用计算方法设计光控抗癌药,实验证明光照下抑制效果提升15倍。
Computational Design and Experimental Validation of Photoactive PARP1 Inhibitors

- 结合分子模拟与机器学习,从500万候选物中筛选光响应抑制剂。
- 实验验证其中1种化合物在绿光照射下对PARP1抑制力提升15倍。
- 适合药物研发与光控治疗领域研究者参考。
光激活药物为局部疾病治疗提供了新途径,但需同时优化光物理与生物特性,开发难度高。本文利用基于原子级模拟与机器学习的新方法,对500万种假想光活性配体进行筛选。流程包括:蛋白-配体对接识别光暗条件下的差异结合;机器学习力场与量子化学计算预测pK_a、吸收光谱及热半衰期;图神经网络代理模型扩展筛选;基于机器学习力场的激发态非绝热动力学估算量子产率;自由能微扰(FEP)优化结合预测。最终优先选择数种合成可行的候选物,预期具备红移吸收、秒至分钟级热半衰期,且异构体依赖性地在可见光下调控PARP1结合。合成10种化合物并验证其光行为与抑制常数。其中化合物1在519 nm绿光照射下,对PARP1抑制常数由14.4 ± 1.9 μM升至208.8 ± 28.3 μM,提升15倍。结果验证了计算指导筛选红移型PARP1光抑制剂的有效性,也揭示水相中快速热弛豫的现有局限。
原文摘要 · Abstract (English)
Light-activated drugs are a promising way to treat localized diseases for which existing treatments have severe side effects. However, their development is complicated by the set of photophysical and biological properties that must be simultaneously optimized. Here we used computational techniques to find a set of promising candidates for the photoactive inhibition of the poly(ADP-ribose) polymerase 1 (PARP1) cancer target. Using our recently developed methods based on atomistic simulation and machine learning (ML), we screened a set of 5 million hypothetical photoactive ligands. Our workflow used protein-ligand docking to identify candidates with differential PARP1 binding under light and dark conditions; ML force fields and quantum chemistry calculations to predict p$K_\mathrm{a}$, absorption spectra, and thermal half-lives; graph-based surrogate models to screen additional compounds; excited-state nonadiabatic dynamics with ML force fields to estimate quantum yields; and free energy perturbation (FEP) to refine binding predictions. From these predictions, we prioritized a small set of synthetically feasible candidates expected to have red-shifted absorption spectra, thermal half-lives on the order of seconds to minutes, and isomer-dependent PARP1 binding under visible-light control. We synthesized 10 candidates and experimentally characterized their photobehavior and PARP1 inhibition constants. Among the validated compounds, \textbf{1} showed a 15-fold increase in inhibition of PARP1 upon green-light irradiation at 519 nm (208.8 $\pm$ 28.3 $μ$M vs 14.4 $\pm$ 1.9 $μ$M). These results validate the computation-guided screening strategy for identifying red-shifted PARP1 photoinhibitors, while also underscoring current limitations such as rapid thermal relaxation in aqueous media.
Thank you to arXiv for use of its open access interoperability. PaperDance 不是 arXiv 官方产品;中文卡片由大模型生成,请以原文为准。