Ranjan Nihar, Kellish Patrick, King Ada, Arya Dev P
Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University , Clemson, South Carolina 29634, United States.
NUBAD LLC , 900 B West Faris Road, Greenville, South Carolina 29605, United States.
Biochemistry. 2017 Dec 12;56(49):6434-6447. doi: 10.1021/acs.biochem.7b00929. Epub 2017 Nov 29.
Small molecules that modulate biological functions are targets of modern day drug discovery efforts. In a common platform fragment-based drug discovery, two fragments that bind to adjacent sites on a target are identified and are then linked together using different linkers to identify the linkage for optimum activity. What are not known from these studies are the effects these linkers, which typically contain C, H, and O atoms, have on the properties of the individual fragment. Herein, we investigate such effects in a bisbenzimidazole fragment whose derivatives have a wide range of therapeutic applications in nucleic acid recognition, sensing, and photodynamic therapy and as cellular probes. We report a dramatic effect of linker length and composition of alkynyl (clickable) Hoechst 33258 derivatives in target binding and cell uptake. We show that the binding of Hoechst 33258-modeled bisbenzimidazoles (1-9) that contain linkers of varying lengths (3-21 atoms) display length- and composition-dependent variation in B-DNA stabilization using a variety of spectroscopic methods. For a dodecamer DNA duplex, the thermal stabilization varied from 0.3 to 9.0 °C as the linker length increased from 3 to 21 atoms, respectively. Compounds with linker lengths of ≤11 atoms (such as compounds 1 and 5) are localized in the nucleus, while compounds with long linkers (such as compounds 8 and 9) are distributed in the extranuclear space, as well, with possible interactions with extranuclear targets. These findings provide insights into future drug design by revealing how linkers can influence the biophysical and cellular properties of individual drug fragments.
调节生物功能的小分子是现代药物研发工作的目标。在基于片段的药物发现这一常见平台中，会识别出与靶点上相邻位点结合的两个片段，然后使用不同的连接子将它们连接在一起，以确定具有最佳活性的连接方式。这些研究中尚不清楚的是，这些通常含有碳、氢和氧原子的连接子对各个片段的性质有何影响。在此，我们在一种双苯并咪唑片段中研究此类影响，该片段的衍生物在核酸识别、传感、光动力疗法以及作为细胞探针方面具有广泛的治疗应用。我们报道了炔基（可点击）Hoechst 33258衍生物的连接子长度和组成对靶点结合及细胞摄取的显著影响。我们表明，使用多种光谱方法，含有不同长度（3 - 21个原子）连接子的Hoechst 33258模拟双苯并咪唑（1 - 9）与B - DNA的结合显示出长度和组成依赖性变化。对于一个十二聚体DNA双链体，随着连接子长度从3个原子增加到21个原子，热稳定性分别从0.3℃变化到9.0℃。连接子长度≤11个原子的化合物（如化合物1和5）定位于细胞核中，而具有长连接子的化合物（如化合物8和9）也分布在核外空间，可能与核外靶点相互作用。这些发现通过揭示连接子如何影响单个药物片段的生物物理和细胞性质，为未来的药物设计提供了见解。
