization (SSI), matrix-assisted laser desorption/ionization (MALDI), and liquid chromatography-tandem mass spectrometry (LC-MS/MS). These techniques were applied to profile, detect, and quantify a wide range of metabolites and biomolecules across different biological contexts. At York University, we employed sandpaper spray ionization mass spectrometry for the rapid and comprehensive analysis of maple leaves infected with distinct fungal species. This approach demonstrated the capability of this high-throughput and solvent-efficient screening technique to differentiate fungal infections by analyzing directly from the leaf surface without requiring sample preparation. The study highlighted SSI-MS as a powerful tool for in situ metabolomic analysis of plant-pathogen interactions, enabling the detection of key metabolic changes associated with different fungal infections. Additionally, we developed a MALDI-high resolution MS method for the absolute quantification of the phytoalexins camalexin and scopoletin in Arabidopsis thaliana, providing novel insights into the plant’s biochemical responses to environmental stressors. Furthermore, a semi-quantitative version of this method was employed to perform relative quantification of a broader set of phytoalexins in wild-type and mutant Arabidopsis thaliana plants lacking key transcription factors involved in their production. In collaboration with Nucro-Technics Laboratories, we developed an ultra-sensitive immunoprecipitation-LC-MS/MS method for the quantification of low-abundance proteins in rat serum. This approach significantly enhances detection precision and sensitivity, allowing for the accurate quantification of trace-level proteins (≥ 1 ng/mL) in plasma while requiring small sample volumes (≤ 50 μL). This method meets the increasing demand for highly sensitive and reliable biomolecular assays in clinical and pharmaceutical research. These applications underscore the adaptability and efficacy of modern mass spectrometry in tackling diverse biological questions, ranging from plant-pathogen interactions to clinical biomolecule analysis. The methodologies developed and optimized in this dissertation provide valuable tools for MS-based metabolite profiling, biomolecule quantification, and the exploration of complex biological matrices. This research lays the foundation for future advancements in high-throughput screening, precision medicine, and plant metabolic studies.
Access status: Open Access ,
Pioneering The Development Of CRISPR-Guided Photooxidation Of Guanine For Guanine-To-Cytosine Conversion In Cellular DNA
(2025-07-23) Frias, Nicole Adrianna; Hili, Ryan
Adapted as an RNA-guided genome-editing system, CRISPR/Cas9 has served promising potential in the treatment of human genetic diseases. Specifically, enzymatic base editors can effectively catalyze single-nucleotide conversions in cellular DNA through the use of a catalytically-dead Cas9 and a deaminase. Current base editors primarily consist of cytosine and adenine base editors, which can create C-to-T and A-to-G conversions through deamination of the substrate, respectively. However, the use of enzyme-based approaches can give rise to exasperated levels of non-specific editing. Therefore, new base editors are needed to expand the mutagenic repertoire of current base editing technologies, as well as reduce off-target effects associated with current editors. For this, the photooxidation of guanine was explored as a method of achieving precise G-to-C conversions in the cellular genome. The development of the first chemical base editor could therefore allow for the utmost spatiotemporal precision, potentially alleviating the off-target effects associated with enzymatic editors.
Access status: Open Access ,
Protein Structure Dynamics In Gram Negative Bacterial Secretion Systems
(2025-04-10) Nicholas Joseph Bragagnolo; Audette, Gerald F.
