Browsing by Author "Hong, Jiyong"

Macrocycles have received growing appreciation for their potential in probing a broader biological space, and there are a significant number of bioactive macrocycles in nature. In addition, a macrocyclic scaffold provides interesting features, including high binding affinity and target selectivity due to the pre-organized conformation. Despite the therapeutic potential and valuable pharmacological characteristics, this class of scaffolds has been poorly exploited in the field of drug discovery because of synthetic challenges and incompatibility to the conventional Lipinski’s rule of five. Therefore, efficient approaches for the generation of diverse and complex macrocycles are needed to develop novel macrocyclic agents.

In an attempt to construct a diverse set of macrocycles, we designed a natural product-like macrocycle library containing a tetrahydropyran core. Our strategy for the generation of the library is based on the tandem allylic oxidation/oxa-conjugate addition for the stereoselective synthesis of a 2,6-cis-tetrahydropyran ring. The incorporation of various building blocks and the utilization of diverse macrocyclization methods were carried out to rapidly increase skeletal diversity and complexity. Appendage diversification was performed to further modulate the physicochemical properties of the macrocycles. Cheminformatic analyses demonstrated that our macrocycle library covers a distinct chemical space compared to drug-like space, while significantly overlapping

with macrocyclic natural product space.

We also explored a modular strategy for the synthesis of a macrocycle from nature, forazoline A, polyketide natural product. Forazoline A exhibits potent in vivo efficacy against the fungal pathogen Candida albicans displaying a synergistic effect with amphotericin B. Our approach towards the synthesis of forazoline A relied on the construction of three major fragments with the desired stereochemistry and the assembly of those fragments. In the dissertation, the synthetic studies of cyclohexane, thiazolidine, and alkyl chain fragments were introduced. Construction of the highly functionalized cyclohexane moiety was efficiently accomplished utilizing Mukaiyama aldol, Bayer–Villeger reaction, and addition of lithium dimethyl cuprate. Synthesis of the thiazolidine fragment was investigated via oxa-conjugate addition and Pummerer-type rearrangements. Finally, the alkyl chain fragment was synthesized through epoxidation, regioselective ring opening, and β-ketoester formation.

Histone deacetylases (HDACs) have been shown to play key roles in tumorigenesis, and

have been validated as effective enzyme target for cancer treatment. Largazole, a marine natural

product isolated from the cyanobacterium Symploca, is an extremely potent HDAC inhibitor that

has been shown to possess high differential cytotoxicity towards cancer cells along with excellent

HDAC class-selectivity. However, improvements can be made in the isoform-selectivity and

pharmacokinetic properties of largazole.

In attempts to make these improvements and furnish a more efficient biochemical probe

as well as a potential therapeutic, several largazole analogues have been designed, synthesized,

and tested for their biological activity. Three different types of analogues were prepared. First,

different chemical functionalities were introduced at the C2 position to probe the class Iselectivity profile of largazole. Additionally, docking studies led to the design of a potential

HDAC8-selective analogue. Secondly, the thiol moiety in largazole was replaced with a wide

variety of othe zinc-binding group in order to probe the effect of Zn2+ affinity on HDAC

inhibition. Lastly, three disulfide analogues of largazole were prepared in order to utilize a

different prodrug strategy to modulate the pharmacokinetic properties of largazole.

Through these analogues it was shown that C2 position can be modified significantly

without a major loss in activity while also eliciting minimal changes in isoform-selectivity. While

the Zn2+-binding group plays a major role in HDAC inhibition, it was also shown that the thiol

can be replaced by other functionalities while still retaining inhibitory activity. Lastly, the use of

a disulfide prodrug strategy was shown to affect pharmacokinetic properties resulting in varying

functional responses in vitro and in vivo.

v

Largazole is already an impressive HDAC inhibitor that shows incredible promise.

However, in order to further develop this natural product into an anti-cancer therapeutic as well as

a chemical probe, improvements in the areas of pharmacokinetics as well as isoform-selectivity

are required. Through these studies we plan on building upon existing structure–activity

relationships to further our understanding of largazole’s mechanism of inhibition so that we may

improve these properties and ultimately develop largazole into an efficient HDAC inhibitor that

may be used as an anti-cancer therapeutic as well as a chemical probe for the studying of

biochemical systems.

