College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada.
Biochim Biophys Acta Gen Subj. 2023 Jun;1867(6):130347. doi: 10.1016/j.bbagen.2023.130347. Epub 2023 Mar 21.
SIMR1281 is a potent anticancer lead candidate with multi- target activity against several proteins; however, its mechanism of action at the molecular level is not fully understood. Revealing the mechanism and the origin of multitarget activity is important for the rational identification and optimization of multitarget drugs.
We have used a variety of biophysical (circular dichroism, isothermal titration calorimetry, viscosity, and UV DNA melting), biochemical (topoisomerase I & II assays) and computational (molecular docking and MD simulations) methods to study the interaction of SIMR1281 with duplex DNA structures.
The biophysical results revealed that SIMR1281 binds to dsDNA via an intercalation-binding mode with an average binding constant of 3.1 × 10 M. This binding mode was confirmed by the topoisomerases' inhibition assays and molecular modeling simulations, which showed the intercalation of the benzopyrane moiety between DNA base pairs, while the remaining moieties (thiazole and phenyl rings) sit in the minor groove and interact with the flanking base pairs adjacent to the intercalation site.
The DNA binding characteristics of SIMR1281, which can disrupt/inhibit DNA function as confirmed by the topoisomerases' inhibition assays, indicate that the observed multi-target activity might originate from ligand intervention at nucleic acids level rather than due to direct interactions with multiple biological targets at the protein level.
The findings of this study could be helpful to guide future optimization of benzopyrane-based ligands for therapeutic purposes.
SIMR1281 是一种有效的抗癌先导化合物，对多种蛋白质具有多靶点活性；然而，其在分子水平上的作用机制尚不完全清楚。揭示其作用机制和多靶点活性的起源对于合理识别和优化多靶点药物非常重要。
我们使用了多种生物物理（圆二色性、等温滴定量热法、粘度和 UV-DNA 熔解）、生化（拓扑异构酶 I 和 II 测定）和计算（分子对接和 MD 模拟）方法来研究 SIMR1281 与双链 DNA 结构的相互作用。
生物物理结果表明，SIMR1281 通过嵌入结合模式与 dsDNA 结合，平均结合常数为 3.1×10 M。这种结合模式得到了拓扑异构酶抑制测定和分子建模模拟的证实，该模拟显示苯并吡喃部分嵌入 DNA 碱基对之间，而其余部分（噻唑和苯基环）位于小沟中并与嵌入位点相邻的侧翼碱基对相互作用。
SIMR1281 的 DNA 结合特性，如拓扑异构酶抑制测定所证实的那样，可以破坏/抑制 DNA 功能，这表明观察到的多靶点活性可能源于配体在核酸水平上的干预，而不是由于与蛋白质水平上的多个生物靶标直接相互作用。
本研究的发现可能有助于指导未来基于苯并吡喃的配体的优化，以达到治疗目的。
