Department of Chemistry and Physical Sciences, Pace University, New York, NY 10038, USA.
Department of Mathematics and Department of Research Computing, Princeton University, Princeton, NJ 08544, USA.
Molecules. 2019 Apr 21;24(8):1574. doi: 10.3390/molecules24081574.
The human telomeric G-quadruplex (G4) is an attractive target for developing anticancer drugs. Natural products protoberberine alkaloids are known to bind human telomeric G4 and inhibit telomerase. Among several structurally similar protoberberine alkaloids, epiberberine (EPI) shows the greatest specificity in recognizing the human telomeric G4 over duplex DNA and other G4s. Recently, NMR study revealed that EPI recognizes specifically the hybrid-2 form human telomeric G4 by inducing large rearrangements in the 5'-flanking segment and loop regions to form a highly extensive four-layered binding pocket. Using the NMR structure of the EPI-human telomeric G4 complex, here we perform molecular dynamics free energy calculations to elucidate the ligand selectivity in the recognition of protoberberines by the human telomeric G4. The MM-PB(GB)SA (molecular mechanics-Poisson Boltzmann/Generalized Born) Surface Area) binding free energies calculated using the Amber force fields bsc0 and OL15 correlate well with the NMR titration and binding affinity measurements, with both calculations correctly identifying the EPI as the strongest binder to the hybrid-2 telomeric G4 wtTel26. The results demonstrated that accounting for the conformational flexibility of the DNA-ligand complexes is crucially important for explaining the ligand selectivity of the human telomeric G4. While the MD-simulated (molecular dynamics) structures of the G-quadruplex-alkaloid complexes help rationalize why the EPI-G4 interactions are optimal compared with the other protoberberines, structural deviations from the NMR structure near the binding site are observed in the MD simulations. We have also performed binding free energy calculation using the more rigorous double decoupling method (DDM); however, the results correlate less well with the experimental trend, likely due to the difficulty of adequately sampling the very large conformational reorganization in the G4 induced by the protoberberine binding.
人类端粒 G-四链体（G4）是开发抗癌药物的有吸引力的靶标。天然产物原小檗碱生物碱已知能结合人类端粒 G4 并抑制端粒酶。在几种结构相似的原小檗碱生物碱中，表小檗碱（EPI）在识别人类端粒 G4 与双链 DNA 和其他 G4 方面表现出最大的特异性。最近，NMR 研究表明，EPI 通过诱导 5'-侧翼片段和环区域的大重排，形成高度广泛的四层结合口袋，特异性识别杂交-2 形式的人类端粒 G4。利用 EPI-人类端粒 G4 复合物的 NMR 结构，我们在这里进行分子动力学自由能计算，以阐明人类端粒 G4 对原小檗碱的配体选择性。使用 Amber 力场 bsc0 和 OL15 计算的 MM-PB（GB）SA（分子力学-泊松 Boltzmann/广义 Born）表面面积）结合自由能与 NMR 滴定和结合亲和力测量很好地相关，两种计算都正确地将 EPI 识别为杂交-2 端粒 G4 wtTel26 的最强结合物。结果表明，考虑 DNA-配体复合物的构象灵活性对于解释人类端粒 G4 的配体选择性至关重要。虽然 G-四链体-生物碱复合物的 MD 模拟（分子动力学）结构有助于解释为什么 EPI-G4 相互作用比其他原小檗碱更优，但在 MD 模拟中在结合部位附近观察到与 NMR 结构的结构偏差。我们还使用更严格的双去耦方法（DDM）进行了结合自由能计算；然而，结果与实验趋势相关性较差，可能是由于很难充分采样原小檗碱结合诱导的 G4 中非常大的构象重排。
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