!Drug discovery typically involves structure-based drug design based on three-dimensional protein structures and hit/lead compound identification and optimization. Herein, this technique was used to overcome several obstacles associated with the developing of antibiotics, anticancer agents, and antifungals and reveal critical insights into the corresponding structure-activity relationships (SARs).Phospho-N-acetyl-muramyl-pentapeptide translocase (MraY) is an important membrane enzyme involved in the early-stage biosynthesis of bacterial peptidoglycans. As the inhibition of MraY leads to bacterial cell lysis, such MraY inhibitors (e.g., muraymycin) hold great promise for antibiotic development. However, the structural complexity of muraymycin makes its synthesis and practical applications challenging. Hence, we synthesized several muraymycin analogs with reduced structural complexity and better synthetic tractability and identified the moieties responsible for their biological activity to facilitate the development of muraymycin-derived antibiotics. Translesion synthesis (TLS) is a major mechanism that enables bypass replication over DNA lesions and promotes the formation of mutagenic DNA. Rev1/Pol ζ–mediated TLS plays an important role in cisplatin-induced mutations, and thus, the Rev1/Pol ζ interface is an attractive target for small-molecule TLS inhibitors. Herein, we aimed to develop TLS inhibitors as potential anticancer agents based on the recently reported inhibitor of the Rev1-Rev7 interaction, JH-RE-06. Despite its high potency, JH-RE-06 is poorly soluble in aqueous media and is therefore a limitation for further development. To overcome this limitation and identify novel anticancer agents, we prepared various JH-RE-06 analogs and studied the related SARs, to determine the critical functional groups for improving the biological activity improvement and aqueous solubility. Currently, fungal infections, which are particularly dangerous to immunocompromised patients, are a frequent cause of a death. However, the similarities between the eukaryotic physiologies of fungal pathogens and their hosts render targeting of the pathogen without causing side effects in the host challenging. Calcineurin (CN) plays a major role in invasive fungal diseases and is therefore a promising target for antifungal drug development. FK506, which is an approved CN inhibitor, exhibits promising activity but an insufficient selectivity because of its strong immunosuppressive effect. Therefore, in developing antifungal agents, we exploited the major structural differences between the CN-FK506-FKBP12 ternary complexes of humans and fungi and developed FK506/520 analogs targeting these complexes. The synthesized analogs retained the parent antifungal efficacy while exhibiting lower immunosuppressive activities and improved therapeutic efficacies both in vivo and in vitro.

Natural products have a significant influence on the development of chemical treatments for diseases as well as the exploration of biological pathways and are still a major pipeline for novel drug discovery. However, their use has diminished in past decades, because of technical barriers to secure compounds. Recently, the development of new techniques, such as combinatorial chemistry and high-throughput screening, revitalizes the value of natural products. In this regard, the synthetic studies of natural products and their analogs for biological evaluations are still important for utilizing them.

Subglutinols A and B were reported as natural immunosuppressive products. Our group reported the first total synthesis of subglutinols A and B and also revealed that subglutinol A effectively blocks T-cell proliferation and survival in vitro and in vivo. However, subglutinols cannot be easily obtained from natural sources and synthesis of these molecules is challenging because of their structural complexity. Therefore, our aim has been to develop structurally simple and readily synthesized subglutinol-derived chemical probes for the investigation of autoimmune mechanisms. In attempts to develop a more efficient biological probe as well as a potential therapeutic, we designed and synthesized subglutinol A analogs, and then evaluated their biological activities. Our efforts have resulted in the identification of simple analog 2.170, based on several in vitro experiments, which led to the evaluation of in vivo efficacy in EAE mouse model. Although the analog 2.170 treated mice were worse than the DMSO control group, we were able to find the reason by immune profiling. We hope this study could be a good starting point to develop new immunosuppressants.

Grayanoids are isolated from the plants of Ericaceae and exhibit a wide variety of biological activities. Recently, the potent antinociceptive activities of rhodojaponins, which belong to the diterpenoids of grayanoids, were reported. Although over 290 natural grayanoids have been identified, only one total synthesis was reported in 1994. Rhodojaponins possess a 5/7/6/5 membered fused ring system, which is the featuring structure of grayanane diterpenoids. Therefore, a unique structural feature and remarkable biological activities determine these molecules as a great target for the total synthesis. Our synthetic efforts focused on the conjugate addition to establish the quaternary carbon center and the Conia-ene reaction to obtain the 6/5 bicyclic system. These synthetic strategies will contribute to the completion of the total synthesis of rhodojaponins in the future.

