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Identification of modulators of deoxyribonucleotide pools and replication stress in cancer


Regulation of intracellular deoxyribonucleotide triphosphate (dNTP) pools are critical for DNA replication and repair. DNA replication is a highly demanding process, which requires precise timing and supply of adequate unmodified dNTPs. Imbalanced dNTP pools can lead to genomic instability and result in cancer development. Several studies have reported cancer cells are more susceptible than normal cells to perturbations in the quantity, quality and balance of dNTP pools. Therefore, therapeutic agents targeting dNTP synthesis have been used for treatment of several types of cancer. Despite these studies, the molecular mechanisms that regulate quantity and quality of dNTP pools are not completely understood. Studying the crosstalk between metabolic and signaling mechanisms for regulation of dNTP pools are required to develop better pharmacological interventions against cancer.

Dysregulation of dNTP pools can occur in different ways -

Modulators of dNTP pools’ quantity: Similar to other major branches of cellular

metabolism, nucleotide biosynthesis consists of redundant and convergent biosynthetic pathways. dNTPs required for DNA replication and repair can be produced by the de novo pathway (DNP) or by the nucleoside salvage pathway (NSP). Therefore, both pathways are required to be targeted simultaneously to achieve therapeutic efficacy.


Modulators of dNTP pools’ quality: Reactive oxygen species (ROS), generated by both

endogenous and exogenous routes can pose a significant threat to cellular integrity by inducing oxidative damage. This results in DNA base modifications, formation of apurinic/apyrimidinic lesions, which can be mutagenic and lead to DNA damage. Hence, pharmacological intervention by redox modulators is being investigated as promising anti-cancer therapy.

Regulation of dNTP pools by signaling pathways: Dysregulation of quantity or quality of dNTP pools lead to transient disruption of replication fork progression, termed as replication stress (RS), defined by accumulation of unprotected single-stranded DNA (ssDNA) at stalled replication forks. In order to protect genomic integrity, cells activate the replication stress response (RSR) pathway to limit the amount of ssDNA and subsequent DNA damage. However, the metabolic consequences of RSR on nucleotide metabolism are poorly understood.

This thesis focuses on development of pharmacological modulators to regulate dNTP pools. Further it explores the interconnections between these dNTP pool modulators and replication stress to establish combination therapies against cancer.

In Chapter 1, we identified metabolic alterations in response to ATR inhibition in acute lymphoblastic leukemia, and developed a combination therapy targeting the metabolic vulnerabilities.

In Chapter 2, we developed a novel dCK (the rate-limiting enzyme of NSP) inhibitor, with improved metabolic stability and bioavailability. We studied preclinical pharmacokinetics and dose-response relationships of dCK inhibitor for translation to first in-human clinical trials.

In Chapter 3, we evaluated a series of novel isoquinoline based thiosemicarbazone compounds to discover a highly potent copper ionophore which induces oxidative stress and DNA damage against aggressive solid tumor models.

In Chapter 4, we designed and applied a metabolic modifier screen which identified multiple protein kinase inhibitors as having non-canonical targets within pyrimidine metabolism.

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