Defense Date


Graduation Date

Fall 1-1-2017


One-year Embargo

Submission Type


Degree Name



Medicinal Chemistry


School of Pharmacy

Committee Chair

Aleem Gangjee

Committee Member

Marc W. Harrold

Committee Member

Patrick T. Flaherty

Committee Member

Kevin Tidgewell

Committee Member

Lauren O'Donnell


This dissertation describes an introduction, background and research progress in the areas of agents designed as (a) selective Pneumocystis jirovecii dihydrofolate reductase (pjDHFR) inhibitors for pneumocystis pneumonia (PCP) infection; (b) inhibitors of microtubule polymerization and multiple receptor tyrosine kinase (RTK) for potential treatment of cancer; and (c) substrates for tumor-targeted therapy for cancer.

PCP is a host species-specific infection. Most of the drugs, synthesized and evaluated so far, have been tested against Pneumocystis carinii dihydrofolate reductase (the causative organism in rats), which would not necessarily be effective against pjDHFR (the causative organism in humans). Trimethoprim-sulfamethoxazole (TMP-SMX) combination, which has been used for PCP for decades, has major limitations due to low inhibitory potency of TMP, side-effects of SMX and emergence of resistant strains expressing mutated dihydropteroate synthase enzyme (target of SMX). For patients unresponsive or resistant to this treatment, newer drugs are critically needed. The absence of an X-ray crystal structure of pjDHFR poses a large gap in drug discovery efforts. The status quo, as it pertains to designing selective inhibitors for an enzyme, is to exploit the amino acid differences between the active sites of the desired and undesired target enzyme. Structure based design, using a pjDHFR homology model and through identification of amino acid differences between pjDHFR and hDHFR active sites, has been presented in the text. Novel synthetic strategies were developed for efficient synthesis of 6- and 7-substituted 5-methyl-pyrrolo[2,3-d]pyrimidine-2,4-diamines, N6-substituted pyrido[3,2-d]pyrimidine-2,4,6-triamines, 6-(arylthio)pyrido[3,2-d]pyrimidine-2,4-diamines and 7-(arylthio)pyrido[3,2-d]pyrimidine-2,4-diamines.

In cancer chemotherapy, the two major limitations are the dose-limiting toxicities of clinically used agents and development of resistant to the treatment. Combination chemotherapy with antiangiogenic agents and microtubule targeting agents has shown an advantage against both these drawbacks. Single agents with both antiangiogenic activity and cytotoxicity would afford a therapy that circumvents pharmacokinetic problems of multiple agents, avoids drug-drug interactions, lowers the drug dose, decrease overlapping toxicities, and delays or prevents tumor cell resistance. The work in this dissertation discusses the development of fused pyrimidines, aimed to inhibit tubulin polymerization as well as act as antiangiogenic agents which inhibit one or more of the receptor tyrosine kinases (RTKs)- vascular endothelial growth factor receptor-2 (VEGFR2), platelet derived growth factor receptor-β (PDGFRβ) and epidermal growth factor receptor (EGFR), using molecular modeling studies. This work also reviews the synthesis pyrrolo[3,2-d]pyrimidines and thieno[3,2-d]pyrimidines and discusses novel synthetic strategies for substituted pyrrolo[3,2-d]pyrimidines and thieno[3,2-d]pyrimidines.

Cancer cells transport folates through reduced folate carrier (RFC), Proton-Coupled Folate Transporter (PCFT) and/or Folate receptors (FR). Among several targeting strategies for cancer cells, selectively targeting through PCFT and FRs, over RFC have been successfully investigated. The next valid step in the field is to carry out a structure based design of agents to gain selectivity for PCFT and/or FRs transport over RFC and thus avoid dose-limiting toxicities. Absence of X-ray crystal structures for PCFT and RFC make this step impossible. The work in this dissertation discusses our efforts to fulfil this gap in the literature by developing a 3D QSAR pharmacophore for PCFT and RFC.

PMX, the most widely used antifolate has three disadvantages: (i) transport by RFC; (ii) dependence on its polyglutamylation for potency; and (iii) development of resistance due to mutagenesis in the target enzyme (thymidylate synthase). This dissertation focuses on development of substituted-pyrrolo[3,2-d]pyrimidines to combat the above-mentioned drawbacks of PMX, using the X-ray crystal structures of intracellular targets and transporters and using the basic principles of scaffold hopping and bioisosteric replacements. The work described herein discusses our efforts to obtain agents with inhibition of two or more intracellular targets to inhibit de novo purine biosynthesis. Synthetic efforts for the development of pyrrolo[3,2-d]pyrimidines with different linkers and aryl substitutions have been discussed.