The discovery of new drug scaffolds is a time-consuming and costly process. As new technologies are developed and implemented into the drug discovery process, these costs are being lessened. Of these methods, computer-aided drug discovery is the most widely implemented as it reduces the number of compounds that need to be explored synthetically. Computer-aided drug discovery has also become a powerful tool as it envelops a wide range of computational methods that can be used to identify or optimize lead compounds for various disease states or drug targets.The first part of the dissertation presents the design, synthesis, and biological evaluation of sulfonyl piperazine LpxH inhibitors. The emergence of widespread antibiotic resistance among Gram-negative pathogens has led to an urgent need for a new class of antibiotics to fight multidrug-resistant Gram-negative bacteria. Lipid A is a critical component of lipopolysaccharides present on the outer membrane of Gram-negative bacteria that prevents penetration of the membrane by external detergents and antibiotics. The biosynthesis of lipid A occurs through the Raetz pathway via 9 distinct enzymes, one of which is known as LpxH. The dual mechanism of cell killing due to the inhibition of LpxH and its presence in the majority of Gram-negative bacteria makes it an attractive target for novel antibiotics. Based on the structure of AZ1, a small molecule inhibitor of LpxH identified by AstraZeneca, we have synthesized and evaluated a series of sulfonyl piperazine LpxH inhibitors. Our study allowed for the establishment of a comprehensive structure-activity relationship of the various components of AZ1. We also obtained the first crystal structure of Klebsiella pneumoniae LpxH in complex with a sulfonyl piperazine LpxH inhibitor which illuminated how this class of LpxH inhibitors fits into the binding pocket of LpxH and guided the design of inhibitors with increased potency. Our findings will be instrumental in the discovery of new antibiotics against multidrug-resistant Gram-negative pathogens. The second part of the dissertation describes the modification of existing TRPM8 ligands and the search for alternative scaffolds towards the development of a new TRPM8 agonist for the treatment of dry eye disease. As the use of technology continues to increase, so does the incidence of dry eye disease, especially in younger individuals. Modulation of the transient receptor potential cation channel TRPM8 has been implicated as a route for the treatment of dry eye disease as TRPM8 plays a critical role in basal tear production, eye blinking, and is the sensor for eye dryness. Current well-known modulators of TRPM8 such as menthol, icilin, and WS-12, are not suitable for ocular use as they have undesirable physical properties and have off-target effects on other transient receptor potential channels. The recently discovered small molecule cryosim-3 which was identified as a TRPM8 specific agonist provides a good starting point for the development of a new agonist suitable for ocular studies. Through the use of cryo-electron microscopy, molecular docking, and virtual screening, we have begun to understand the different binding orientations of various TRPM8 ligands. This information has aided us in probing new chemical space for the identification of a TRPM8 agonist with improved potency, selectivity, and physical properties over existing agonists.

Part I: Extensive studies for treating hypercholesterolemia, one of the major causes of human morbidity throughout the world, have led to the development of statin drugs-the most prevalent drug prescribed today. In addition to statins, SCH 351448 has attracted considerable interest from many synthetic groups as it is the only selective activator of low-density lipoprotein receptor (LDL-R) containing structural features such as a C2-symmetry and 2,6-cis-tetrahydropyrans. Even though direct dimerization has been the most efficient method for the construction of C2-symmetric macrodiolides, total syntheses of SCH 351448 were only achived by stepwise dimerizations. In this chapter, attempts were made to exploit the inherent C2-symmetric macrodioloide via direct dimerization using various single monomeric units, but they did not prove to be viable. Therefore, formal synthesis of SCH 351448 was accomplished through two tandem sequences; cross-metathesis/conjugate addition and allylic oxidation/conjugate addition reactions, to stereoselectively construct 2,6-cis-tetrahydropyrans embedded in SCH 351448. The 1,4-syn aldol and the Suzuki coupling reactions were effective for the construction of the monomeric units. This convergent route should be broadly applicable to the synthesis of a diverse set of analogues of SCH 351448 for further biological studies.

