Part I. Development of an isoxylitone analog as an antiepileptic drug candidate. Delphinium denudatum is a medicinal plant traditionally used to treat a variety of conditions in Central Asia. Its interesting anticonvulsant effects were determined to be a property of the compound isoxylitone. Prior work from our group in collaboration with the Poulter group from Western University investigated this compound and generated a large number of isoxylitone analogs in order to optimize its antiepileptic activity. This led to the discovery of the prodrug 13 and the active form 15 shown below, which emerged as the most potent. In this work, the library of analogs was further expanded with 22 new compounds with several which matched the activity of 13 and 15, such as compounds 22 and 37, which led to valuable new insights on the activity of these analogs, and suggested other possible future improvements. In addition, efforts were continued regarding developing compound 15 as a clinical trial candidate. Optimization of the synthesis was performed to drastically reduce costs and waste of chemicals, as well as accelerating the duration of the synthesis. The purification of the final product was also greatly facilitated by the direct synthesis of 15, compared to the prior process of first preparing 13 and hydrolyzing the ester. Efforts were exerted to gather additional knowledge on the characteristics of the compound, with structural and conformational analysis via X-ray crystallography and NOE NMR as well as accelerated stability studies to test the viability of 15 in long-term storage under various conditions. All the information gathered throughout this work supported 15 and its sodium salt as excellent clinical trial candidates as treatments for epilepsy. Part II. Synthesis of SOX9 inhibitors as promoters of recovery from spinal cord injury. According to the World Health Organization, 250 to 500 thousand people develop a spinal cord injury each year with a large portion resulting in tetraplegia. A common misconception is that this is permanent because the damaged nerves cannot be repaired. In fact, nerves can and do regrow after being damaged, but cannot do so after spinal cord injuries due to formation of scar tissues which physically and chemically prevents the healing. The Brown group at Western University identified the SOX9 transcription factor as an important promoter of the formation of this scar and showed that SOX9 inhibitors could improve recovery and mobility in mice affected by spinal cord injuries. In collaboration with their group, previous work in our lab performed and SAR study on the lead compounds ZO2(1) and STL26 (2), shown below. The different sections of the molecule have been designated units A to D, to simplify discussion. Initial work by our group established an efficient method to prepare a library of analogs of the lead compounds. A number of compounds were prepared, which primarily investigated small amines as unit A and phenols with small aliphatic substituents as unit D. The initial SAR data confirmed the validity of STL26 as lead compound, as most alterations to the structure were detrimental to the SOX9 inhibitory activity. The objective of this work was to build on these preliminary SAR results, and expand the library of analogs. Larger substituents were introduced in unit A and D and showed that any group larger or smaller than diethylamide in unit A was detrimental to the activity, but that there seemed to be ample space to increase the size of the unit D isopropyl group. Analogs investigating unit B showed that adding substituents at most of the positions was detrimental, as well as changing the relative positions of unit A and B to be ortho or para to each other. However, the C4 on ring B seemed to be very tolerant to various electron donating or withdrawing functional groups. During this SAR study, a recurring theme was the awful solubility of the compounds in water, which heavily complicated their administration to mice during the bioassays. While none of the analogs tested proved superior to 2, the knowledge accrued during this work painted a clear path forward on which areas of the structure could be safely altered to improve solubility without negative impacts on SOX9 inhibition. Some additional efforts were put into obtaining an accurate three-dimensional structure of an active STL26 (2) analog, and information on the primary conformation in solution. Achieving these goals required the use of NOE NMR experiments and X-ray crystallography. One conformation was discovered to be strongly favoured as a result of an intramolecular hydrogen bond even in protic solvents. Subsequently, a small number of additional analogs were prepared containing modifications that would strongly favor or hinder the preferred conformation, in order to better understand its role in the inhibitory activity. The presence of this hydrogen bond appeared to be key to the activity of the compounds.

