Herlah Barbara, Goričan Tjaša, Benedik Nika Strašek, Grdadolnik Simona Golič, Sosič Izidor, Perdih Andrej
National Institute of Chemistry, Hajdrihova 19, SI 1000 Ljubljana, Slovenia.
University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI 1000 Ljubljana, Slovenia.
Comput Struct Biotechnol J. 2024 Jul 6;23:2995-3018. doi: 10.1016/j.csbj.2024.06.037. eCollection 2024 Dec.
The 4,6-substituted-1,3,5-triazin-2(1)-ones are promising inhibitors of human DNA topoisomerase IIα. To further develop this chemical class targeting the enzyme´s ATP binding site, the triazin-2(1)-one substitution position 6 was optimized. Inspired by binding of preclinical substituted 9-purine derivative, bicyclic substituents were incorporated at position 6 and the utility of this modification was validated by a combination of molecular simulations, dynamic pharmacophores, and free energy calculations. Considering also predictions of Deepfrag, a software developed for structure-based lead optimization based on deep learning, compounds with both bicyclic and monocyclic substitutions were synthesized and investigated for their inhibitory activity. The SAR data showed that the bicyclic substituted compounds exhibited good inhibition of topo IIα, comparable to their mono-substituted counterparts. Further evaluation on a panel of human protein kinases showed selectivity for the inhibition of topo IIα. Mechanistic studies indicated that the compounds acted predominantly as catalytic inhibitors, with some exhibiting topo IIα poison effects at higher concentrations. Integration of STD NMR experiments and molecular simulations, provided insights into the binding model and highlighted the importance of the Asn120 interaction and hydrophobic interactions with substituents at positions 4 and 6. In addition, NCI-60 screening demonstrated cytotoxicity of the compounds with bicyclic substituents and identified sensitive human cancer cell lines, underlining the translational relevance of our findings for further preclinical development of this class of compounds. The study highlights the synergy between simulation and AI-based approaches in efficiently guiding molecular design for drug optimization, which has implications for further preclinical development of this class of compounds.
4,6-二取代-1,3,5-三嗪-2(1)-酮是有前景的人DNA拓扑异构酶IIα抑制剂。为了进一步开发针对该酶ATP结合位点的这类化合物，对三嗪-2(1)-酮的6位取代进行了优化。受临床前取代的9-嘌呤衍生物结合的启发，在6位引入了双环取代基，并通过分子模拟、动态药效团和自由能计算相结合的方式验证了这种修饰的效用。还考虑了Deepfrag（一种基于深度学习开发的用于基于结构的先导优化的软件）的预测结果，合成了具有双环和单环取代的化合物，并研究了它们的抑制活性。构效关系（SAR）数据表明，双环取代的化合物对拓扑异构酶IIα表现出良好的抑制作用，与单取代的类似物相当。在一组人蛋白激酶上的进一步评估显示了对拓扑异构酶IIα抑制的选择性。机理研究表明，这些化合物主要作为催化抑制剂起作用，一些在较高浓度下表现出拓扑异构酶IIα中毒效应。STD NMR实验和分子模拟的结合，为结合模型提供了见解，并突出了Asn120相互作用以及与4位和6位取代基的疏水相互作用的重要性。此外，NCI-60筛选证明了具有双环取代的化合物的细胞毒性，并鉴定出敏感的人癌细胞系，强调了我们的发现对于这类化合物进一步临床前开发的转化相关性。该研究突出了模拟和基于人工智能的方法在有效指导药物优化的分子设计方面的协同作用，这对这类化合物的进一步临床前开发具有重要意义。
