<p dir="ltr">Methods of protein engineering and mutation to achieve selective and designed enzymatic function are often challenged by issues with foldamer stability. Molecular nanocages present an exciting new opportunity for biomimetic-defined cavities capable of biomolecule recognition and catalysis. While many different types of molecular cages exist, covalent organic molecular cages offer great flexibility and control over the design of the cage. Furthermore, the covalent linkages provide a robust framework resistant to degradation and stable in many chemical environments. Lastly, covalent organic cages may be designed for the precise placement of functional groups, including group placement inside the cage cavity for molecular recognition and binding. I report our recent advances in developing new synthetic methods for robust organic molecular cages with well-defined cavities and tunable functions for artificial enzyme catalysis and recognition. The basic design philosophy for such protein-mimetic structures will be introduced for the scalable synthesis of these macromolecules. Herein, we report two approaches to a [8+12] triazine-linked organic cage and a similar [8+12] triazine and boroxine-linked cage. While our first approach attempts a kinetically controlled tethered cage formation, our second method relies on the principles of dynamic covalent chemistry in the thermodynamically controlled self-assembly of the final cage structure.</p>

<p>  </p> <p>Alkyl radicals are powerful intermediates for the generation of carbon-carbon bonds, which play an indispensable role in the synthesis of natural products, pharmaceuticals, and pesticides. Traditionally, there are two main methods for the generation of alkyl radicals. The first is C-H bond functionalization via hydrogen-atom-transfer (HAT). HAT processes have been used as an effective approach for selectively activating C-H bonds via radical pathways. The other strategy to explore the generation of alkyl radicals is C-X bond functionalization via halogen-atom-transfer (XAT). Alkyl halides are one of the largest classes of building blocks in synthesis and they can be obtained from the corresponding alcohols. The most straightforward and effective way to form such alkyl radicals is the direct homolytic cleavage of C-X bonds. In past decades, photoredox catalysis has emerged as a powerful and greener tool for the synthesis of radicals under mild reaction conditions, which has brought tremendous attention. Although remarkable success has been made in this field, some methods still require costly transition metal catalysts or toxic reagents. Herein, we display a series of visible light-induced approaches under transition-metal free conditions or using earth-abundant metals. These novel photo-induced transformations and corresponding mechanistic work will be discussed in the following order:</p> <p>We will first present our work on metal-free visible-light-promoted C(sp3)-H functionalization of aliphatic cyclic ethers using trace O2.  This reaction uses a trace amount of aerobic oxygen as the sole green oxidant under blue light at room temperature to achieve the synthesis of sulfone and phosphate derivatives in good to excellent yields using cyclic ethers and vinyl sulfones. Then, we report on a photo-induced C(sp3)-H chalcogenation of amide derivatives and ethers via a ligand-to-metal charge-transfer. This reaction converts secondary and tertiary amides, sulfonamides, and carbamates into the corresponding amido-<em>N,S</em>-acetal derivatives in good yields, using an earth abundant metal catalyst under mild conditions.</p> <p>Finally, we present a photoredox polyfluoroarylation of alkyl halides via halogen atom transfer. This method converts primary, secondary, and tertiary unactivated abundant alkyl halides into the corresponding polyfluoroaryl compounds in good yields and has good functional group compatibility.</p>

No description available.

<p dir="ltr">LeadGlow (<b>LG</b>) was reported in 2009 for its ability to both sensitively and selectively detect Pb²⁺ in aqueous solutions. Utilizing the synthetic approach of <b>LG</b>, it is possible to generate a class of novel fluorophores. A derivative of first-generation <b>LG </b>was synthesized and reported here for the first time, intuitively named <b>LG2</b>. Both compounds contain interesting photophysical properties that have not been extensively researched prior to this work. Because of this, photophysical properties of both <b>LG</b> and <b>LG2</b> are unveiled here for the first time. These properties were investigated by determinations of quantum yield (QY), average fluorescence lifetime, and DFT calculations. <b>LG</b> was found to have a higher QY (0.057) than <b>LG2</b> (0.011); however, <b>LG2</b> displays an average fluorescence lifetime (3.186 ns) 5x greater than that of <b>LG</b>. Both <b>LG </b>and <b>LG2</b> are synthesized via Hg²⁺-facilitated desulfurization of their respective thiocarbonyls, resulting in a turn-on fluorescence feature. The thiocarbonyl-containing fluorophores (<b>SLG </b>and <b>SLG2</b>) display quenched fluorescence compared to their oxo-derivatives (<b>LG </b>and <b>LG2</b>), this work attempts to investigate the mechanism(s) responsible.<b> </b>A whole class of LeadGlow compounds can be synthesized and could be potentially used as fluorescence-based sensors.</p>