Part II: Histone deacetylases (HDACs) play a significant role in tumorigenesis and have been recognized as one of the target enzymes for cancer therapy. Extensive studies in small molecules inhibiting HDAC enzymes have resulted in pan-HDAC inhibitor suberoylanilide hydroxamic acid (SAHA) and class I HDAC inhibitor FK228, approved by FDA in 2006 and 2009, respectively. Recently, largazole, a natural product was isolated from Symploca sp. presented HDAC inhibitory activity. Due to its unique differential cytotoxicity, potency, and class selectivity, structure-activity relationship (SAR) studies of largazole have been achieved to improve the potency and class selectivity. In addition to such biological activities, pharmacokinetic characteristics and isoform selectivity should be improved for the therapeutic potential of cancer therapy. In this chapter, two types of largazole analogues were synthesized by a convergent route that involved an efficient and high yielding multistep sequence. The synthesis of three disulfide analogues to improve pharmacokinetics and five linker analogues to enhance HDAC isoform selectivity is disclosed. The evaluation of biological studies is in progress.

This dissertation focuses on three main projects that include aspects of natural product synthesis, synthetic methodology, as well as the development of a small molecular probe for the study of protein palmitoylation. This first project introduces studies towards the synthesis of manassantins A and B which are potent inhibitors of hypoxia-inducible factor 1 (HIF-1). In addition, the preparation of manassantin A analogues is described along with preliminary structure-activity relationship (SAR) studies providing further insight into the structural requirements for HIF-1 inhibitory activity. The second project describes efforts towards the development of a fluorescence resonance energy transfer (FRET)-based assay system to characterize the palmitoylation of oncogenic Src family kinases. The initial work on this project involves the synthesis of a modified lipopeptide mimicking the critical N-terminus sequence of Src signaling proteins required for activation. Lastly, the third project focuses on the development of an asymmetric organocatalytic method to synthesize 2,7-cis- and 2,7-trans oxepanes as well as its application to the preparation of a simple cyclic ether. Ultimately, the goal of this work would be to extend this methodology to the preparation of complex, biologically active cyclic ethers.

Affecting 1 in 5 Americans, chronic pain has become the most common reason individuals seek out medical care. Those suffering from daily pain often endure mobile restrictions, anxiety, depression, and an overall reduced quality of life. Currently, pain management relies heavily on non-steroidal anti-inflammatory drugs (NSAIDs) and opioid analgesics, but these options only provide relief for ~25% of patients. Opioids, which are considered the most effective at relieving pain, are associated with very serious side effects such as addiction, dependence, and tolerance. As a result of their addictive properties, we now face an epidemic of opioid overdose. Since 1999 the number of deaths resulting from opioid overdose has steadily increased with ~70,000 deaths in 2020. Consequently, the discovery of safe, effective, and non-addictive analgesics is imperative to end this epidemic and treat those suffering from daily pain. As natural products have had a long-standing role in the identification of bioactive compounds for drug development, they may provide an excellent starting point for the development of non-opioid analgesics. Grayanane-type natural products are diterpenoids extracted from the plants of the Ericaceae family. They exhibit a unique 5/7/6/5 ring system and a wide variety of bioactivities. Among them, rhodojaponin III has recently been reported to possess potent analgesic activity in an acute, inflammatory, and diabetic neuropathic pain model. Notably, rhodojaponin III does not affect the endogenous opioid peptidergic system but it’s mechanism of action has yet to be established. As the total synthesis of rhodojaponin III has yet to be reported, we aim to develop an efficient route to access rhodojaponin III for further development as an analgesic and a chemical probe for mechanistic studies. Our synthetic strategy relies on a convergent approach in which two fragments are synthesized separately and then coupled together to provide the skeleton of grayanane-type natural products. Herein, the synthesis of the two fragments will be discussed with an emphasis on the enantioselective construction of the key bicyclo[3.2.1]octane fragment. Synthesis of the bicycle is centered around a copper(I)-mediated conjugate addition to a shielded enoate, cyclization of an alkynyl ketone via Mn(III)-mediated radical cyclization and a stereoselective ketone reduction with SmI2. In addition to natural product synthesis, our efforts towards the development of non-opioid analgesics includes the structure-guided design of adenosine reuptake inhibitors (AdoRIs). The analgesic effect of adenosine has gained recent attraction as an alternative approach for pain-relief. One tactic for increasing extracellular adenosine is to inhibit the intracellular transport by equilibrative nucleoside transporters (ENTs). Consequently, our work takes advantage of the co-crystal structure of hENT1 in complex with two known inhibitors, dilazep and NBMPR, to rationally design novel inhibitors with improved potency, selectivity, and pharmacological properties. Herein, the generation of a small library of hENT1 inhibitors with promising analgesic activity in a streptozotocin (STZ) induced diabetic neuropathic pain model will be reviewed. Additionally, the design and synthetic progress towards a macrocyclic inhibitor and hENT3 selective compounds will be discussed.

