Chen Q, Shafer R H, Kuntz I D
Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143-0446, USA.
Biochemistry. 1997 Sep 23;36(38):11402-7. doi: 10.1021/bi970756j.
Ligands capable of specific recognition of RNA structures are of interest in terms of the principles of molecular recognition as well as potential chemotherapeutic applications. We have approached the problem of identifying small molecules with binding specificity for the RNA double helix through application of the DOCK program [Kuntz, I. D., Meng, E. C., and Shoichet, B. K. (1994) Acc. Chem. Res. 27, 117-123], a structure-based method for drug discovery. A series of lead compounds was generated through a database search for ligands with shape complementarity to the RNA deep major groove. Compounds were then evaluated with regard to their fit into the minor groove of B DNA. Those compounds predicted to have an optimal fit to the RNA groove and strong discrimination against DNA were examined experimentally. Of the 11 compounds tested, 3, all aminoglycosides, exhibited pronounced stabilization of RNA duplexes against thermal denaturation with only marginal effects on DNA duplexes. One compound, lividomycin, was examined further, and shown to facilitate the ethanol-induced B to A transition in calf thymus DNA. Fluorine NMR solvent isotope shift measurements on RNA duplexes containing 5-fluorouracil provided evidence that lividomycin binds in the RNA major groove. Taken together, these results indicate that lividomycin recognizes the general features of the A conformation of nucleic acids through deep groove binding, confirming the predictions of our DOCK analysis. This approach may be of general utility for identifying ligands possessing specificity for additional RNA structures as well as other nucleic acid structural motifs.
就分子识别原理以及潜在的化疗应用而言，能够特异性识别RNA结构的配体备受关注。我们通过应用DOCK程序[昆茨，I. D.，孟，E. C.，和肖伊谢特，B. K.（1994年）《化学研究述评》27卷，第117 - 123页]来解决识别对RNA双螺旋具有结合特异性的小分子这一问题，DOCK程序是一种基于结构的药物发现方法。通过数据库搜索与RNA深大沟具有形状互补性的配体，生成了一系列先导化合物。然后评估这些化合物与B型DNA小沟的契合度。对那些预测与RNA沟具有最佳契合度且对DNA有强烈区分作用的化合物进行了实验研究。在测试的11种化合物中，有3种，均为氨基糖苷类，对RNA双链体热变性表现出明显的稳定作用，而对DNA双链体仅有轻微影响。对其中一种化合物青紫霉素进行了进一步研究，结果表明它能促进小牛胸腺DNA中乙醇诱导的B型向A型转变。对含有5 - 氟尿嘧啶的RNA双链体进行的氟核磁共振溶剂同位素位移测量提供了证据，表明青紫霉素结合在RNA大沟中。综合这些结果表明，青紫霉素通过深沟结合识别核酸A构象的一般特征，证实了我们DOCK分析的预测。这种方法可能普遍适用于识别对其他RNA结构以及其他核酸结构基序具有特异性的配体。