Bacteria use a variety of secretion systems that enhance their virulence. The conjugative type IV secretion system attributes transmission of mobile DNA elements in bacteria, whereas type IV pili are akin to the type II secretion system and are responsible for host adhesion and twitching motility. Understanding the structure and function of components in these systems has the potential to elucidate the mechanisms of bacterial commensalism and antagonism, and would aid in the development of inhibitors to bacterial pathogenesis by disrupting the tools virulent species use for stable, long-term infections. The entry exclusion protein of the F-like type IV secretion system, TraG, consists of a membrane-bound N-terminal domain and a periplasmic C-terminal domain, denoted TraG*. TraG* is essential in preventing redundant DNA transfer through interaction with a cognate TraS in the inner membrane of the recipient cell to prevent conjugation when the recipient cell carries the same plasmid. Using a multitude of biophysical methods including thermofluor, circular dichroism, collision induced unfolding mass spectrometry, and small angle X-ray scattering, the structural dynamics of TraG* was investigated. This allowed for the characterisation of the 50 N-terminal residues, the 77 C-terminal residues, and the TraS-interacting region of the protein as highly dynamic, providing evidence for the mechanism of the long-distance interactions made by TraG. This dissertation also describes the 1.3 Å crystal structure of the N-terminally truncated Type IV pilin of Pseudomonas aeruginosa from strain P1 (ΔP1), the first structure of its phylogenetically linked group (group Ia) to be reported. The structure was solved from X-ray diffraction data collected 20 years ago with a molecular replacement search model generated using AlphaFold. Comparisons of the ΔP1 structure to other Type IV pilins using ProSMART indicated that there are cases of higher structural homology between different phylogenetic groups of P. aeruginosa than there are between pilins from the same phylogenetic group, indicating that the classification of pilins based on structural homology may be necessary in developing anti-virulence drugs and vaccines.
Access status: Open Access ,
Chemical Approaches To Study Modified Nucleic Acids
(2025-04-10) Cauley-Le Fevre, Morgan Beatty Pierre; Hili, Ryan
Chemical modifications govern the fate and function of nucleic acids. The methylation of the N-6 position of adenosine (m6A) in RNA is the most studied naturally occurring modification. Methylation of this position is regulated by a complex, dynamic interplay between enzymes known as methyltransferases (writers) and demethylases (erasers). Modifications on functional nucleic acid polymers (aptamers), have also been reported to increase binding affinity and stability in vivo towards a particular target. Ligase-catalyzed OligOnucleotide polymERization (LOOPER) is a method to access hetermultivalent aptamers, and the method was successful in the evolution of a modified aptamer towards human α-thrombin. However, LOOPER requires a platform to produce these modified aptamers at scale. Chapter 2 of this thesis focusses on my work to create such a platform, using solid-phase DNA synthesis and orthogonal protecting groups. Two protecting groups were synthesized, and one, allyloxy carbonyl (alloc) was taken forward for this platform due to the ease of the solution-phase deprotection step. Synthesis of the modified phosphoramidite equipped with alloc was undertaken, and the phosphoramidite was eventually incorporated into an oligonucleotide. The protecting group was successfully removed on-instrument, however several coupling protocols to install the chemical modifiers for the aptamer were ultimately unsuccessful. In Chapter 3 of this thesis, I focussed on the optimisation of some hit compounds towards m6A demethylase ALKBH5, which has been shown to be up- or down-regulation in a variety of cancerous and non-cancerous disease. Selective inhibition of the protein would greatly facilitate knowledge generation around its associated pathologies. From two DNA-encoded library hits towards the protein, hit optimization synthesis of two molecules was performed. A fluorescence polarization (FP) assay to determine IC50 data from these compounds was produced and was successfully validated. Unfortunately, with little material of the two compounds generated, only limited FP data was generated, and the results were inconclusive.
Access status: Open Access ,
Photo-Oxidative Sequencing Approach For Methylated Guanosine In RNA
(2025-04-10) Chung Kim Chung, Kimberley Alexandra; Hili, Ryan
In recent years, RNA-modifying enzymes have gained significant attention due to their impact on critical RNA-based processes, and consequently human pathology. However, identifying sites of modifications throughout the cellular transcriptome remains challenging largely due to the lack of accurate and sensitive detection technologies. Indeed, N2-methylation at guanosine such as N2-methylated guanosine (m2G) and N2,N2-dimethylated guanosine (m22G) are prevalent modifications found in RNA but their functional studies are limited due to the absence of sequencing methods. While m22G creates termination during reverse transcription and can often be detected during sequencing due to its high error signature, m2G does not affect Watson−Crick−Franklin base pairing, and therefore cannot be distinguished from unmodified guanosine. Although computational predictors exist for m2G, there are no direct sequencing method available. In this thesis, the first chemistry-based sequencing method for N2-methylated guanosine at the single-nucleotide level is described. This method takes advantage of the chemoselectivity of photoredox chemistry to enable selective photo-oxidation of m2G and m22G in the presence of guanosine. Under blue light, using riboflavin as a photocatalyst and selectfluor as an oxidant, N2-methylated guanosines convert into their respective 2,5-diamino-4H-imidazol-4-one (Iz) and 8-oxoguanine (OG) products resulting in different mutation signature after sequencing. The limitation and scope of this method were further evaluated and extended to explore other methylated guanosine types such as m1G and generate the first database of high confidence m2G sites in multiple RNA types in human lung cancer cell line.