The small Molecule Drug Discovery field has been heavily dependent on suppressor discovery by structural binding prediction. Despite all successes in targeting different types of molecular targets in cells, many are considered undruggable. Over 85% of proteins and over 99% of RNAs are still considered hard to drug in cancer. The main challenge in suppressing their activity would be their unknown or super complicated structures. In addition, many of them present a dynamic 3D structure with no pocket. Since computational structural-based drug discovery has been developed for proteins with rigid structures and obvious pockets, it has not been successful in discovering small molecule candidate drugs against dynamic or unknown structures. In addition, structurally binding to some targets like RNAs does not guarantee their activity inhibition. Therefore, there has been a need for a computational approach to discover drugs against hard-to-drug targets with no structural information involved. I introduce a new small molecule drug discovery approach using Artificial Intelligence (AI), specifically Deep Learning (DL). This method does not require any input data from the sequence or the 3D structure of the target. Rather than targeting biomolecules' structure, AI models learn the biology of suppressing the target's activity called functional-based modeling. In three different projects, we prove the efficiency of AI-based functional-based drug discovery compared to traditional computational drug discovery. First, the collection of one of the biggest molecular datasets for molecular machine learning. MolData is one of the biggest categorized molecular datasets ever published for AI drug discovery. Second, I introduce RiboStrike, an AI-based model capable of discovering candidate drugs against micro RNAs. RiboStrike is the state-of-the-art model capable of discovering small molecule candidate drugs against RNA regardless of their size, structure, and coding functionality. We successfully discovered three candidate drugs against the functionality of miR21. Third, I introduce AMPdeep, an AI-based approach to discovering the hydrolysis of Anti-microbial Peptides (AMPs).

Subcutaneous administration of biological drugs has become highly attractive as it offers the possibility for patient self-administration. Coacervates as a subcutaneous drug delivery system provide a way to decrease injection volumes thereby reducing the risk of injection site pain. The aim with this thesis was to investigate possible coacervation between polyelectrolytes and peptide drugs under various physicochemical conditions. In this project, hyaluronic acid (HA) and carboxymethylcellulose (CMC) and their ability to coacervate with polymyxin B (PB) and vancomycin (VA) was studied. Furthermore, the release of these peptide drugs from the formulations into a release medium mimicking the subcutaneous environment was studied using UV spectroscopy. Studies showed successful coacervation between VA-CMC, PB-CMC and PB-HA. VA-CMC and PB-CMC coacervates were formed at higher peptide-polyelectrolyte charge ratios and lower ionic strengths at pH 7. The increase in charge ratio seemed to eliminate steric effects caused by the polyelectrolyte chains that most likely hindered coacervation. Furthermore, PB-CMC and PB-HA formed gel-like coacervates in the pH range of 11.73-11.84 at 1:1 charge ratio and ionic strengths 0-70mM. At such high pH values, the obtained formulations were most likely a result of PB-PB aggregation or charge regulation. From drug release studies one could conclude that VA-CMC exhibits direct release followed by a slower prolonged release profile. PB-CMC coacervates, liquid and gel, showed a sustained release profile while the PB-HA gel formulation resulted in direct release. Unfortunately, due to limitations with the experimental release rate set-up, the conclusions drawn can not be considered 100% reliable.