<p>  </p> <p>Seven-membered ring structures are one of the most important structural motifs found widely in natural products and bioactive molecules. Although several [5+2]-cycloaddition reactions have been developed to construct these seven membered cores, asymmetric cycloaddition reactions are less explored. Described in Chapter-1 is a base mediated intramolecular diastereoselective [5+2]-cycloaddition reaction that afforded highly functionalized seven membered rings in good yields and excellent diastereoselectivities. The high diastereoselectivity is controlled by the alkyl stereocenter and the chain length of the alkene tether. The existing chirality of the substrate can direct the stereochemical outcome of the [5+2]-cycloaddition reaction. Furthermore, this methodology has been applied to synthesize various potent HIV-1 protease inhibitors. </p> <p>COVID-19 pandemic has profoundly affected life around the globe and costed us 6 million lives. Therefore, there is an urgent need for rational design of new drug candidates to specifically target different SARS-CoV-2 proteins. Recently, Pfizer developed an FDA-approved antiviral therapeutic agent, Paxlovid, targeting SARS-CoV-2 3CLpro. Chapter-2 discusses a concise synthetic route to synthesize active component of Paxlovid, Nirmatrelvir, in 6-steps without any epimerization. We have also developed a series of potent covalent inhibitors targeting SARS-CoV-2 3CLprotease and compared the antiviral activities of these inhibitors with that of Nirmatrelvir. </p> <p>In the final chapter, a concise partial synthesis of the segment A of (-)-Rafonin is discussed. (-)-Rasfonin is an antitumor agent that induces apoptosis in <em>ras</em>-dependent cells. We have proposed an asymmetric chiron approach to install the α-pyranone ring of rasfonin. Our goal is to perform SAR studies on this natural product by designing various analogues. </p>

<p>Continuous flow synthesis provides an efficient, rapidly scalable, safer, and improved synthetic route over traditional batch synthesis owing to enhanced heat and mass transfer. High throughput experimentation (HTE) is a powerful tool to discover novel reaction conditions and optimize challenging transformations in significantly small amount of time and by exploring multiple arrays of reactions. The utilization of desorption electrospray ionization mass spectrometry (DESI-MS) couple to HTE enables the exploration of 384 unique reaction conditions in just ~7 minutes. Chapter 1 highlights the different organic transformations and the target-based synthesis that have been studied using the HTE in the literature. Validation of the HTE-DESI-MS was investigated by performing a large set of aldol reactions on triacetic acid lactone (TAL), a compound well studied for use as a bio-based platform molecule which can be transformed to a range of valuable agrochemicals, commodity chemicals and intermediates for pharmaceutical industry. Two different active pharmaceutical ingredients namely, HSN-608 and Lorazepam have been synthesized using continuous manufacturing. HTE-DESI MS tools were utilized for rapid reaction screening for Sonogashira couplings for the development of telescoped continuous flow synthesis of an alkynyl naphthyridine anti-cancer agent, HSN-608. It is a fms-like tyrosine kinase 3 (FLT-3) inhibitor, a drug-lead compound for potential treatment of acute myeloid leukemia. Furthermore, a 5-step continuous flow synthesis involving N-acylation, cyclization, N-oxidation, polonovski-type rearrangement, and hydrolysis has been developed for Lorazepam, an essential generic active pharmaceutical ingredient under shortage. Different synthetic routes scouting, and impurity profiling was done to propose the novel route that was further developed under continuous flow conditions with optimization of each step.</p>