Access status: Open Access ,
Zinc And Aluminum Complexes Bearing Monoanionic Bidentate Cyclic Guanidine-Ethenolate Or Amidine-Ethenolate Ligands For The Ring Opening Polymerization Of Lactide
(2025-04-10) Campos Rivera, Lya Evelyn; Lavoie, Gino G.
Aluminum and zinc complexes bearing bidentate guanidine-ethenolate ligands are reported and used in the solvent-free polymerization of rac-lactide at 130 °C. Solid-state structures of the zinc complexes showed a distorted tetrahedral geometry. Solid-state structures of the bischelated aluminum complex showed dynamic trigonal pyramidal and square-based pyramidal geometries. The spectra provide evidence of hydroxy and L1H end group for PLA generated from Zn(L1)2 with and without BnOH, as well as from Zn(L1)Et with BnOH. These terminated PLA chains result from water contaminants present in LA. However, it remains challenging to determine whether AMM or CIM is the dominant mechanism. In contrast, Zn(OBn)2, both with and without BnOH, generated polymers with hydroxy, OBn, and macrocycles sodium adducted cationized open chain polymers. The presence of OBn end groups indicates that the polymerization proceeded through CIM. All spectra indicated transesterification side reactions present due to peak separations of m/z 72 g/mol. The π-accepting properties of the guanidine moiety in the Zn(Lx)2 complexes, as estimated by the 31P NMR chemical shift of the corresponding N-heterocyclic carbene–phosphinidene adduct, resulted in a negative correlation in the rate for the ROP of LA polymerization using zinc complexes produced polylactic acid (PLA) with a heterotactic bias (Pr = 0.52–0.65) with molecular weights comparable to those obtained in the SnOct2 control experiment. The most active zinc catalyst reported herein, Zn(L1)2 is only about three times less active than SnOct2, for the ROP of rac-LA at 130 ℃. For the polymerization of L-LA under industrial conditions, at 150 ℃, Zn(L1)2 is only about 14.4 times slower compared to Sn(Oct)2, and about only 2.5 times slower compared to Herres-Pawlis et al. zinc(II) Schiff base complex. Interestingly, the addition of benzyl alcohol as a co-initiator for the polymerization using Zn(L1)Et readily produced Zn(L1)2 and Zn(OBn)2, with both complexes giving comparable activities. Polymerization studies showed that Zn(OBn)2 is only 2.5 times less active than Sn(Oct)2 but with twice as large molecular weights. The Zn(L5)Et complex, in the presence of BnOH, resulted in a reaction rate three times faster than the monochelated guanidine-ethenolate Zn(L1)Et complex, due to the enhanced Lewis acidity of the metal center caused by the presence of the CAAI fragment. MALDI-TOF MS was used to determine the end groups of the polymer chain.
Access status: Open Access ,
Exploring The Evolution Process And Requirements For Molecular Recognition Via Highly Functionalized Aptamers
(2025-04-10) Movahedi, Matina; Hili, Ryan
Expanding the chemical diversity of oligonucleotide libraries has allowed the evolution of synthetic nucleic acid polymers with enhanced molecular recognition and catalytic abilities. Thus, synthetic methods that enable the sequence-defined incorporation of diverse chemical modifications in developing novel or improved nucleic acid polymers and selection methods that facilitate efficient enrichment of high-quality aptamers are of particular importance in identifying novel or improved nucleic acid polymers for diagnostics and therapeutics. In this thesis, the advancement of ligase-catalyzed oligonucleotide polymerization (LOOPER) is discussed as a method to increase the chemical diversity of oligonucleotide libraries and its application towards the evolution of modified aptamers. An evaluation of the use of different ligases, scope and number of modifications, sequence space, and evolutionary outcomes from in vitro selections is provided, along with a critical lens on challenges to be addressed for the method to mature into a more widely adapted technology. Further to this, a variety of selection methods are discussed striving towards efficient single-round aptamer selection. The successful single-round aptamer selection against Thrombin is an inspiring outcome for future selections.