Part I. Development of an isoxylitone analog as an antiepileptic drug candidate. Delphinium denudatum is a medicinal plant traditionally used to treat a variety of conditions in Central Asia. Its interesting anticonvulsant effects were determined to be a property of the compound isoxylitone. Prior work from our group in collaboration with the Poulter group from Western University investigated this compound and generated a large number of isoxylitone analogs in order to optimize its antiepileptic activity. This led to the discovery of the prodrug 13 and the active form 15 shown below, which emerged as the most potent. In this work, the library of analogs was further expanded with 22 new compounds with several which matched the activity of 13 and 15, such as compounds 22 and 37, which led to valuable new insights on the activity of these analogs, and suggested other possible future improvements. In addition, efforts were continued regarding developing compound 15 as a clinical trial candidate. Optimization of the synthesis was performed to drastically reduce costs and waste of chemicals, as well as accelerating the duration of the synthesis. The purification of the final product was also greatly facilitated by the direct synthesis of 15, compared to the prior process of first preparing 13 and hydrolyzing the ester. Efforts were exerted to gather additional knowledge on the characteristics of the compound, with structural and conformational analysis via X-ray crystallography and NOE NMR as well as accelerated stability studies to test the viability of 15 in long-term storage under various conditions. All the information gathered throughout this work supported 15 and its sodium salt as excellent clinical trial candidates as treatments for epilepsy. Part II. Synthesis of SOX9 inhibitors as promoters of recovery from spinal cord injury. According to the World Health Organization, 250 to 500 thousand people develop a spinal cord injury each year with a large portion resulting in tetraplegia. A common misconception is that this is permanent because the damaged nerves cannot be repaired. In fact, nerves can and do regrow after being damaged, but cannot do so after spinal cord injuries due to formation of scar tissues which physically and chemically prevents the healing. The Brown group at Western University identified the SOX9 transcription factor as an important promoter of the formation of this scar and showed that SOX9 inhibitors could improve recovery and mobility in mice affected by spinal cord injuries. In collaboration with their group, previous work in our lab performed and SAR study on the lead compounds ZO2(1) and STL26 (2), shown below. The different sections of the molecule have been designated units A to D, to simplify discussion. Initial work by our group established an efficient method to prepare a library of analogs of the lead compounds. A number of compounds were prepared, which primarily investigated small amines as unit A and phenols with small aliphatic substituents as unit D. The initial SAR data confirmed the validity of STL26 as lead compound, as most alterations to the structure were detrimental to the SOX9 inhibitory activity. The objective of this work was to build on these preliminary SAR results, and expand the library of analogs. Larger substituents were introduced in unit A and D and showed that any group larger or smaller than diethylamide in unit A was detrimental to the activity, but that there seemed to be ample space to increase the size of the unit D isopropyl group. Analogs investigating unit B showed that adding substituents at most of the positions was detrimental, as well as changing the relative positions of unit A and B to be ortho or para to each other. However, the C4 on ring B seemed to be very tolerant to various electron donating or withdrawing functional groups. During this SAR study, a recurring theme was the awful solubility of the compounds in water, which heavily complicated their administration to mice during the bioassays. While none of the analogs tested proved superior to 2, the knowledge accrued during this work painted a clear path forward on which areas of the structure could be safely altered to improve solubility without negative impacts on SOX9 inhibition. Some additional efforts were put into obtaining an accurate three-dimensional structure of an active STL26 (2) analog, and information on the primary conformation in solution. Achieving these goals required the use of NOE NMR experiments and X-ray crystallography. One conformation was discovered to be strongly favoured as a result of an intramolecular hydrogen bond even in protic solvents. Subsequently, a small number of additional analogs were prepared containing modifications that would strongly favor or hinder the preferred conformation, in order to better understand its role in the inhibitory activity. The presence of this hydrogen bond appeared to be key to the activity of the compounds.

A novel approach to access N-Aryl nitrones via copper catalyzed coupling of benzyl alcohols with nitrosobenzenes is described. The results of mechanistic studies are conflicting but suggest this reaction proceeds through either redox process or a nucleophilic nitroso hydrate intermediate formed in situ, which was previously unprecedented. The unique electronics of this process allow access to nitrones with excellent step and atom economy, which are otherwise difficult to make using conventional methods. In this work, a total of 22 nitrones have been made. 15 of which from pure starting materials with yields ranging from 26 - 89 % and another 7 from two step, one pot reactions where the nitrosobenzenes were made in situ from commercially available anilines and reacted in a subsequent step to produce the nitrone in 8 - 46 % yield. In addition to the nitrone forming reaction occurring in the second step of a two-step sequence, we have also shown that subsequent reactions can be done on newly formed nitrones in one pot. This was demonstrated with a newly synthesized nitrone and a donor-acceptor cyclopropane in a [3+3] annulation reaction forming the cycloadduct in 90% yield. / Thesis / Master of Science (MSc) / With over 250 000 cases of resistant bacterial infections reported, and more than 5 400 directly causing Canadian deaths in 2018, we are currently facing an antibiotic crisis[67]. A particularly worrying class of resistance involves Gram-negative bacteria, as their highly impermeable outer membrane poses added complexity to their evolved resistance mechanisms[68]. The outer membrane restricts the chemical matter able to cross, making the bacteria intrinsically resistant to small molecule antibiotics and other compounds which may have intracellular targets[69],[70]. This barrier is therefore a major bottleneck for cellular mechanistic studies and compound mechanism of action, as these small molecules cannot gain entry to the cell. To circumvent this issue, outer membrane permeabilizing compounds must be discovered so that these systems can be more effectively studied. Commonly used membrane active compounds such as colistin and its derivatives, interact with both the outer and inner membranes of Gram-negative bacteria, and are toxic to cells[71]. Therefore, molecules that are outer membrane selective and nontoxic to Gram negative bacteria would be useful tools to expedite the study of biological systems.

No description available.

