Unwinding of the DNA double helix and the separation of newly replicated DNA are controlled by DNA topoisomerases, enzymes involved in the cleavage and passing of strands of DNA (33, 34). The topoisomerase I enzymes cut a single strand of the helix and allow topologically constrained DNA to relax, but separation of the strands does not occur. Both strands can be concurrently cleaved by the topoisomerase II enzymes, and this cleavage allows separation of the strands (33, 34).
DNA topoisomerases I and II are both molecular targets in cancer chemotherapy. Until 1988 the only established inhibitors of topoisomerase I were camptothecin and its derivatives (35). In the presence of a camptothecin, the enzyme creates characteristic single-stranded protein-associated DNA breaks and inhibition of the DNA resealing event (35, 36, 37). Structure-activity relationships of substituted camptothecins suggest that the molecules interact with an asymmetrical receptor site on the enzyme or enzyme-DNA complex (36). The correlation of antitumor activity of a series of camptothecins against the murine leukemias with their activity as inhibitors of the enzyme was considered indicative that the antitumor activity of the camptothecins is the result of topoisomerase I inhibition (36).
In contrast, topoisomerase II is inhibited by many agents, including the DNA intercalating anthracyclines, 4'-(9-acridinylamino)-methanesulfon-m-anisidide (m-AMSA), and the demethylepipodophyllotoxins etoposide (VP-16) and teniposide (VM-26) (38, 39, 40, 41). The enzyme effects site-specific DNA cleavage that continues only in the presence of the drug. Sensitivity to the drug increases with intracellular enzyme content (41). Those cells with diminished enzyme content are resistant to the drug. Topoisomerase II, in the presence of the inhibitor, creates both single- and double-stranded protein-associated DNA breaks. The DNA breaks have been postulated to require a ternary complex of enzyme, DNA, and drug (34, 35). When the two DNA intercalators mitoxantrone and m-AMSA were assayed by inhibition of clonogenicity, mitoxantrone was significantly more toxic than m-AMSA, and it was proposed that this difference in cytotoxicity was related to persistence of the ternary complex (42).
Topoisomerase II-DNA binding agents create mean graph patterns that are grouped by COMPARE, and selected examples are presented. Alkylating agents also occasionally appeared within the top 10 matches. As with the antimetabolites, all COMPARE studies presented here with topoisomerase II agents were performed at the GI50 level.
Doxorubicin (Adriamycin)
The Table shows the top 10 matches to the anthracycline seed, doxorubicin (Adriamycin). All matches were topoisomerase II inhibitors.
| Compound | NSC Number | 2D Structure | 3D Structure | Cell Inhibition Data |
|---|---|---|---|---|
| doxorubicin (Adriamycin) | 123127 | 2D | 3D | Cell Data |
m-AMSA (Amsacrine)
The COMPARE list created by using m-AMSA as a probe is shown in the Table. The four topoisomerase II interactive agents menogaril, mitoxantrone, VM-26, and VP-16 appear within the top 10 but are accompanied by topoisomerase I interactive topotecan and alkylating agents piperazinedione, dianhydrogalactitol, hepsulfam, and piperazine alkylator.
| Compound | NSC Number | 2D Structure | 3D Structure | Cell Inhibition Data |
|---|---|---|---|---|
| m-AMSA | 249992 | 2D | 3D | Cell Data |
| menogaril | 269148 | 2D | 3D | Cell Data |
| mitoxantrone | 301739 | 2D | 3D | Cell Data |
| VM-26 | 122819 | 2D | 3D | Cell Data |
| VP-16 | 141540 | 2D | 3D | Cell Data |
| topotecan | 609699 | 2D | 3D | Cell Data |
Anthrapyrazoles and Anthracenediones
The anthrapyrazoles are a series of 5-[(aminoalkyl)amino]-substituted anthra[1,9-cd]pyrazol-6(2H)-ones that differ from the anthracenediones [e.g., dihydroxyanthracenedione (DHAD)] in that a pyrazole ring has been fused to the anthracene system in place of a carbonyl group (43). Development of the compounds was pursued with the goal of noncardiotoxic agents that retain the antitumor activity of anthracyclines. Two members of this series, anthrapyrazole (NSC 355644) and oxanthrazole (piroxantrone, NSC 349174), are in the standard agent database. The anthrapyrazoles are strong DNA-binding agents (44) that are topoisomerase II inhibitors. DHAD is the only anthracenedione in the standard agent database.
When anthrapyrazole derivative NSC 355644 was used as the seed to produce the COMPARE shown in the Table, all matching compounds were topoisomerase II agents. The rankings were dominated by the anthrapyrazoles and anthracyclines with the closest matches being the structurally very similar anthrapyrazole derivative NSC 349174 (oxanthrazole) and the anthracenedione DHAD.
| Compound | NSC Number | 2D Structure | 3D Structure | Cell Inhibition Data |
|---|---|---|---|---|
| anthrapyrazole | 355644 | 2D | 3D | Cell Data |
| oxanthrazole | 349174 | 2D | 3D | Cell Data |
| DHAD (mitoxantrone) | 301739 | 2D | 3D | Cell Data |
VM-26
With VM-26 used as a seed in the Table, VP-16 was the closest match. VM-26 (teniposide) and VP-16 (etopside) are structurally similar demethylepipodophyllotoxin topoisomerase II inhibitors, and they are the only demethylepipodophyllotoxins in the database. The remaining nine matches are all known topoisomerase II active agents.
| Compound | NSC Number | 2D Structure | 3D Structure | Cell Inhibition Data |
|---|---|---|---|---|
| VM-26 | 122819 | 2D | 3D | Cell Data |
| VP-16 | 141540 | 2D | 3D | Cell Data |