Abstract
BackgroundHuman topoisomerase I catalyzes the relaxation of DNA supercoils in fundamental cell processes like transcription, replication and chromosomal segregation. It is the only target of the camptothecin family of anticancer drugs. Among these, topotecan has been used to treat lung and ovarian carcinoma for several years. Camptothecins reversibly binds to the covalent intermediate DNA-enzyme, stabilizing the cleavable complex and reducing the religation rate. The stalled complex then collides with the progression of the replication fork, producing lethal double strand DNA breaks and eventually cell death.Methodology/Principal FindingsLong lasting molecular dynamics simulations of the DNA-topoisomerase I binary complex and of the DNA-topoisomerase-topotecan ternary complex have been performed and compared. The conformational space sampled by the binary complex is reduced by the presence of the drug, as observed by principal component and cluster analyses. This conformational restraint is mainly due to the reduced flexibility of residues 633–643 (the region connecting the linker to the core domain) that causes an overall mobility loss in the ternary complex linker domain. During the simulation, DNA/drug stacking interactions are fully maintained, and hydrogen bonds are maintained with the enzyme. Topotecan keeps the catalytic residue Lys532 far from the DNA, making it unable to participate to the religation reaction. Arg364 is observed to interact with both the B and E rings of topotecan with two stable direct hydrogen bonds. An interesting constrain exerted by the protein on the geometrical arrangement of topotecan is also observed.Conclusions/SignificanceAtomistic-scale understanding of topotecan interactions with the DNA-enzyme complex is fundamental to the explaining of its poisonous effect and of the drug resistance observed in several single residue topoisomerase mutants. We observed significant alterations due to topotecan in both short-range interactions and long-range protein domain communications.
Highlights
Human topoisomerase I catalyzes the relaxation of DNA supercoils in fundamental cell processes like transcription, replication and chromosomal segregation [1,2]
The root mean square deviations (RMSD) value reaches an average value of about 3 Ain both simulations during the first nanoseconds, showing strong oscillations during the whole simulation time
The analysis shows that the conformational space visited by the linker in the native system is strongly reduced by the presence of topotecan, since fewer clusters are visited by the ternary system and the conformations in these have a higher degree of similarity
Summary
Human topoisomerase I (hTop1) catalyzes the relaxation of DNA supercoils in fundamental cell processes like transcription, replication and chromosomal segregation [1,2]. Due to its high toxicity, CPT cannot be used as an antitumor agent and a number of derivatives have been developed and are currently used in clinical therapy; among these, topotecan (TPT; Hycamtin, GlaxoSmithKline) is widely used to treat lung and ovarian carcinoma [11]. Human topoisomerase I catalyzes the relaxation of DNA supercoils in fundamental cell processes like transcription, replication and chromosomal segregation. It is the only target of the camptothecin family of anticancer drugs. The stalled complex collides with the progression of the replication fork, producing lethal double strand DNA breaks and eventually cell death
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
