Interaction between human telomere and a carbazole derivative: a molecular dynamics simulation of a quadruplex stabilizer and telomerase inhibitor.
The mechanism of inhibition of telomerase by drugs is a key factor in an understanding of guanine-quadruplex complex stabilization during human cancer. This study describes a simulated annealing docking and molecular dynamics simulation to investigate a synthesized potent inhibitor, 3,6-bis(1-methyl-4-vinylpyridinium iodine) carbazole (BMVC), which stabilizes the quadruplex structure of the human telomeric DNA sequence d[AG3(T(2)AG(3))3] and inhibits telomerase activity. The compound was predicted to selectively interact with the quadruplex structure. During our simulation, the binding affinities were calculated and used to predict the best drug-binding sites as well as enhanced selectivity compared with other compounds. Our studies suggest that the simulation results quite coincide with the experimental results. In addition, molecular modeling shows that a 2:1 binding model involving the external binding of BMVC to both ends of the G-quartet of d[AG(3)(T(2)AG)3))3] is the most stable binding mode and this agrees with the absorbance titration results that show two binding sites. Of particular interest is that one pyridinium ring and carbazole moiety of the BMVC can stack well at the end of G-quartet. This implies that BMVC is a good human quadruplex stabilizer and also a good telomerase inhibitor.
Yang
Dah-Yen
DY
Department of Life Sciences and Institute of Genome Sciences, Institute of Bioinformatics, and Structural Biology Program, National Yang-Ming University, Taipei 112, Taiwan.
Chang
Ta-Chau
TC
Sheu
Sheh-Yi
SY
D002227:Carbazoles / Q000737:chemistry* / Q000494:pharmacology; D003198:Computer Simulation; D054856:G-Quadruplexes; D006801:Humans; D008958:Models, Molecular; D015394:Molecular Structure; D011726:Pyridinium Compounds / Q000737:chemistry* / Q000494:pharmacology; D019098:Telomerase / Q000037:antagonists & inhibitors*; D016615:Telomere / Q000737:chemistry*
C486012:3,6-bis(1-methyl-4-vinylpyridium)carbazole diiodide; D002227:Carbazoles; D011726:Pyridinium Compounds; D019098:Telomerase