Access status: Open Access ,
Characterizing the Interactions of Aptamers with their Ligands using Isothermal Titration Calorimetry and Fluorescence Spectrometry
(2025-04-10) Thavaseelan, Kabisan; Johnson, Philip E.
Aptamers are short single-stranded DNA or RNA molecules that are selected to bind a target often with high affinity and specificity. Some of these targets include small molecules, proteins, nucleic acids, cells and tissues. Isothermal Titration Calorimetry (ITC) and Fluorescence Spectrometry were employed to characterize the binding interactions of aptamers with their ligands. This dissertation comprises two separate research projects; in the first project, ITC was used to explore how the binding affinity of structure-switching aptamers toward their ligand varies when altering the NaCl concentration. It was shown that the binding affinity of MN19, a variant of the cocaine-binding aptamer, decreases when the NaCl concentration is increased from 140 mM to 1000 mM. The affinity increases again when the NaCl concentration is increased to 2000 mM. The next project showcases the use of fluorescence spectrometry to characterize the interactions of methylene blue with different aptamers. Methylene blue is a redox-reporter which is used in Electrochemical aptamer-based biosensing platforms. It was shown that methylene blue binds to the MN19 aptamer, and therefore, it was of interest to see if methylene blue binds to other aptamers and to explore any similarities in their aptamer structures. Fluorescence spectrometry was used to see if methylene blue binds to other aptamers by measuring the change in fluorescence intensity of methylene blue and if binding occurred, the binding affinity was quantified. It was determined that methylene blue may be interacting and binding tightly to DNA aptamer structures which includes bulges and stem-loops but may be binding very weakly to duplex DNA such as the Dickerson Drew Dodecamer and a Hexamer.
Access status: Open Access ,
A Passive Air Sampling Technique For Ultra-Trace Quantitation Of Gas-Phase Perfluoroalkyl Carboxylic Acids
(2024-11-07) Vanhauwaert, Eric; VandenBoer, Trevor ; Young, Cora
Perfluoroalkyl carboxylic acids (PFCAs) are persistent chemicals distributed ubiquitously in the environmental despite their anthropogenic origin. Recent studies have shown that atmospheric transport is an important transport mechanism for PFCAs. Despite this, measuring mixing ratios of gaseous PFCAs in the atmosphere has been an analytical challenge, limiting the availability of atmospheric measurements. A new nylon-based passive air sampling (PAS) technique addresses many of these challenges by offering a cost effective, low-labour solution. These samplers were calibrated for trifluoroacetic acid (TFA) in an atmospheric chamber and field measurements were compared to measurements from an ambient ion monitoring ion chromatography mass spectrometer, where good agreement was found. They were also deployed in various locations in Canada for gas-phase PFCA measurements which revealed many different trends, including the wastewater treatment plant as a point source of gas-phase TFA. These measurements have enhanced our understanding of PFCAs with calibrated, cost-effective samplers capable of ultra-trace measurements.
Access status: Open Access ,
The Utility Of Hydrogen Deuterium Exchange Mass Spectrometry For Characterization Of Proteins And Their Interactions.
(2024-11-07) Wolf, Esther Zvia; Wilson, Derek
Mass spectrometry (MS) offers immense versatility to the structural biology field. Particularly, Hydrogen Deuterium Exchange MS (HDX-MS) can overcome obstacles encountered by more traditional, higher resolution structural characterization methods. What happens when your protein system is just too big, dynamic, dilute, or poorly soluble? Recent advancements in structural prediction and HDX-MS automation have enabled some of the fastest data turnaround to date. This work follows many different scenarios where HDX-MS and MS have been employed, including protein-peptide interactions of the Bcl-2 family, affinity ranking and prediction of a focused small molecule library targeting WDR5, USP3 binding characterization of a small molecule screen hit, the detection of proteolysis targeting chimera (PROTAC)-induced ternary complex formation, and epitope mapping of antibodies targeting the SARS-CoV-2 Spike protein, all made possible by the collaboration of the Dickinson Lab (University of Chicago), Icosagen (Estonia), the Ingerman-James Lab (University of North Carolina at Chapel Hill), and the Structural Genomics Consortium.