Muscarinic receptors are G-protein-coupled receptors that mediate the response to acetylcholine released from parasympathetic nerves. Although five mAChR subtypes (M1-M5) share a high degree of homology, they display different physiological effects including controlling smooth muscle tone to neurotransmitter release in the CNS. Hence these receptor subtypes have been investigated as potential therapeutic targets for agents capable of treating Alzheimer's Disease, Parkinson's Disease, peptic ulcer disease, COPD, urinary incontinence, and muscle spasms. Our interest in the development of subtype selective muscarinic ligands led to previous reports detailing the identification of substituted lactones as lead muscarinic compounds. Later work involved molecular modifications of those leads that included the addition of aromatic groups with a variety of substitution patterns. These efforts led to an increase in receptor affinity and produced a lactone-based muscarinic ligand with an IC50 of 340nM. As a continuation of that work, additional novel ligands were designed based on the general pharmacophoric elements proposed for the lactone-based ligands. In that model, the lactone oxygens serve as H-bond acceptor moieties while different nitrogen containing heterocycles provide the requisite cationic group. These groups may be separated by linker groups of varying sizes. In order to synthesize the lactone-based ligands mentioned above, efficient synthetic routes are required for key precursors. These include but are not limited to: 1. A novel high yield synthesis of the hydroxyethyl-lactone precursor was designed using a carefully controlled Prins reaction. The method readily quenches a cationic intermediate and simultaneously protects hydroxyl groups in a single step. A mechanism for the new route to the precursor is proposed and its use in the preparation of the target compounds is presented 2. Microwave-assisted synthesis of various sterically hindered N-aryl piperazines has been developed allowing quick access to structurally diverse muscarinic ligands These synthesis along with other newly developed routes enabled ready access to 59 novel muscarinic ligands. The ligands were tested in a general muscarinic binding assay. The result was analyzed and SAR study was performed to direct ligand design. As a result of this work, ligand affinity was improved by over 100 folds compare to the lead molecules. Several promising compounds were selected and selectivity tested. / Pharmaceutical Sciences

RNase P is a bacterial ribozyme that catalyzes the maturation of tRNA and is conserved across Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). RNase P consists of a RNA component and a protein component, RnpA. In Gram-positive bacteria, RnpA itself possesses ribonuclease activity. The Dunman group demonstrated that inhibition of RnpA activity alone or as part of the RNase P complex was sufficient to inhibit RNA degradation and exert antimicrobial activity in MRSA. Because of its low amino acid homology to mammalian homologs, RnpA may represent a novel, selective antimicrobial target for MRSA. A high throughput screen by the Dunman group identified a number of compounds which inhibit RnpA activity, including RNPA1000. However, RNPA1000 demonstrated cytotoxic effects at higher concentrations and required a high dose to achieve efficacy in a murine model of MRSA infection. We therefore selected another “hit” from the screen (RNPA2000), which contains metabotoxic hydrazide, thiourea and furan moieties, as the starting point for hit to lead activities. We sought to replace these groups, as well as the isopropylphenoxy group, to provide enhanced inhibitory potency against RNase P and RnpA, as well as lowered MIC values against MRSA1000. We designed and synthesized analogs posessing bioisosteres for these moieties and evaluated their effects in an RNase P assay as well as a RNA degradation assay. Compounds with acceptable results in both assays were tested for their antimicrobial effects in MRSA cultures. As a result of this work, several compounds with improved potency for RnpA inhibition were identified, although improved MIC was not seen. Two compounds demonstrated synergy with mupirocin, an isoleucyl-tRNA synthase inhibitor, which may represent a potential way to re-sensitize resistant bacteria to mupirocin. / Pharmaceutical Sciences