Despite natural products play a crucial role in drug discovery and chemical biology, these compounds are often available in limited quantities. Therefore, there is a need for efficient methods that allow access to the natural products as well as analogues for the evaluation of biological activity, investigation of structure activity relationships, and generation of more improved bioactive molecules. This dissertation consists of two parts focused on synthetic studies towards biologically active natural products and their analogues.

Part I: Since bioactive diterpenoid pyrones produced by microbes have limitless potential in pharmaceutical applications, a considerable effort has been devoted to the synthesis of diterpenoid pyrones and the identification of their structure-activity relationships. This chapter describes our synthetic studies towards the first total synthesis of NF00659B1, the 4,5-seco-tricyclic diterpene α-pyrone. Our synthetic efforts are focused on an efficient construction of the key intermediate oxepanol and installation of the α-pyrone moiety by Cu(I)-mediated intermolecular SN2’ reaction. Using efficient synthetic methods, we have been investigating the unknown absolute and relative stereochemistry of NF00659s. In addition, these synthetic strategies will contribute to a more thorough elucidation of their bioactivities. Due to their bioactivities, NF00659s are expected to be promising new anticancer drugs. Part II: Hypoxia-inducible factor 1 (HIF-1) plays a significant role in the adaptation of tumor cells to hypoxia by activating the transcription of genes involved in critical aspects of cancer, making it a leading target for the treatment of cancer. Despite several small molecules have been reported to inhibit the HIF-1 signaling pathway, these compounds exhibit relatively low HIF-1 inhibitory activity. In addition, most of them lack the desired selectivity or toxicity profiles required for a useful therapeutic agent. Therefore, development of potent and selective HIF-1 inhibitors is urgently needed. Manassantin A, a dineolignan isolated from Saururus cernuus L. (Saururaceae) has been shown to be a potent inhibitor of HIF-1α in vitro with minimal cytotoxicity. Previously, we reported a convergent and efficient synthesis of manassantin A, which enables the creation of various analogues. This chapter describes our medicinal chemistry efforts for design, synthesis, and biological evaluation of manassantin analogues to establish structure-activity relationships of the natural product as well as identification of potential lead compounds with reduced structural complexity and improved drug-like properties. In addition, we have developed chemical probes by modifying structure of the natural product to determine the molecular mechanisms of manassantin-mediated HIF-1 inhibition. In conclusion, we expect that these two projects will provide efficient synthetic approaches to the natural products and their analogues as well as invaluable tools to identify the mechanisms of action of the natural products.

The dissertation focuses on three main projects which complement the studies towards the total syntheses of biologically active natural products as well as the development of stereoselective synthesis of 2,6-disubstituted piperidines.

The first project introduced the first total synthesis of largazole, which is a marine natural product isolated from cyanobacterium of genus Symploca sp. in 2008. It consists of an unusual 16-membered macrocycle incorporating a 4-methylthiazoline linearly fused to a thiazole and an ester of 3-hydroxy-7-mercaptohept-4-enoic acid unit, part of which has been identified to be essential for the potent histone deacetylase (HDAC) inhibitory and consequently antiproliferative activities. Structure-activity relationship (SAR) studies suggest that thiol group generated by hydrolysis of the thioester moiety is the warhead and is critical for its HDAC inhibitory and antiproliferative activity. The biological evaluation of the analogues focusing on macrocycle and linker chain between sulfur atom and macrocycle suggests that the four-atom linker between the macrocycle and the octanoyl group in the side chain and the (S)-configuration at C17-position are critical to potent HDAC inhibitory activity of largazole. In contrast, the valine residue in the macrocycle can be replaced with alanine without compromising activity to a large extent. These SAR results would provide insights into structural requirements for HDAC inhibitory activity including the observed HDAC selectivity of largazole and help in the design of isoform-specific HDAC inhibitors based on largazole.