Access status: Open Access ,
Exploring the heterogeneous uptake of gas-phase PFCAs to the condensed phase
(2024-07-18) Indos, Dylan James; Young, Cora
Perfluoroalkyl carboxylic acids (PFCAs) are a class of per- and polyfluoroalkyl substances (PFAS) which are completely fluorinated, accompanied by a carboxylic head functional group. With varying toxic effects on animals, plants, and humans, it has become imperative to understand the fate of these compounds in the atmosphere. The most important aspect in helping define a chemical’s environmental fate is its physicochemical properties and partition tendencies. Partitioning of a gas phase chemical from air to water begins with the heterogeneous uptake of the gas-phase molecule onto the liquid’s surface. Heterogeneous reactions are important in identifying sinks and the fate of atmospheric gas-phase chemicals. Currently there exists no experimental gas-phase uptake data for gas-phase PFCAs onto liquid surfaces which limits our understanding on their fate, movement, and sinks in the atmosphere. This work will aim to fill in gaps of knowledge for the heterogeneous uptake of a short chain PFCA, TFA, onto various liquid surfaces.
Access status: Open Access ,
Crystalline and amorphous cobalt-based metal oxides for water oxidation reaction – structure, composition, morphology and electrochemical
(2024-07-18) Thekkoot, Sreena Raju; Morin, Sylvie
Cu, Ni, and Fe-substituted cobalt-based amorphous materials (CoOx, CuCo2Ox, Ni0.5Cu0.5Co2Ox, Fe0.1Cu0.9Co2Ox, and Fe0.1Ni0.9Co2Ox) were prepared by thermal decomposition method and employed as electrocatalysts for oxygen evolution reaction (OER). These materials were characterized by scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HR-TEM) and X-ray photoelectron spectroscopy (XPS). CuxCo3-xO4 (0 ≤ x ≤ 1), NixCu1-xCo2O4 (0 ≤ x ≤ 0.75) and FeyCux-yCoxO4 (x=1, 1.5 and y = 0.1, 0.15) were also by thermal decomposition method. Surface area measurements were performed using cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The catalytic activity of spinel oxides and amorphous metal oxides for OER was analyzed by CV, while kinetic studies were carried out using a rotating disc electrode (RDE). TEM and HR-TEM analysis were performed on polarized and nonpolarized CuCo2O4. The study clearly indicates that the as-prepared CuCo2O4 possesses a higher degree of crystallization compared to the polarized sample. The crystallite size of the samples measured by TEM and XRD analysis is very similar. Surface area measurements indicate that the incorporation of Cu and Ni increased the surface area of amorphous and crystalline samples. The incorporation of Fe increased the surface area of the amorphous samples, while an opposite trend was observed in the case of spinel oxides. XPS analysis indicates that the surface of both amorphous and crystalline samples contains different species and the metal ions exist in different oxidation states. Catalytic activity was measured as a function of geometric and real surface area. Both amorphous and spinel oxides were found to be active for OER. However, when corrected for real surface area, spinel oxides provided much higher current density compared to amorphous samples. Our study indicates that spinel oxides outperform amorphous samples for OER.
