Protoberberines represent a new structural class of organic cations with selective cytotoxicity against CNS cancer cells. Their cytotoxic mechanisms have been demonstrated to involve poisoning of human DNA topoisomerases. Using purified topoisomerases, protoberberines are shown to poison both topoisomerases I and II (TOP1 and TOP2). These dual poisons of topoisomerases represent an emerging class of new anticancer agents with potential improved activity over either TOP I - or TOP2-specific poisons. The overall goal of this proposal is to understand the molecular mechanisms by which protoberberines differentially poison human TOP I and TOP2. Toward this goal, over one hundred protoberberines have been synthesized and evaluated for door ability to poison topoisomerases and kill a broad range of tumor cells. In addition to these biochemical and cell biological studies, we also have initiated biophysical studies of protoberberine interactions with DNA. Preliminary studies have suggested that a mixed mode of DNA binding (incorporating both minor groove-directed and intercalative interactions) is responsible for the dual poisoning activities of protoberberines. We hypothesize that the minor groove-directed interaction is critical for TOP I poisoning, while the intercalative interaction is important in TOP2 poisoning.
The Specific Aims of this proposal are: (a) To characterize and cross-correlate the DNA binding and topoisomerase poisoning properties of protoberberines. These studies are designed to provide evidence supporting the role of specific drug-DNA interactions (i.e. minor groove-directed versus intercalative) in differential topoisomerase poisoning. (b) To determine the role of minor groove-directed interactions in TOP I poisoning. Specifically, we will test the possibility that minor groove binding induces a DNA structural perturbation that results in stimulation of TOP1-mediated DNA cleavage. (c) To characterize specific drug-DNA and drug-enzyme interactions within the ternary cleavable complex using various biochemical methods, such as affinity labeling and protein modification interference. These studies are designed to assess the individual molecular interactions that govern the formation and stabilization of the ternary cleavable complex. Our proposed studies using this new class of topoisomerase poisons will enhance our understanding of the molecular basis for topoisomerase poisoning, which has been established as the key molecular event responsible for the antitumor activity of a broad -range of naturally occurring and synthetic compounds.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Project (R01)
Project #
Application #
Study Section
Experimental Therapeutics Subcommittee 1 (ET)
Program Officer
Fu, Yali
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Medicine & Dentistry of NJ
Schools of Medicine
United States
Zip Code
Feng, Wei; Satyanarayana, Mavurapu; Tsai, Yuan-Chin et al. (2009) 12-Substituted 2,3-dimethoxy-8,9-methylenedioxybenzo[i]phenanthridines as novel topoisomerase I-targeting antitumor agents. Bioorg Med Chem 17:2877-85
Zhu, Shejin; Ruchelman, Alexander L; Zhou, Nai et al. (2006) 6-Substituted 6H-dibenzo[c,h][2,6]naphthyridin-5-ones: reversed lactam analogues of ARC-111 with potent topoisomerase I-targeting activity and cytotoxicity. Bioorg Med Chem 14:3131-43
Zhu, Shejin; Ruchelman, Alexander L; Zhou, Nai et al. (2005) Esters and amides of 2,3-dimethoxy-8,9-methylenedioxy-benzo[i]phenanthridine-12-carboxylic acid: potent cytotoxic and topoisomerase I-targeting agents. Bioorg Med Chem 13:6782-94
Daroui, Parima; Desai, Shyamal D; Li, Tsai-Kun et al. (2004) Hydrogen peroxide induces topoisomerase I-mediated DNA damage and cell death. J Biol Chem 279:14587-94
Ruchelman, Alexander L; Singh, Sudhir K; Ray, Abhijit et al. (2004) 11H-Isoquino[4,3-c]cinnolin-12-ones; novel anticancer agents with potent topoisomerase I-targeting activity and cytotoxicity. Bioorg Med Chem 12:795-806
Ruchelman, Alexander L; Kerrigan, John E; Li, Tsai-Kun et al. (2004) Nitro and amino substitution within the A-ring of 5H-8,9-dimethoxy-5-(2-N,N-dimethylaminoethyl)dibenzo[c,h][1,6]naphthyridin-6-ones: influence on topoisomerase I-targeting activity and cytotoxicity. Bioorg Med Chem 12:3731-42
Ruchelman, Alexander L; Zhu, Shejin; Zhou, Nai et al. (2004) Dimethoxybenzo[i]phenanthridine-12-carboxylic acid derivatives and 6H-dibenzo[c,h][2,6]naphthyridin-5-ones with potent topoisomerase I-targeting activity and cytotoxicity. Bioorg Med Chem Lett 14:5585-9
Desai, Shyamal D; Zhang, Hui; Rodriguez-Bauman, Alexandra et al. (2003) Transcription-dependent degradation of topoisomerase I-DNA covalent complexes. Mol Cell Biol 23:2341-50
Yu, Younong; Singh, Sudhir K; Liu, Angela et al. (2003) Substituted dibenzo[c,h]cinnolines: topoisomerase I-targeting anticancer agents. Bioorg Med Chem 11:1475-91
Kerrigan, John E; Pilch, Daniel S; Ruchelman, Alexander L et al. (2003) 5H-8,9-dimethoxy-5-(2-N,N-dimethylaminoethyl)dibenzo[c,h][1,6]naphthyridin-6-ones and related compounds as TOP1-targeting agents: influence of structure on the ternary cleavable complex formation. Bioorg Med Chem Lett 13:3395-9

Showing the most recent 10 out of 21 publications