The second project involved the synthesis of cytotoxic mycobactin-like siderophore-brasilibactin A and its unnatural diastereomers, which are then identified to unambiguously confirm that brasilibactin A possesses the 17S, 18R absolute stereochemistry at β-hydroxy acid fragment. The convergent synthetic strategy has been applied to the synthesis of a more water-soluble analogue-Bbtan, iron-binding studies of which suggest brasilibactin A may play an important role in the iron-uptake mechanism in mycobacteria and related organisms.

The third project elucidated a convergent stereoselective synthesis of 2,6-cis- and 2,6-trans-piperidines through a reagent-controlled organocatalytic aza-Michael reaction promoted by the gem-disubstituent effect introduced by 1,3-dithiane. The reaction was applicable to a broad range of substrates and proceeded with good stereoselectivities (up to 20:1 dr) and yields. The 1,3-dithiane group allowed for rapid access to substrates, promoted the intramolecular aza-Michael reaction via the gem-disubstituent effect, and improved the yield of the reaction. This synthetic method should be broadly applicable to the efficient synthesis of a diverse set of bioactive natural products with 2,6-disubstituted piperidines.

Medium-sized cyclic ethers are challenging synthetic targets due to enthalpic and entropic barriers. Methods for the stereoselective synthesis of α,α΄-disubstituted medium-sized cyclic ethers began to appear with the discovery of naturally-occurring, ladder-shaped polycyclic ethers, such as brevetoxin B, and monocyclic ethers, such as (+)-laurencin. Despite the progress made in this field, limitations remain including competing formation of smaller ring sizes and scarcity of catalytic methods. Our aim has been to develop stereoselective syntheses for 7- and 8-membered cyclic ethers which have potential for application in natural product synthesis. The C-O bond disconnection was selected for the methods described within because cyclization and stereoinduction could be achieved simultaneously. In the case of 7-membered cyclic ethers, an organocatalytic oxa-conjugate addition reaction promoted by the gem-disubstituent (Thorpe−Ingold) effect has been developed to stereoselectively provide α,α′-trans-oxepanes. A gold(I)-catalyzed alkoxylation reaction has also allowed access to α,α′-cis-oxocenes. This method has been probed for feasibility in the stereoselective synthesis of (+)-intricenyne, an 8-membered cyclic ether belonging to the C15 nonterpenoid acetogenin natural product class. These methods have the potential to become general and efficient routes to highly functionalized oxepanes and oxocenes.

Nature provides an abundant source of small molecules that can be used to interrogate biological systems. However, these compounds are often available in limited quantities from natural sources and must be synthesized in order to: 1) accumulate useful amounts for further study; 2) provide an efficient means to introduce structural modifications to achieve analogues. Part I demonstrates the asymmetric total synthesis of (-)-clavosolide A, showcasing the tandem allylic oxidation/oxa-Michael reaction in the stereoselective formation of the 2,3-trans-2,6-cis-tetrahydropyran core. Part II demonstrates the total synthesis of the immunosuppressive compounds, subglutinols A and B through reductive deoxygenation and cross-metathesis/intramolecular SN2ʹ reactions from a common intermediate to form the substituted 2,3-trans-2,5-trans-tetrahydrofuran and 2,3-trans-2,5-cis-tetrahydrofuran cores (subglutinol A and B respectively. Preliminary structure-activity relationships as well as biological studies are presented.

Purpose

Methods

Results

Conclusions

Substituted tetrahydropyrans are prevalent in natural products that show interesting biological and pharmacological activities. Therefore, demand for new synthetic approaches for the construction of substituted tetrahydropyrans has recently increased. Specifically, quick and facile access to substrates, excellent stereoselectivity and yield, versatility in substrate scope, and mild reaction conditions compatible with various functional groups are highly desirable characteristics in tetrahydropyran synthesis.

