Design, Synthesis, and Biological Evaluation of Novel Indenoisoquinolines as Potential Anticancer Agents

Daniel Edward Beck, Purdue University


The research in this thesis is focused on the design, synthesis, and biological evaluation of indenoisoquinolines that inhibit the human topoisomerase IB enzyme (Top1). At present, there are only two FDA-approved cancer chemotherapeutic drugs that target this enzyme. These agents bind to a covalent Top1-DNA cleavage complex intermediate that is formed when Top1 relaxes supercoiled DNA. The effect of this stabilization is that a DNA replication fork can “collide” with the cleavage complex, which produces cytotoxic DNA damage products. Although the present arsenal of Top1 inhibitors is effective in the treatment of solid tumors, their common camptothecin-based structure is plagued by physicochemical and pharmacological issues. For these reasons, alternative structures with Top1 inhibitory activity are currently needed. The objectives of this research were to: (1) establish new and improved synthetic routes to three clinically studied Top1 inhibitors that are based on an indenoisoquinoline scaffold; (2) investigate the structure-activity relationships (S.A.R.) of indenoisoquinolines substituted with carbohydrate-derived and carbohydrate-mimetic moieties; (3) seek out bioisosteric replacements for the nitro group in the highly active 3-nitroindenoisoquinoline Top1 inhibitor series; and (4) design and test dimeric indenoisoquinolines that could potentially inhibit both Top1 and DNA repair enzyme tyrosyl DNA phosphodiesterase 1 (TDP1). Three compounds discovered in the Cushman laboratory are under investigation in humans and canines as potential anticancer drugs. Indotecan (LMP400) and indimitecan (LMP776) are being studied in Phase I clinical trials, and one of these two agents may be promoted to a Phase II trial in the future. LMP744 is being studied in canines, and it will likely be studied in man. As the three agents enter into and progress through clinical trials, increasing supplies of the drugs will be required to support their studies. New synthetic routes to the three drugs were devised to overcome problems with their present manufacturing routes, including the requirement for column chromatography purifications. The new routes overcome several problems and provide the drugs in greater overall yields. In the second effort, thirty-two new indenoisoquinolines substituted with linear and cyclic carbohydrate-derived or carbohydrate-mimetic moieties were designed and synthesized as potential Top1 inhibitors. The rationale for this substitution and the design process were aided by the X-ray crystal structures of an indenoisoquinoline and an indolocarbazole glycoside bound separately to the Top1-DNA cleavage complex. Aromatic ring substitution with 2,3-dimethoxy-8,9-methylenedioxy or a 3-nitro group was found to exert beneficial effects on antiproliferative and Top1 inhibitory activities. While the length of the linear carbohydrate side chains clearly correlates with antiproliferative activity, the relationship between stereochemistry and biological activity is less clearly defined. The potencies of 12 of the new indenoisoquinolines equaled or exceeded that of camptothecin. The third effort was focused on making improvements to a promising class of indenoisoquinoline Top1 inhibitors, albeit one with a potentially serious toxicology risk. 3-Nitroindenoisoquinolines often exhibit potent antiproliferative effects on cancer cells and display high Top1 inhibitory activity; however, their 3-nitro group could be reduced in vivo to species with nonspecific and harmful protein and DNA reactivity. The undesirable nitro toxicophore was replaced by ten other functional groups that could retain the desired biological activities and minimize potential safety risks. The data reveal that fluorine and chlorine may substitute for the 3-nitro group with minimal loss to Top1 inhibitory and antiproliferative activities. The new information gained from these efforts was then used to guide the design of additional novel indenoisoquinolines that, in some cases, exhibit growth and Top1 inhibitory activities on par with analogous 3-nitroindenoisoquinolines. Finally, in the fourth effort, dimeric indenoisoquinolines were designed using the available S.A.R. data for their Top1 and TDP1 inhibitory activities. The dimers, or bis(indenoisoquinolines), were decorated with the 2,3-dimethoxy-8,9-methylenedioxy aromatic ring substitution pattern on each monomer with the expectation of conferring high Top1 inhibitory activity. The polyaminoalkyl linker chains uniting two monomers were modulated to vary both the number of basic amines and length. Contrary to expectation, the Top1 inhibitory activities of the new compounds were weaker than those for aromatic ring-unsubstituted analogues. However, each of the dimeric compounds did exhibit inhibitory activity towards TDP1. These results can educate the future design of improved dual Top1-TDP1 inhibitors.




Cushman, Purdue University.

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