The proteasome is a large protein complex which is responsible for the majority of protein degradation in eukaryotes. Following FDA approval of the first proteasome inhibitor bortezomib for the treatment of multiple myeloma (MM) in 2003, there has been an increasing awareness of the significant therapeutic potential of proteasome inhibitors in the treatment of cancer. As of 2017, three proteasome inhibitors are approved for the treatment of MM but in clinical trials with patients bearing solid tumors these existing proteasome inhibitors have demonstrated poor results. Notably, all three FDA-approved proteasome inhibitors rely on the combination a peptide backbone and reactive electrophilic warhead to target the proteasome, and all three primarily target the catalytic subunits conferring the proteasome’s chymotrypsin-like (CT-L) activity. It is our hypothesis that compounds with non-peptidic structures, non-covalent and reversible modes of action, and unique selectivity profiles against the proteasome’s distinct catalytic subunits could have superior pharmacodynamic and pharmacokinetic properties and may bear improved activity against solid tumors relative to existing proteasome inhibitors. In an effort to discover such compounds we have employed an approach which combines computational drug screening methods with conventional screening and classic medicinal chemistry. Our efforts began with a computational screen performed in the lab of Dr. Chang-Guo Zhan. This virtual screen narrowed a library of over 300,000 drug-like compounds down to under 300 virtual hits which were then screened for proteasome inhibitory activity in an in vitro assay. Despite screening a relatively small pool of compounds, we were able to identify 18 active compounds. The majority of these hits were non-peptide in structure and lacked any hallmarks of covalent inhibition. The further development of one compound, a tri-substituted pyrazole, provided us with a proteasome inhibitor which demonstrated cytotoxic activity in a variety of human solid cancer cell lines as well as significant anti-tumor activity in a prostate cancer mouse xenograft model. We have also evaluated the in vitro pharmacokinetic properties of our lead compound and investigated its ability to evade cross-resistance phenomena in proteasome inhibitor-resistant cell lines. We believe that our lead compound as well as our drug discovery approach itself will be of interest and use to other researchers. We hope that this research effort may aid in the further development of reversible non-peptide proteasome inhibitors and may eventually deliver new therapeutic options for patients with difficult-to-treat solid tumors.

This dissertation thesis consists of a series of chapters that are interwoven by solving interesting biological problems, employing various computational methodologies. These techniques provide meaningful physical insights to promote the scientific fields of interest. Focus of chapter 1 concerns, the importance of computational tools like docking studies in advancing structure based drug design processes. This chapter also addresses the prime concerns like scoring functions, sampling algorithms and flexible docking studies that hamper the docking successes. Information about the different kinds of flexible dockings in terms of accuracy, time limitations and success studies are presented. Later the importance of Induced fit docking studies was explained in comparison to traditional MD simulations to predict the absolute binding modes. Chapter 2 and 3 focuses on understanding, how sickle cell disease progresses through the production of sickled hemoglobin and its effects on sickle cell patients. And how, hydroxyurea, the only FDA approved treatment of sickle cell disease acts to subside sickle cell effects. It is believed the primary mechanism of action is associated with the pharmacological elevation of nitric oxide in the blood, however, the exact details of this mechanism is still unclear. HU interacts with oxy and deoxyHb resulting in slow NO production rates. However, this did not correlate with the observed increase of NO concentrations in patients undergoing HU therapy. The discrepancy can be attributed to the interaction of HU competing with other heme based enzymes such as catalase and peroxidases. In these two chapters, we investigate the atomic level details of this process using a combination of flexible-ligand / flexible-receptor virtual screening (i.e. induced fit docking, IFD) coupled with energetic analysis that decomposes interaction energies at the atomic level. Using these tools we were able to elucidate the previously unknown substrate binding modes of a series of hydroxyurea analogs to human hemoglobin, catalase and the concomitant structural changes of the enzymes. Our results are consistent with kinetic and EPR measurements of hydroxyurea-hemoglobin reactions and a full mechanism is proposed that offers new insights into possibly improving substrate binding and/or reactivity. Finally in chapter 4, we have developed a 3D bioactive structure of O6-alkylguanine-DNA alkyltransferase (AGT), a DNA repair protein using Monte Carlo conformational search process. It is known that AGT prevents DNA damage, mutations and apoptosis arising from alkylated guanines. Various Benzyl guanine analouges of O6- methylguanine were tested for activity as potential inhibitors. The nature and position of the substitutions methyl and aminomethyl profoundly affected their activity. Molecular modeling of their interactions with alkyltransferase provided a molecular explanation for these results. The square of the correlation coefficient (R2 ) obtained between E-model scores (obtained from GLIDE XP/QPLD docking calculations) vs log(ED)values via a linear regression analysis was 0.96. The models indicate that the ortho-substitution causes a steric clash interfering with binding, whereas the meta-aminomethyl substitution allows an interaction of the amino group to generate an additional hydrogen bond with the protein. Using this model for virtually screening studies resulted in identification of seven lead compounds with novel scaffolds from National Cancer Institute Diversity Set2.