The first part of the dissertation details studies of the tandem and organocatalytic oxa-conjugate addition reactions in conjunction with a dithiane coupling reaction promoted by the gem-disubstituent effect for the stereoselective synthesis of 2,3,6-trisubstituted tetrahydropyrans. The reactions were applicable to a broad range of substrates and proceeded with excellent stereoselectivity. It is of note that the present protocol provides an access to thermodynamically less favorable 2,6-trans-tetrahydropyrans through a reagent controlled, organocatalytic oxa-conjugate addition. In addition, a temperature-dependent configurational switch allowed the preparation of both 2,3-trans-2,6-trans- and 2,3-cis-2,6-cis-tetrahydropyrans from a common substrate. The synthetic utility of a combination of the tandem and organocatalytic oxa-conjugate addition reaction and the dithiane coupling reaction was demonstrated in the formal synthesis of the cytotoxic macrolide (+)-leucascandrolide A, which possesses both the 2,6-cis-disubstituted tetrahydropyran and the 2,3-trans-2,6-trans-tetrahydropyran. We also demonstrated the potential of the organocatalytic 1,6-oxa-conjugate addition for the formation of the 2,6-cis-tetrahydropyran in the total synthesis of (+)-dactylolide.

The second part describes the facile and efficient approach to the synthesis of 2,6-cis-4-hydroxy-tetrahydropyrans via a tandem CM/thermal SN2′ reaction. The strategic placement of the hydroxy group at C(4) in the tether resulted in an enhancement of the diastereoselectivity in ring closure. The mildness of the thermal conditions allowed for the synthesis of 2,6-cis-4-hydroxy tetrahydropyrans from base-sensitive substrates without the use of protecting groups. The tandem reaction enabled a protecting-group-free synthesis of (±)-diospongin A.

The identification of a promising lead compound is a crucial step for the drug development. Despite of a number of approaches, the optimization of promising hit compounds is still challenging. Structure-based drug design approach is a well established and widely used strategy based on the 3D atomic structure of proteins. The combined use of screening and computational method boost the search for lead compounds and optimization.

The first part of the dissertation details studies of the development of translesion synthesis (TLS) inhibitors. Translesion synthesis is a major mechanism to enable bypass replication over DNA lesions. Lesion bypass is carried out by specialized TLS polymerases that use damaged DNA as templates and insert nucleotides opposite lesions, promoting mutagenic DNA synthesis. Since Rev1/Pol ζ-mediated translesion synthesis plays an important role in cisplatin-induced mutations, Rev1/Pol ζ interface is an attracted target for inhibition of TLS by small molecules. An ELISA assay has identified two promising hits for inhibition of Rev1/Rev7 interaction: quinolone scaffold RE01 and perhexiline maleate RE02. Our efforts for design, synthesis, and biological evaluation of analogs have led to the establishment of structure-activity relationships. Also, we have been developing novel synthetic approaches to extend a diversity of analogs and improve the activity. As an important step toward our goal of sensitizing cancer cells to cisplatin, additional in vitro studies reveal that RE01 sensitizes cancer cells to cisplatin and shows less mutation frequency than RE02, suggesting that RE01 is highly potent inhibitor of Rev1-mediated translesion synthesis. Moreover, the crystal structure of RE01-bound Rev1 along with modeling studies would facilitate the structural optimization of hit compound to improve the potency.

The second part describes the synthesis and biological evaluation of LpxH inhibitors. Lipid A has a critical role in host response to bacterial infection and thus is required for the growth and survival of most Gram-negative bacteria. An effective therapeutic targeting lipid A biosynthesis can cure Gram-negative bacterial infections and sensitize infectious bacteria to other antibiotics. Essential and most widespread lipid A enzyme LpxH is an attractive target for the development of novel antibiotics. The AstraZeneca compound LH01 has been identified as an EcLpxH inhibitor. Based on the LH01 structure, we have prepared and evaluated a series of analogs for HiLpxH inhibition and the development of co-crystal structure. LpxH activity assays result in the identification of more potent inhibitors against EcLpxH, not HiLpxH. In addition, we have developed the photo-induced crosslinking probe to elucidate the binding mode of analogs. With the potential of analogs, we hope our analogs show good potency against different LpxH orthologs.

The development process of lead compounds shown in this dissertation

highlights accomplishments as well as challenges, along with the value of structure-based lead optimization.

