Defense Date
11-28-2023
Graduation Date
Spring 5-10-2024
Availability
One-year Embargo
Submission Type
dissertation
Degree Name
PhD
Department
Medicinal Chemistry
School
School of Pharmacy
Committee Chair
Aleem Gangjee
Committee Member
Patrick T. Flaherty
Committee Member
Kevin Tidgewell
Committee Member
Rehana Leak
Committee Member
Jane Cavanaugh
Committee Member
James Drennen
Keywords
Inhibition, 1C metabolsim, antifolate, SHMT2, multitarget, SHMT1, GARFTase, AGF347
Abstract
With over 6 million death counts, cancer is the second leading cause of death in the United States. Lung cancer was the leading cause of cancer death, accounting for 23% (136,084 death count) of all cancer deaths. Other than that, colon and rectal (9%, 51,869 death count), pancreas (8%, 46,774 death count), female breast (7%, 42,275 death count), prostate (5%, 32,707 death count), and liver and intrahepatic bile duct (5%, 28,227 death count). Other cancers individually accounted for less than 5% of cancer deaths. Although cancer death rates decreased about 27% from 2001 to 2020, the therapeutic options are limited by the diversity of cancer heterogeneity and resistance to chemotherapy is poses challenges to existing therapeutic options and patient non-compliance due to adverse side effects of chemotherapy. This dissertation describes the design, synthesis, and biological evaluation of pyrimidine-based antifolates as tumor selective, cytosolic and mitochondrial multitargeted one-carbon metabolism inhibitors for tumor therapy. The goal is to attain a single tumor selective chemotherapeutic, preclinical, antifolate, with effectiveness both in early and late-stage cancer and to circumvent existing cancer therapy resistance and toxicity to antifolates in the clinic.
Clinically used all antifolates, methotrexate (MTX; DHFR inhibitor), pemetrexed (PMX; TS and GARFTase inhibitor), pralatrexate (PTX; DHFR inhibitor), and raltitrexed (RTX; TS inhibitor), are limited by two major disadvantages: (1) dose-limiting toxicities due to ubiquitous transport via the reduced folate carrier (RFC) and (2) drug-resistance; mutation and/or overexpression of RFC and target enzymes resulting in inadequate transport, reduced cellular retention, and decreased potency. In the last two decades, the role of mitochondrial one-carbon (1C) metabolism, and simulations targeting cytosolic and mitochondrial serine hydroxy methyl transferase (SHMT) isoforms have evolved as an effective therapeutic mechanism. Moreover, SHMT2 has been repeatedly reported as an onco-driver in different types of cancer and only dual inhibition of both cytosolic and mitochondrial SHMT1 and 2 isoform ensures death of cancer cells. Yet, none of the clinically used antifolates target either of the SHMT isoforms.
RFC transport of antifolates is responsible for nonselective targeting related dose limiting toxicities and is also one of the prominent mechanisms of the development of antifolate resistance. Folate receptors (FR) and the proton coupled folate transporter (PCFT) are two other folate transporters, that are sparsely expressed in healthy tissue but overexpressed in a wide variety of cancers (epithelial ovarian cancer (EOC), NSCLC, renal, endometrial, colorectal, breast cancers, hematologic malignancies, etc.). Using the recently published PMX bound chicken PCFT and human RFC crystal structure, the aim was to design classical antifolates for FRs and PCFT selective transport over RFC and inhibit 1C metabolism both in cytosol (de novo purine biosynthesis and SHMT1) and mitochondria (SHMT2). Successful design and identification of such small molecule, single agents, will potentially have multi-targeting mode of action in both cytosolic and mitochondrial compartment and thus overcome the development of drug resistance by simultaneously attacking the tumor at multiple sites.
Previously reported pyrrolo[2,3-d]pyrimidine analogs were potent cytosolic 1C metabolism inhibitors. In this study, the design and synthesis of 5-substituted pyrrolo[3,2-d]pyrimidines and their structural basis of selective multi-transport (PCFT and FR) as well as targeting 1C metabolism (GARFTase/AICARFTase and/or SHMT2 enzymes) both in cytosol and mitochondria to circumvent the dose-limiting toxicity and tumor resistance associated with the most prescribed antitumor agents like pemetrexed are reported.
This dissertation exemplifies the use of various structural features such as a pyridyl ring, thiophene ring, fluoro, and methyl groups as high impact medicinal chemistry design strategies. The pyridyl ring, fluorine and methyl substitutions in the phenyl and thiophene rings has been used to introduce both conformational flexibility and restriction, whereas the combined stereo-electronic effects of the pyridyl and fluoro groups are also assessed. For the first time, the crystal structure of both SHMT2 and GARFTase in complex with potent 5-substituted pyrrolo[3,2-d]pyrimidine antifolates has been reported. Molecular modeling studies have been used to rationalize the probable features to design and synthesize potent, selective analogs and the development of one preclinical candidate AGF-347 are discussed.
Language
English
Recommended Citation
Nayeen, M. (2024). TARGETING CANCER- ONE CARBON AT A TIME: DESIGN AND SYNTHESIS OF PYRIMIDINE BASED HETEROCYCLES AS POTENTIAL CANCER CHEMOTHERAPEUTICS (Doctoral dissertation, Duquesne University). Retrieved from https://dsc.duq.edu/etd/2347
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