<p>  </p> <p>A concise and scalable total synthesis of the therapeutically relevant methyl ester of the prostaglandin D₂ metabolite, tricyclic-PGDM, was accomplished in 8 steps from a known and easily accessed cyclopentene-diol derivative. The route features three key transition metal catalyzed steps. These steps include: a nickel catalyzed Ueno-Stork type dicarbofunctionalization which generates two consecutive stereocenters on the central cyclopentane core, a late-stage palladium-catalyzed carbonylative oxaspirolactonization, and a <em>Z</em>-selective cross metathesis to introduce the <em>Z</em>-butenoate side chain- a motif difficult to introduce through traditional protocols and which caused significant issues in the previous total syntheses of tricyclic-PGDM. Through this route, we have accumulated 75 mg of material for an ¹⁸O tricyclic-PGDM clinical assay which previously suffered from a material shortage. In addition to completing the synthesis, we generalized the <em>Z</em>-selective cross metathesis and nickel catalyzed Ueno-Stork protocols to numerous other substrates further demonstrating the utility of these transformations. </p> <p><br></p> <p>Protein arginine methyltransferases (PRMTs) catalyze the transfer of methyl groups from the cofactor SAM to arginine residues on various cytosolic and nuclear proteins. Of the nine members of the PRMT family, PRMT5 has been the most extensively studied and has been shown to regulate processes such as the DNA damage response, cell proliferation, and mRNA translation. Although numerous pathways have been identified that regulate PRMT5 activity, the cytosolic protein MEP50 has been identified as a key regulator in many diseases. PRMT5 and MEP50 interact to form a hetero-octameric complex, which can modulate the activity of PRMT5 for many cellular processes. Two new generations of PRMT5:MEP50 inhibitors were strategically designed and synthesized, which do not suffer from chemical instability like our previously most potent analogues. Our best compounds have IC₅₀ values ranging from 512 to 2.5 nM in LNCaP cells, and were confirmed to target the PRMT5:MEP50 interaction through BiFC analysis.</p>

Malaria, the disease caused by Plasmodium sp., claims the lives of over 1 million people every year, with Plasmodium falciparum causing the highest morbidity. Rapidly acquiring drug resistance is threatening to exhaust our antimalarial drug arsenal and already requires the utilization of combination drug therapy in most cases. The global need for novel antimalarial chemical scaffolds has never been greater. Screening of natural product libraries is known to have higher hit rates than synthetic chemical libraries. This elevated hit rate is somewhat attributed to the greater biodiversity available in natural products. Marine life is the most biodiverse system on the planet, containing 34 of the 36 known phyla of life, and is expected to be a rich source of novel chemotypes. In collaboration with the Harbor Branch Oceanographic Institute in Ft. Pierce we have screened a library of over 2,800 marine macroorganism peak fractions against Plasmodium falciparum using the SYBR green I fluorescence-based assay. In this screening process we have identified six compounds from five novel chemical scaffolds all of which have low micromolar to submicromolar IC50 values and excellent selectivity indices. Additionally, one of these chemical scaffolds, the bis(indolyl)imidazole, was selected for further in vitro pharmacological and structure-activity relationship (SAR) profiling, key steps in the challenging process of identifying a new antimalarial drug lead compound.

The Wittig reaction has constantly evolved during the last half-century and is one of the most strategic, reliable, widely-applicable carbon-carbon olefin bond forming processes available in organic synthesis. The reaction allows for olefination with complete positional selectivity, relatively high chemoselectivity and may be conducted in many cases with predictable stereocontrol. Triphenylphosphoranylides are ubiquitously employed and despite the myriad benefits these reagents bestow there are known disadvantages to their use—most prominently related to issues surrounding stereoselectivity and phosphine oxide removal which is notoriously problematic. Trialkylphosphoranylides, by contrast, undergo olefination in the presence of carbonyls with high (E)-stereoselectivity and the corresponding short chain trialkylphosphine oxides are water soluble. Previous work in our group has shown that semi-stabilised ylids of this type readily undergo olefination with a broad range of aldehydes under mild aqueous conditions. This aqueous Wittig reaction was then extended to the synthesis of substituted styrenes using aqueous formalin. In the search for ever milder conditions for the Wittig reaction we were also able to develop an organocatalytic Wittig reaction which was amenable to a bioorthogonal process. Thus, we were able to perform the first Wittig reaction in vivo by feeding the two reactants to Castylegia sepium. Alkenals (colloquially enals) are strategic intermediates in organic synthesis; their importance is growing each year due to the expanding breadth of iminium and vinylogous enamine organocatalysis. Unfortunately their preparation remains problematic requiring labour and reagent intensive multi-step sequences. A new pincolacetal-phosphonium salt (DualPhos) for the stereoselective two-carbon homologation of aldehydes has been developed which allows for the one-pot homologation of aldehydes to enals under aqueous and/or anhydrous conditions; its application to the total synthesis and stereochemical reassignment of phomolides G & H is discussed. / Thesis / Doctor of Philosophy (PhD)