Access status: Open Access ,
Structural Modifications of Dithienophospholes for Applications as Functional Materials
(2024-03-16) Asok, Nayanthara; Baumgartner, Thomas
Recent breakthroughs in synthetic chemistry have revolutionized main-group molecules, elevating them from mere laboratory curiosities to powerful materials with broad applications. A primary focus has been on electron-accepting or -deficient materials, driven by their historical limitations in availability and stability, which have hindered practical applications. The incorporation of heavier main-group elements, including Si, Ge, P, As, Sb, Bi, S, Se, and Te, has proven advantageous for electron-accepting materials due to their polarizable molecular orbitals (MOs) readily accessible to electrons and nucleophiles. This foundation has spurred research in materials chemistry across various applications, encompassing optoelectronic devices (OLEDs, OPVs), energy storage (batteries, capacitors), fluorescent sensors (biological, physiological), catalysis, and synthesis. Among main-group-element-based materials, organophosphorus compounds hold a privileged status, with their frontier orbitals easily modifiable through chemical, structural, or electronic means at the phosphorus center itself, without necessitating kinetic stabilization. The five-membered phosphorus-based heterocycle, phosphole, is particularly captivating in this context. Extensive studies have unveiled the intricate σ*-π* interaction within phospholes, endowing them with intriguing electron-accepting properties, while preserving morphological and physiological stability for practical utilization. Furthermore, phosphorus introduces easily accessible, low-lying antibonding orbitals, leading to Lewis acidic phosphorus species, a departure from the conventional perception of phosphorus as an electron-rich element. These species exhibit unconventional chemical reactivity through hypervalency. This thesis advances conjugated materials by employing the unique structures and electronics of organophosphorus compounds. It discusses how these materials can be harnessed to design functional materials with exceptional electronic, chemical, and structural properties, contributing to the realm of functional materials.
Access status: Open Access ,
Machine Learning Estimation of Reaction Energy Barriers and its Applications in Astrochemistry
(2024-03-16) Ji, Hongchen; Fournier, Rene Andre
We developed a machine learning model for fast estimating reaction energy barriers. The model was trained on data for 11,730 elementary reactions and barriers computed with an estimated accuracy of 2.3 kcal/mol by Grambow and coworkers. Although it was trained, and then applied, only for reactions involving atoms of H, C, N and O, our model can readily be generalized to molecules and reactions involving other elements. We designed and tested many molecular representations. Our best model has 363 features calculated from the chemical composition, structure, and energy of products and reactants that can all be obtained at a small computational cost. A Kernel Ridge Regression with Laplacian kernel was found to give the best fit to the data. It makes predictions with a mean absolute error of 4.1 kcal/mol for barriers smaller than 40 kcal/mol. We used this machine learning model to estimate the barriers of 136,081 hypothetical association reactions between molecules known to exist in the circumstellar envelopes and interstellar medium, where temperatures range between 10 and 150 K. A screening procedure identified reactions likely to occur (those with near zero barriers) that could play a role in the formation of relatively complex organic molecules (those with at least one double bond and containing at least one atom each of the elements H, C, N and O). Reactions identified as the most promising were investigated with density functional theory and coupled cluster quantum chemical methods to obtain reaction pathways and energies of reactants, intermediates, transition states and products with an accuracy of roughly 1 kcal/mol. We found no barrierless reaction but found two reactions with low barriers leading to the formation of N-methyleneformamide (CH2NCHO) and imine acetaldehyde (NHCHCHO). These molecules have not yet been observed in space. The low barriers that we calculated, and the possibility that these reactions would be facilitated by adsorption on ice covered dust grains in the interstellar medium, suggest that these two molecules may exist in space and could be detected by determinations of rotational constants from spectroscopic lines in the microwave region.
Access status: Open Access ,
Structural and Functional Insights into the F Plasmid Type IV Secretion System proteins TrbI and TrbB
(2024-03-16) Apostol, Arnold Jan; Audette, Gerald F.
Bacteria have evolved elaborate mechanisms to thrive in stressful environments. One mechanism that bacteria utilize are secretion systems that can traverse protective lipid cell membranes and serve as mediators for a diverse set of goals, including the secretion of toxins implicated with target host pathogenesis. F-like plasmids in gram-negative bacteria encode for the multi-protein Type IV Secretion System (T4SSF) that is functional for bacterial proliferation and adaptation through the process of conjugation. The periplasmic protein TrbB is believed to have a stabilizing chaperone role in the T4SSF assembly, with TrbB exhibiting disulfide isomerase (DI) activity. In the current report, we demonstrate that residues W57-K181, which include the active thioredoxin motif, are sufficient for DI activity. Moreover, a structural model of GST-TrbBWT based on ColabFold-AlphaFold2 and Small Angle X-Ray Scattering data indicate that TrbBWT’s N-terminus is disordered, and this disordered nature likely contributes to the protein’s dynamicity and recalcitrance to crystallization. A truncation construct, TrbB57-181, was designed and found to exhibit higher physicochemical stability using 1H-15N Heteronuclear Single Quantum Correlation spectroscopy and Circular Dichroism spectroscopy. Binding studies of TrbB and other T4SSF proteins TrbI and TraW were performed, and results do not support the inference of a stable complex forming in vitro. Comparative studies of TrbB, TraF, and TrbI also provide insights into the structure of these T4SSF component proteins. Lastly, crystallization trials of GST-TrbBWT and GST-TrbI provide leads for future crystallization campaigns.