<p dir="ltr">Post-translational modification (PTM) is an important biological process by which cells regulate their signaling pathways. De-regulation of these signaling pathways often leads to many diseases. Protein AMPylation is a recently discovered PTM that caught a great amount of attention for its involvement in neurodevelopment and neurodegeneration. However, the mechanisms by which protein AMPylation modulates these biological processes remain mostly unknown. FIC domain protein adenylyltransferase (FICD)<b> </b>is one of the only two known AMPylators in eukaryotes, and its physiological role remains largely unexplored. By using a chemical approach, we identified two direct substrates of FICD: Peroxiredoxin 1 (PRX1) and Peroxiredoxin 2 (PRX2). These are antioxidant enzymes responsible for protecting cells from oxidative stress, which has been implicated in many neurodegenerative diseases. In addition, we found that FICD-mediated AMPylation increased PRX1 and PRX2 enzymatic activity <i>in vitro</i> and their protein levels in cells. These findings established a link between FICD-mediated AMPylation and oxidative stress, suggesting a potential neuroprotective role of FICD in neurodegenerative diseases.</p><p dir="ltr">Protein phosphorylation is another PTM that has been under extensive study due to its widespread role in cell signaling in many biological processes such as growth, division, metabolism, membrane transport, etc... Deregulation of protein kinases, which catalyze phosphorylation reaction, is often implicated in many diseases, including cancer. To elucidate disease mechanisms and explore alternative therapeutic targets, identifying direct protein substrates of a given disease-relevant kinase is crucial but remains a major challenge. Conventional methods to study phosphorylation involved the use of radiolabeled ATP, which poses health hazards and lacks reliability due to rapid decay of radioactive isotope. In this research, we developed an alternative method with a series of novel γ-modified ATP analog probes bearing a phospho-alkyne reporter handle, and their effectiveness and efficiency for<i> </i><i>in vitro</i> phosphorylation of recombinant proteins and proteomic substrate labeling in cell lysate were examined.</p>

<p dir="ltr">Cancer is the second leading cause of death worldwide, and there is a continued need for effective treatments to combat the disease. A key challenge in cancer therapy persists in the form of therapeutic resistance. While kinase inhibitors (KIs) have shown promise in treating cancer patients with dysregulated protein kinases, treatment failures are common, highlighting the urgent need to address this issue. Despite the approval of 80 protein kinase inhibitors by the United States Food and Drug Administration (FDA), and numerous others in clinical trials, the chemical space explored for protein kinase inhibitors remains limited. Most FDA-approved kinase inhibitors share common core moieties, such as indazole, quinoline, pyrazole, and pyrimidine, indicating a lack of diversification in drug development in this area.</p><p dir="ltr">Efforts to expand the chemical space have led to the identification of a novel 3<i>H</i>-pyrazolo-[4,3-<i>f</i>]quinoline core by the Sintim group. This scaffold can be efficiently synthesized through the Doebner–Povarov multicomponent reaction using readily available ketones, heteroaromatic aldehydes, and 5-aminoindazole. This multicomponent chemistry affords small molecules which inhibit disease-associated protein kinases with sub-nanomolar IC₅₀ values. Additionally, the scaffold presents a unique opportunity to tune for selectivity via judicious substitution patterns, allowing us to target numerous disease-driving kinases, such as FLT3, haspin, and CLK, with the use of simple multi-component chemistry.</p><p dir="ltr">From this work emerged lead amide-containing compound HSK205, which potently inhibits FLT3 and haspin and shows impressive potencies against FLT3-driven acute myeloid leukemia cell lines, with GI₅₀ values between 2 and 20 nM. Western blot analyses indicate that HSK205 inhibits the phosphorylation of FLT3 and histone H3 (substrate of haspin) in Molm-14 AML cells. Further exploration led to the discovery of lead CLK inhibitors, such as HSK1132 and HSK3110, which inhibit the growth of multiple myeloma cell lines <i>in vitro</i> with GI₅₀ values as low as 17 nM. Additionally, these compounds are orally bioavailable and reduce the growth of multiple myeloma RPMI-8226 xenograft model in mice by 69%.</p>

