Minor groove-directed and intercalative ligand-DNA interactions in the poisoning of human DNA topoisomerase I by protoberberine analogs
Minor groove-directed and intercalative ligand-DNA interactions in the poisoning of human DNA topoisomerase I by protoberberine analogs
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DOI：
10.1021/bi971272q
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发表时间：
1997-10-14
期刊：
影响因子：
2.9
通讯作者：
Liu, LF
中科院分区：
文献类型：
--
作者：
Pilch, DS;Yu, C;Liu, LF
用光谱、量热法、DNA裂解、电泳法和计算机模拟技术研究了3种原小檗碱类似物8-脱甲基小檗碱(DMC)、5，6-二氢-8-脱甲基小檗碱(DHDMC)和巴马汀的DNA结合和拓扑异构酶中毒性质，它们的B-和/或D-环的化学结构不同。DNA拓扑异构酶介导的切割分析表明，这些化合物对哺乳动物II型拓扑异构酶没有毒性。相比之下，三种原小檗碱类似物对人拓扑异构酶I的毒性顺序如下：DHDMC>；DMC>；巴马汀。三种原黄连素类似物与DNA的结合诱导了负流动的线性二向色性信号以及宿主双链的解离。这两个观察结果与原黄连素与双链DNA结合的插层模式一致。然而，对DMC和DHDMC的DNA结合性能的比较表明，原黄连素类似物并不像经典的DNA嵌入剂那样具有典型的DNA嵌入剂的行为。DMC和DHDMC的结合性质只是B环5，6位的饱和状态不同。具体地说，DMC B环中5-6双键的饱和，从而将其转化为DHDMC分子，与增强的DNA解离以及DNA结合偏好的逆转有关，从具有不可接近或闭塞的小沟槽的DNA双链{Poly[d(G-C)](2)}到具有可进入或畅通的小沟槽的DNA双链{Poly[d(A-T)](2)和Poly[d(I-C)](2)}。此外，对DHDMC和巴马汀的DNA结合性能的比较表明，将DHDMC D-环上的11-甲氧基部分转移到9位，从而将其转化为巴马汀，与具有畅通小槽的双链以及具有闭塞小槽的双链的结合亲和力降低有关。这些DNA结合特性与原黄连素的“混合模式”DNA结合模型是一致的，在该模型中，配体分子的一部分插入到双螺旋中，而配体分子的非插入部分突出到宿主双链的小槽中，在那里它可以与排列在小槽的底部和/或壁上的原子相互作用。此外，B环5，6位的饱和导致A环相对于由C环和D环形成的平面倾斜，似乎稳定了宿主双链体与原黄连素配体的次要凹槽定向部分之间的相互作用。对DHDMC-聚[d(A-T)](2)络合物的计算机模拟研究表明，这种相互作用可能涉及配体A环与主链上排列在主体双链小槽上的主链糖原子之间的van der Waals接触。上面提到的拓扑异构酶I中毒的等级表明，这种微小的沟槽定向相互作用可能在原黄连素类似物引起的拓扑异构酶I中毒中发挥重要作用。综上所述，我们的研究结果与最近由少量沟槽结合的三苯并咪唑引起的拓扑异构酶I中毒有关[Sun，Q.，Gatto，B.，Yu，C.，Liu，A.，Liu，L.F.，&LaVoie，E.J.(1995)J.Med.化学。38,3638-3644]，提示在拓扑异构酶I的中毒过程中，微小的沟槽导向的配体-DNA相互作用可能具有普遍意义。
Spectroscopic, calorimetric, DNA cleavage, electrophoretic, and computer modeling techniques have been employed to characterize the DNA binding and topoisomerase poisoning properties of three protoberberine analogs, 8-desmethylcoralyne (DMC), 5,6-dihydro-8-desmethylcoralyne (DHDMC), and palmatine, which differ in the chemical structures of their B- and/or D-rings. DNA topoisomerase-mediated cleavage assays revealed that these compounds were unable to poison mammalian type II topoisomerase. By contrast, the three protoberberine analogs poisoned human topoisomerase I according to the following hierarchy: DHDMC > DMC > palmatine. DNA binding by all three protoberberine analogs induced negative flow linear dichroism signals as well as unwinding of the host duplex. These two observations are consistent with an intercalative mode of protoberberine binding to duplex DNA. However, a comparison of the DNA binding properties for DMC and DHDMC, which differ only by the state of saturation at the 5,6 positions of the B-ring, revealed that the protoberberine analogs do not ''behave'' like classic DNA intercalators. Specifically, saturation of the 5-6 double bond in the B-ring of DMC, thereby converting it to the DHDMC molecule, was associated with enhanced DNA unwinding as well as a reversal of DNA binding preference from a DNA duplex with an inaccessible or occluded minor groove {poly[d(G-C)](2)} to DNA duplexes with accessible or unobstructed minor grooves {poly[d(A-T)](2) and poly[d(I-C)](2)}. In addition, a comparison of the DNA binding properties for DHDMC and palmatine revealed that transferring the 11-methoxy moiety on the D-ring of DHDMC to the 9 position, thereby converting it to palmatine, was associated with a reduction in binding affinity for both duplexes with unobstructed minor grooves as well as for duplexes with occluded minor grooves. These DNA binding properties are consistent with a ''mixed-mode'' DNA binding model for protoberberines in which a portion of the ligand molecule intercalates into the double helix, while the nonintercalated portion of the ligand molecule protrudes into the minor groove of the host duplex, where it is thereby available for interactions with atoms lining the floor and/or walls of the minor groove. Furthermore, saturation at the 5,6 positions of the B-ring, which causes the A-ring to be tilted relative to the plane formed by rings C and D, appears to stabilize the interaction between the host duplex and the minor groove-directed portion of the protoberberine ligand. Computer modeling studies on the DHDMC-poly[d(A-T)](2) complex suggest that this interaction may involve van der Waals contacts between the ligand A-ring and backbone sugar atoms lining the minor groove of the host duplex. The hierarchy of topoisomerase I poisoning noted above suggests that this minor groove-directed interaction may play an important role in topoisomerase I poisoning by protoberberine analogs. In the aggregate, our results presented here, coupled with the recent demonstration of topoisomerase I poisoning by minor groove-binding terbenzimidazoles [Sun, Q., Gatto, B., Yu, C., Liu, A., Liu, L. F., & LaVoie, E. J. (1995) J. Med. Chem. 38, 3638-3644], suggest that minor groove-directed ligand-DNA interactions may be of general importance in the poisoning of topoisomerase I.