Access status: Open Access ,
Alkylidene Dihydropyridines as Useful Intermediates for Functionalization of 4-Alkylpyridines
(2024-03-16) Shi, Jiaqi; Orellana, Arturo
Pyridines are widely used and extensively studied heterocyclic compounds in industry and academia. Developing mild and selective methods for functionalizing pyridines would facilitate the synthesis of more structurally diverse pyridine derivatives, which could aid the development of potential drug candidates and streamline the drug discovery process. Through a “soft-enolization” logic, 4-alkylpyridines can be readily converted to corresponding alkylidene dihydropyridines (ADHPs), enabling mild and selective palladium-catalyzed allylation and dehydrogenation, as previously shown by our group. During the mechanistic study of the allylation reaction, prompted by the low enantioselectivity of pyridine allylation using optically active ligands, our group demonstrated that ADHPs are “soft” nucleophiles towards the allylpalladium(II) complex. We thus began employing this class of intermediates as soft nucleophiles in other reactions. Here I will first discuss the work towards enantioselective allylation of 4-alkylpyridines. Then I will describe the conjugate addition of ADHPs to a,b-unsaturated ketones that are activated by triethylsilyl triflate. Finally, I will introduce the approach to unite piperidine and pyridine with a carbon atom through addition of ADHPs to protonated pyridines with subsequent transfer hydrogenation reaction.
Access status: Open Access ,
Advancing Kinetic Capillary Electrophoresis for High-Efficiency Screening of Oligonucleotide Libraries in Drug Discovery
(2024-03-16) Le, An Thi Hoai; Krylov, Sergey N.
Identifying protein binders is the first step in drug discovery. The combinatorial approach, in which a library of compounds is subjected to affinity screening against a target protein, is a major way for identifying protein binders. Oligonucleotide libraries constitute the largest source of material for such affinity screening. Selecting protein binders from such libraries requires a highly efficient method for separation of protein−oligonucleotide complexes from the excess of unbound oligonucleotides. Kinetic Capillary Electrophoresis (KCE) is a rapidly advancing technique in affinity applications. It reportedly has superior partitioning efficiency, but screening oligonucleotide libraries by KCE has many challenges which must be addressed before KCE can compete with conventional surface-based screening. The goal of my research is to transform KCE into a versatile technology for screening protein binders from oligonucleotide libraries. To overcome the nonbinder background issue in KCE-based partitioning, I introduce Ideal-Filter Capillary Electrophoresis (IFCE), where binders and nonbinders travel in opposite directions. While successfully implementing IFCE conditions to be compatible with physiological buffers, a remarkable partitioning efficiency of 109 is achieved, the highest recorded so far. Further, I develop the first quantitative characterization of all KCE-based partitioning modes for a diverse range of protein target sizes. This systematic analysis provides guidance for CE users on selecting appropriate KCE-based partitioning conditions for a given protein target. Next, I conduct the first experimental investigation into the influence of target concentration on binder selection, aiding researchers in identifying an appropriate range of target concentrations to prevent selection failures. Finally, I gather insights from all these works to demonstrate the first highly efficient KCE-based selection of protein binders from DNA-encoded library of small molecules (DEL). This pioneering achievement showcases the capabilities of KCE-based partitioning within the context of DEL-based drug discovery, marking a significant advancement in the field.
Access status: Open Access ,
Robust MircroRNA detection by Capillary Electrophoresis
(2023-12-08) Hu, Liang; Krylov, Sergey N.
