Small molecules are powerful tools to probe biological systems and cure diseases. In the scope of this dissertation, small molecules were applied to study three distinct disease models: cancer, Sedaghatian-type spondylometaphyseal dysplasia (SSMD), and COVID-19. First, encouraged by the recently reported vulnerability of drug-resistant, metastatic cancers to GPX4 (Glutathione Peroxidase 4) inhibition, we examined the basis for nanomolar potency of proof-of-concept GPX4 inhibitors, which revealed an unexpected allosteric binding site. Through hierarchical screening of a lead-optimized compound library, we identified novel small molecules binding to this allosteric site. Second, a homozygous point mutation in the GPX4 gene was identified in three living patients with SSMD. With a structure-based analysis and cell models of the patient-derived variant, we found that the missense variant significantly changed the protein structure and caused substantial loss of enzymatic function. Proposed proof-of-concept treatments were subsequentially validated in patient fibroblasts. Our further structural investigation into the origin of the reduced enzymatic activity revealed a key residue modulating GPX4 enzymatic function. We also found that the variant alters the degradation of GPX4, unveiling the native degradation mechanism of GPX4 protein. Third, driven by the recent urgent need for COVID-19 antiviral therapeutics, we utilized the conservation of 3CL protease substrate-binding pockets across coronaviruses to identify four structurally divergent lead compounds that inhibit SARS-CoV-2 3CL protease. With structure-based optimization, we ultimately identified drug-like compounds with < 10 nM potency for inhibiting the SARS-CoV-2 3CL protease and blocking SARS-CoV-2 replication in human cells.

The human body is exposed to a multitude of prevalent viruses, requiring ongoing surveillance and protection by the immune system. Maintenance of human anti-viral adaptive immunity in diverse tissue sites is determined by a multitude of factors and critical for long-term protection against repeat exposure to viral infection. Yet, studies of anti-viral immunity have primarily been limited to animal studies and studies of peripheral blood in humans. Studies in mice have demonstrated that memory T cells in tissues provide superior protection against viral infection compared to circulating T cells, particularly tissue-resident memory T cells (TRM), which remain in tissues long-term without re-entering circulation. However, much remains to be understood about how anti-viral immune responses are maintained in human tissues and how adaptive immune cells in various tissues sites function upon re-exposure to viral antigens. We have established a human tissue resource through a collaboration with LiveOnNY, a local organ procurement organization, to obtain blood and multiple lymphoid and mucosal sites from donors of all ages. Using this tissue resource, we employed comprehensive cellular and molecular analysis to investigate tissue immunity to three prevalent but distinct viruses—influenza A, CMV, and SARS-CoV-2. We compared CD8+ T cells recognizing ubiquitous and longstanding viruses influenza A and CMV across multiple tissue sites of 58 organ donors ages 1-78 years in order to elucidate how covariates of virus, tissue, age, and sex impact the anti-viral immune response. Using flow cytometry, T cell receptor repertoire sequencing, functional assays, and single-cell transcriptional profiling, we showed that virus specificity and tissue localization are the primary drivers of anti-viral T cell immune responses in the human body, with age and sex further influencing T cell subset differentiation. Specifically, virus specificity correlated with virus-specific T cell distribution, memory subset differentiation, and clonal repertoire, while tissue localization determined overall subset distribution and functional responses. We further investigated the tissue-localized immune response to emergent SARS-CoV-2. By examining multiple tissues of organ donors who had recovered from natural infection by SARS-CoV-2, we showed that adaptive memory immune responses persisted months after infection, with memory T and B cells preferentially localized in the lung and lung-associated lymph node. Persisting memory cell populations included tissue-resident T and B cells, particularly in the lung, as well as germinal center B cells in the lung-associated lymph node along with follicular helper T cells, indicating ongoing generation of humoral immunity. Together, these findings highlight the importance of tissue-localized anti-viral immunity and help to define characteristics of site-specific protective immunity that may be leveraged for the development of more effective treatment and prevention strategies.

The SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic has led to widespread socioeconomic and clinical damage. The coalescent response from the global scientific community has been unparalleled, both in speed and furor. Numerous efficacious interventions have been developed and deployed, including several vaccines, antibody therapies, and drugs. Yet, SARS-CoV-2 embodies the quintessential virological issue which threaten these achievements; rapid evolution in the face of selective pressure. This dissertation investigates such adaptations by SARS-CoV-2, and accordingly, modalities to combat this virus despite such evasive measures. To this end, we first studied the antigenic properties of several members of the B.1.1.529 or Omicron lineage of SARS-CoV-2. We observed that B.1.1.529.1 (BA.1), B.1.1.529.1.1 (BA.1.1), and B.1.1.529.2 (BA.2) are the most antibody resistant SARS-CoV-2 variants to-date, while being antigenically unique between each other. Consequently, we turned to explore modalities which may withstand such formidable resistance. We undertook some of the first explorations of a heterologous booster vaccination regimen, finding expanded breadth and potency against SARS-CoV-2, suggesting it may be one simple measure that could be utilized. We also sought to identify broadly neutralizing SARS-CoV-2 antibodies, isolating several with breadth against coronaviruses beyond that of SARS-CoV-2. One of these antibodies, 10-40, was determined to be the broadest receptor-binding domain-directed antibody reported to-date. Finally, we examined an alternative viral target, the 3CL protease. We discovered several SARS-CoV 3CL protease inhibitors that could be repurposed for inhibition of SARS-CoV-2 and determined their crystal structures, which could allow for their use as lead compounds. We further developed and conducted a deep mutational scan of the 3CL protease to examine the activity of all possible single point mutants, revealing that the enzyme had unexpected malleability, as well as several conserved sites that may be targeted by future inhibitors. The SARS-CoV-2 pandemic has been a remarkable trial, but has also served to demonstrate the good that science can do. We hope that this work has been a small contribution among such difficult times.

This dissertation is divided into two main sections describing major portions of my Ph.D. research: (1) development of two enzymatic assays for identifying inhibitors of SARS-CoV-2 RNA dependent RNA polymerase (RdRp) and the associated proofreading exonuclease complexes, two key enzymatic activities of SARS-CoV-2, the virus responsible for the COVID-19 pandemic and (2) the design and implementation of four novel single-color fluorescent DNA sequencing by synthesis (SBS) methods, including the synthesis of many of the key nucleotide analogues required for these studies. In response to the COVID-19 pandemic, the first part of my research is focused on the discovery of potential therapeutics for combating coronavirus infections. Chapter 1 describes the identification of several polymerase and exonuclease inhibitors for SARS-CoV-2 using novel mass spectrometry-based molecular assays. SARS-CoV-2 has an exonuclease complex, which removes nucleotide inhibitors such as Remdesivir that are incorporated into the viral RNA during replication, reducing the efficacy of these drugs for treating COVID-19. Combinations of inhibitors of both the viral RdRp and the exonuclease could overcome this deficiency. Chapter 1 reports the identification of hepatitis C virus NS5A inhibitors Pibrentasvir and Ombitasvir as SARS-CoV-2 exonuclease inhibitors. In the presence of identified exonuclease inhibitors, RNAs terminated with the active forms of the prodrugs like Sofosbuvir, Remdesivir and Favipiravir were largely protected from excision by the exonuclease, while in the absence of exonuclease inhibitors, there was rapid excision. Viral cell culture studies also demonstrate significant synergy using this combination strategy. This study supports the use of combination drugs that inhibit both the SARS-CoV-2 polymerase and exonuclease for effective COVID-19 treatment. Chapters 2-6 describe the single-color DNA SBS studies. Chapter 2 provides essential background on the structure of DNA, the DNA polymerase reaction, and several key DNA sequencing technologies, with an emphasis on the design of nucleotide analogues for the DNA SBS approach. Chapter 3 delineates a one-color fluorescent DNA SBS method based on a set of nucleotide reversible terminators (NRTs) comprising two orthogonal cleavable linkers, one fluorescent dye and one anchor. Chapter 4 describes a one-color hybrid DNA sequencing approach using a set of dideoxynucleotide analogues bearing two orthogonal cleavable linkers, one fluorophore and one anchor as well as a set of unlabeled NRTs. By introducing a pH responsive fluorophore into the design of nucleotide analogues, Chapter 5 demonstrates a novel type of single-color DNA SBS method using a set of NRTs comprising one pH-responsive fluorescent dye or one non-responsive fluorescent dye tethered with one cleavable linker. Chapter 6 presents another option for the single-color DNA sequencing technique using a set of deoxynucleotide analogues comprising the above pH responsive or non-responsive dyes tethered with a cleavable linker, along with a set of unlabeled NRTs. The one-color SBS approaches have the potential for higher sensitivity, miniaturization and cost effectiveness compared with four-color SBS methods. Finally, Chapter 7 summarizes the SARS-CoV-2 antiviral drug discovery and one-color sequencing techniques and discusses potential follow-up research on these projects.