Invasive ductal adenocarcinoma of pancreas, commonly known as “pancreatic cancer”, is a highly malignant neoplasm originating in pancreatic tissues, often metastasizing to nearby organs like liver. Most patients only display nontypical symptoms in the early stages and often have metastasis upon diagnosis. Consequently, pancreatic cancer ranks as the seventh leading cause of cancer-related mortality worldwide and the fourth in the United States.Despite surgery being the sole curative option of human pancreatic cancer, clinical care for most patients remains to be systemic chemotherapy. Gemcitabine has served as the standard first-line chemotherapeutic agent for advanced pancreatic cancer for over two decades, but resistance development poses challenges. Moreover, new standard-of-care regimens such as FOLFIRINOX and gemcitabine/nab-paclitaxel offered modest improvements in survival rates and increased toxicities, and future treatments is founded on targeting tumor microenvironment and cancer-specific cell metabolisms. In 2000, Esumi and colleagues proposed the antiausterity strategy to combat cancer cells’ tolerance of nutrient deprivation conditions resulting from the hypovascular nature of the pancreatic tumor. With the screening method established by Esumi, a diverse array of antiausterity agents have since been isolated or synthesized. In 2020, three daucane-type natural products isolated from Ferula hezarlalehzarica demonstrated potent antiausterity activity against PANC-1 pancreatic cancer cells. However, mechanisms of action for these compounds remain incompletely known, and their structure-activity relationships (SAR) and potential for drug discovery are unclear. Therefore, we focuses on the total syntheses of these natural products as well as the design and preparation of analogs to establish SAR. All three target molecules (compounds 1, 2 and 3) are daucane-type sesquiterpenoids featuring a 5,7-fused bicyclic system with trans ring junction and a quaternary carbon center. In our synthesis, we first aimed to stereoselectively install the quaternary center. While attempts of asymmetric conjugate addition with a Cu/NHC-Ag system failed to provide satisfactory enantiomeric excess, the silicon-tethered radical cyclization-trapping strategy achieved installation of the quaternary carbon center. Compound 1 was then successfully prepared after utilizing a ring-closing metathesis to construct the 5,7-fused bicyclic system. Synthesis of compounds 2 and 3 required establishing the allylic alcohol moiety in the 7-membered ring. Unfortunately, our attempted elimination approaches based on the TBS-protected tetraol intermediate, as well as the Bamford-Stevens reaction and the vinyl triflate formation based on the α-hydroxyketone intermediate, did not afford the desired product. Approaches such as epoxide opening, singlet oxygen, and iodocarbonate cyclization based on the jaeschkeanadiol intermediate or derivatives also proved futile. Eventually, we installed the allylic alcohol moiety via a 6-step sequence involving an elimination with a cyclic sulfate leaving group, and we subsequently improved the efficiency of this pathway by utilizing a 2-step Chugaev elimination. Despite that all esterification attempts to prepare compound 2 failed, we were able to synthesize compound 3 by introducing the ester in the early stage. Four analogs have been prepared by modifying key functional groups (e.g. the ester and endocyclic olefin) within the target molecules, and antiausterity activity of these analogs and compounds 1 and 3 are currently being evaluated. The results will help establish SAR and shed light on designing new derivatives that may provide better solutions to treatments of human pancreatic cancer.

In response to oxygen deprivation, tumor cells express a transcription factor, hypoxia inducible factor 1 (HIF-1). HIF-1 regulates the expression of genes involved in erythropoiesis, angiogenesis, and other adaptive responses to hypoxia, which encourage cell survival and proliferation. Overexpression of HIF-1 causes increased vascularization and tumor growth, while HIF-1 inhibition reverses these processes. The natural products manassantins A and B are potent HIF-1 down-regulators whose molecular mechanisms are unknown. This research aims to establish structure-activity relationships which will aid in both the identification of the chemical moieties necessary for down regulation of HIF-1 and synthesis of manassantin A analogues with reduced structural complexity and increased synthetic accessibility. Preparation and biological characterization of manassantin A analogues is described. A few analogues have been identified with promising lead development potential. Further establishment of their pharmacological profiles will provide insight into the HIF-1 signaling pathway. Our efforts to elucidate the mode of action of manassantin A are described that will aid in the development of these natural products into probes of cancer biology.