<p dir="ltr">Reported herein is a brief summary regarding the previous syntheses of borane-amines, newly developed protocols to synthesize borane-amines, and the material and synthetic applications utilizing borane-amines. Methods to generate borane-amines typically relied on a metathesis-dehydrogenation reaction between ammonium salts and metal borohydrides in organic solvent, typically hazardous tetrahydrofuran (THF). However, due to the poor solubility of inorganic salts in organic solvent, stirring of the reaction mixture becomes difficult and, in turn, scalability is made challenging. We report two new methods to generate borane-amines that both rely on the hydroboration of sodium borohydride and a carbonyl activator, followed by the S_N2-type reaction with the amine to form the requisite borane-amine. The activator for our procedures are either 1) gaseous carbon dioxide or 2) water/ethyl acetate system. The CO₂ mediated protocol was applied to a variety of 1°-, 2°-, 3°-, and heteroaromatic amines as well as phosphines to form the corresponding borane adducts (73-99%). Water was also found to be a green, compatible activator. Interestingly, we had swapped environmentally and health hazardous THF with ethyl acetate (EtOAc) and found the reaction had still proceeded with competitive conversion of amines to the borane-amines (72-97%). The robustness of this reaction was demonstrated with a 1.1 mol scale synthesis of borane pyridine with 87% yield. With increased accessibility of borane-amines established, we sought to investigate their potential applications, including testing their hypergolic properties. Additionally, we utilized borane-ammonia for a sequential reduction/Friedel-Crafts alkylation of benzyl carbonyls. Traditionally an alkyl halide, the scope of the electrophilic aromatic substitution reaction has widened to include alcohols and carbonyls as potential Friedel-Crafts reactants. Few reports exist for the arylation of aldehydes and ketones, while no precedence exists for the arylation of carboxylic acids and esters. Our group previously reported that TiCl₄ is capable of eliminating oxygen from benzyl alcohols, forming a carbocation intermediate. Theoretically, the carbocation formed from TiCl₄ and benzyl alcohols would be vulnerable from attacks from other nucleophiles, including pi bonds from arenes. This was indeed proven to be the case when benzyl alcohol was reacted in 1 equiv. TiCl₄with benzene as the solvent and diphenylmethane was obtained as the sole product. By including borane-ammonia as a hydride source, various aryl carbonyls and aryl carbinols were also reduced to the corresponding alcohol <i>in situ</i>, enabling these substrates to participate in Friedel-Crafts alkylation.</p>

<p dir="ltr">Post-translational modifications (PTMs) play a crucial role in regulating protein function and location. Protein AMPylation, the addition of adenosine monophosphate (AMP), significantly influences protein trafficking, stability, and pathogenic virulence. The Fic Domain family of proteins targets hydroxyl-containing amino acid residues (Ser, Thr, or Tyr), catalyzing the addition of various phosphate-containing moieties such as nucleoside monophosphates (NMPs), phosphocholine, and phosphate. Using gene mining techniques, Dr. Seema Mattoo’s group has identified a clade of Fic domain containing proteins typified by the enzyme originating from <i>Bordetella bronchiseptica</i> (BbFic) which prefers utilizing guanosine triphosphate (GTP) as a substrate over other nucleotides. To understand the physiological role of GMPylation, identifying the proteins modified by BbFic is a first critical step and can be accomplished via mass spectrometry-based proteomics. For a low stoichiometry PTM like GMPylation, however, there is a need to develop chemical tools that enable the targeted enrichment of modified protein. Identifying key interactions between substrate proteins and the BbFic nucleotide binding site will enable development of highly specific molecular tags for Fic substrates.</p><p dir="ltr">The goal of this research project, therefore, is to design chemical probes to tag Fic enzyme substrates, thereby facilitating the identification of GMPylated proteins in chemical proteomics workflows. A set of ATP and GTP analogues carrying either alkyne or azide handles were proposed as possible probes. While 8-azido guanosine showed a high docking score in our in-silico study, literature reports highlight its chemical instability upon exposure to air and light. An alternative probe, the 8-ethynyl guanosine, also showed a high docking score and docks in the same position and orientation as guanosine (the natural ligand) but necessitates synthetically challenging via cross-coupling reactions.</p><p dir="ltr">We considered multiple GMP analogues as potential molecular tags with the assistance of molecular docking with the BbFic enzyme. With predicted binding affinities in hand, we prioritized candidate GTP analogs for synthesis to probe the BbFic-mediated protein GMPylation process. While N6 propargyl guanosine serves as a lead probe for AMPylation, computational analysis reveals challenges with O6 due to its altered hydrogen bond donor/acceptor presentation. The distinctive chemical properties of guanosine, compared to adenosine, require a thorough evaluation of protective group strategies, as not all synthetic methodologies used for ATP analogue synthesis are applicable to GTP analogues. Isolating the triphosphate analogue proved challenging, although purification of the monophosphorylated counterpart is feasible. The Protide analogue benefits from phosphate charge masking, which facilitates purification. While much work remains until the physiological role of GMPylation can be determined, important progress has been made in the design and synthesis of chemical tools for studying this newly discovered PTM.</p>