MicroRNA (miRNA) are short single-stranded RNA molecules that function as post-transcriptional regulators in gene expression, The abnormal expression of small subsets of miRNAs, termed “miRNA fingerprints”, have been found as potential biomarkers in diagnosis of various diseases including cancers. However, none of miRNA-based biomarkers has been approved yet for clinical use due to the lack of a robust quantitative method for miRNA analysis. To address this issue, there have been significant efforts towards developing robust quantitative miRNA detection methods. Among a variety of initiatives, DQAMmiR is a promising approach developed by our lab which is capable of direct, quantitative analysis of multiple miRNAs in capillary electrophoresis (CE). In my PhD project, I have been focusing on investigating and improving the robustness of DQAMmiR to increase its applicability for practical use. Firstly, I demonstrated that DQAMmiR is capable of directly quantitating miRNA in crude cell lysates, indicating its robustness to the change of sample matrices, revealing its great potential to be used to analyzing miRNAs in biological samples directly without the need for complex sample processing. Secondly, I developed a second-generation DQAMmiR by replacing the ssDNA probes with the electrically neutral peptide nucleic acid (PNA) probes, which further improves the robustness of the assay by removing the need for single-stranded DNA binding protein (SSB) in the assay. Thirdly, to increase the applicability of the assay, I introduced a new sample preconcentration technique based on the integration of field-amplified sample stacking (FASS) and isotachophoresis (ITP) prior to CE separation in DQAMmiR, which successfully decreases its limit of quantification (LOQ) by 140 times. Lastly, I investigated the applicability of DQAMmiR for analyzing urinary miRNAs. I demonstrated that the concentration ratio of two miRNAs, miR-16 and miR-21, could be relative stable from different urine samples collected from the same person, although the individual concentrations of these miRNAs varied significantly in these samples. These findings suggests that the ratiometric measurements between multiple miRNAs in urine would serve as better biomarkers than individual miRNA concentrations for clinical diagnostic tests. And DQAMmiR would be an ideal analytical methodology for the development and use of such tests.
Access status: Open Access ,
Instrumental Analysis of Pasylated Asparaginase, JZP-341, A Pre-Clinical Drug Candidate
(2023-12-08) Ghaffari, Shakiba; Krylov, Sergey N.
Bio-betters are second-generation biopharmaceutical drugs that aim to improve the original drug’s pharmacokinetic or pharmacodynamic properties through minor physical modifications. Bio-betters require extensive characterization. Here, we investigate: JZP-341, a long-acting asparaginase bio-better used to treat leukemia. JZP-341 has a disordered proline-alanine-serine (PAS) tail that increases the drug’s size and thereby its serum half-life. A long serum half-life decreases the dosage frequency, providing more freedom to the patient. We assess the structural heterogeneity, charge heterogeneity, and enzyme kinetics of JZP-341 to better understand the effects of the PAS tail on the drug via the methods of capillary electrophoresis (CE), mass spectrometry (MS), and chromatography. We observe size heterogeneity and charge heterogeneity. We also developed a native capillary gel electrophoresis assay and an automated label-free CE-MS enzyme activity assay to study JZP-341. A detailed understanding of the role of PAS tail on JZP-341 requires further assay development and sophisticated equipment.
Access status: Open Access ,
Sustainable Synthesis of 4-acylpyridines through air oxidation of dearomatized 4-alkylpyridines
(2023-12-08) Puzhitsky, Matthew; Orellana, Arturo
Nitrogen containing heterocycles such as pyridines are a frequently encountered motif found in small molecule drugs approved by the FDA. Due to their prevalence in the pharmaceutical industry, green and effective synthetic routes towards these molecules are appealing. We detail a novel synthetic route towards 4-acypyridines via the ambient oxidation of alkylidene dihydropyridines (ADHPs). We then establish the robust and chemoselective nature of this oxidation by exploring substrates with various functional groups and multiple pyridylic sites. Finally, a series of time-course NMR studies reveal how to manipulate the stability of ADHPs by varying the nature of the chloroformate used to make these conjugated intermediates.

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