京都大学 / 0048 / 新制・課程博士 / 博士(薬科学) / 甲第22751号 / 薬科博第125号 / 新制||薬科||14(附属図書館) / 京都大学大学院薬学研究科医薬創成情報科学専攻 / (主査)教授 掛谷 秀昭, 教授 大野 浩章, 教授 高須 清誠 / 学位規則第4条第1項該当 / Doctor of Pharmaceutical Sciences / Kyoto University / DFAM

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Microbial natural products have served a key role in the development of clinically relevant drugs. Despite significant interest, traditional strategies in their characterization have lead to diminishing returns, leaving this field stagnant. Recently developed technologies such as low-cost, high-throughput genome sequencing and high-resolution mass spectrometry allow for a much richer experimental strategy, allowing us to gather data at an unprecedented scale. Naive efforts in analyzing genomic data have already revealed the wealth of natural products encoded within diverse bacterial phylogenies. Herein, I leverage these technologies through the development of specialized computational platforms cognizant of existing natural products and their biosynthesis in order to reinvigorate our drug discovery protocols. As a first, I present a strategy for the targeted isolation of novel and structurally divergent ribosomally synthesized and post-translationally modified peptides (RiPPs). Specifically, this software platform is able to directly compare genomically encoded RiPPs to previously characterized chemical scaffolds, allowing for the identification of bacterial strains producing these specialized, and previously unstudied metabolites. Further, using metabolomics data, I have developed a strategy that facilitates direct identification and targeted isolation of these uncharacterized RiPPs. Through these set of tools, we were able to successfully isolate a structurally unique lasso peptide from a previously unexplored \textit{Streptomyces} isolate. With the technological rise of genomic sequencing, it is now possible to survey polymicrobial environments with remarkable detail. Through the use of metagenomics, we can survey the presence and abundances of bacteria, and further metatranscriptomics is able to reveal the expression of their biosynthetic pathways. Here, I developed a platform which is able to identify microbial peptides exclusively found within the human microbiome, and further characterize their putative antimicrobial properties. Through this endeavour, we identified a bacterially encoded peptide that can effectively protect against pathogenic \textit{Clostridium difficile} infections. With the wealth of publicly available multi-omics datasets, these works in conjunction demonstrate the potential of informatics strategies in the advancement of natural product discovery. / Thesis / Master of Science (MSc) / Biochemistry is the study in which life is built upon a series of diverse chemistry and their interactions. Some of these chemicals are not essential for the maintaining basic metabolism, but are instead tailored for alternative functions best suited to their environment. Often, these molecules mediate biological warfare, allowing organisms to compete and establish dominance amongst their neighbours. Understanding this, several of these molecules have been exploited in our modern pharmaceutical regimen as effective antibiotics. Due to the ever rising reality of antibiotic resistance, we are in dire need of novel antibiotics. With this goal, I have developed several software tools that can both identify these molecules encoded within bacterial genomes, but also predict their effects on neighbouring bacteria. Through these computational tools, I provide an updated strategy for the discovery and characterization of these biologically derived chemicals.

Ginkgolides are naturally occurring compounds that can be extracted from the Ginkgo Biloba tree. Their synthesis remains a significant challenge for organic chemists given their complex structure and their numerous stereocenters (2 adjacent quaternary carbons and up to 12 stereocenters). Both Corey and Crimmins reported the total synthesis of (±)-ginkgolide B in 1988 and 1999 respectively. Corey also published the enantioselective formal synthesis of (±)-ginkgolide B as well as the total synthesis of (±)-ginkgolide A in 1988. However, the total synthesis of Ginkgolide C, the most oxygenated and most complex member of the family, has not yet been published. We report herein the first total synthesis of (±)-ginkgolide C as well as the formal synthesis of (±)-ginkgolide A and (±)-ginkgolide B by intercepting Corey’s intermediate (from his total synthesis of (±)-ginkgolide B). The first key step of our syntheses was the Claisen rearrangement which set the first quaternary carbon. The second key step of the syntheses was a kinetic alkylation which sets the second quaternary carbon. The third key step for our syntheses was an enyne epoxidation which enabled the formation of the E-ring. Starting from the Claisen rearrangement adduct, our target intermediate (towards ginkgolide C) was obtained in 18 steps, after which, (±)-ginkgolide C was synthesized in an additional 6 step (total of 26 linear steps). Starting again from the Claisen rearrangement adduct, Corey’s intermediate (from the total synthesis of (±)-ginkgolide B) was obtained in 15 steps which completed the formal syntheses of (±)-ginkgolide A (in an additional 10 steps) and (±)-ginkgolide B (with 6 additional steps).