Many chronic, age-related disorders could be mitigated by enhancing the activity of enzymes that regulate biochemical signaling pathways, but all known modes of enzyme activation rely on allosteric binding sites, which have only been identified in less than 10% of proteins. Sirtuins (SIRT1-7) are nicotinamide adenine dinucleotide (NAD+)-dependent deacylases playing critical roles in lifespan and age-related diseases. The physiological importance of sirtuins and the reduction in their catalytic activity with the age-related decline in NAD+ levels have stimulated intense interest in designing sirtuin-activating compounds; however, except for substrate-specific allosteric SIRT1 activators, methodologies for rational design of sirtuin-activating compounds are lacking. Here, we introduce methods for the activation of such enzymes that do not rely on allosteric binding sites, and we demonstrate their successful application to the discovery of first-in-class activators of sirtuin enzymes. We establish how all-atom simulations of an enzyme’s active site under the potential of a small molecule modulator can be used to identify molecular properties that achieve desired changes in local enzyme conformational degrees of freedom conducive to the enhancement of catalytic activity. We apply computational high-throughput screening based on this biophysical model for activation of sirtuin enzymes to the major mitochondrial sirtuin SIRT3, which plays a critical role in age-related disorders but does not have a known allosteric site; we thereby identify first-in-class, nonallosteric activators of this enzyme. These compounds are the first reported steady-state activators of the major mitochondrial sirtuin enzyme, and they operate according to a mode of action not shared by any existing drug. Two such compounds can almost double the catalytic efficiency of SIRT3 with respect to NAD+, thus compensating for the loss in SIRT3 activity that occurs due to the age-related decline in NAD+, and they may be developed for therapeutic applications to combat multiple types of age-related disorders. These discoveries establish a foundation for the development of a new class of drugs that function through the activation of enzymes by modulation of local conformational ensembles. Published by the American Physical Society 2024

中文翻译：

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计算驱动的 SIRT3 激活化合物的发现和表征，这些化合物在 NAD+ 耗竭下完全恢复催化活性


许多慢性、与年龄相关的疾病可以通过增强调节生化信号通路的酶的活性来缓解，但所有已知的酶激活模式都依赖于变构结合位点，而变构结合位点仅在不到 10% 的蛋白质中被发现。Sirtuins （SIRT1-7） 是烟酰胺腺嘌呤二核苷酸 （NAD+） 依赖性脱酰酶，在寿命和年龄相关疾病中起关键作用。去乙酰化酶的生理重要性及其催化活性的降低随着 NAD+ 水平与年龄相关的下降而降低，激发了人们对设计去乙酰化酶激活化合物的浓厚兴趣;然而，除了底物特异性变构 SIRT1 激活剂外，缺乏合理设计 sirtuin 激活化合物的方法。在这里，我们介绍了不依赖于变构结合位点的此类酶的激活方法，并展示了它们成功应用于发现 sirtuin 酶的一流激活剂。我们确定了如何在小分子调节剂的电位下对酶活性位点进行全原子模拟来识别分子特性，这些分子特性实现了有利于增强催化活性的局部酶构象自由度的预期变化。我们基于这种生物物理模型应用计算高通量筛选，以激活主要线粒体 sirtuin SIRT3 的 sirtuin 酶，它在年龄相关疾病中起关键作用，但没有已知的变构位点;因此，我们确定了这种酶的同类首创的非变构激活剂。 这些化合物是首次报道的主要线粒体 sirtuin 酶的稳态激活剂，它们根据任何现有药物都没有的作用方式发挥作用。两种这样的化合物几乎可以使 SIRT3 相对于 NAD+ 的催化效率增加一倍，从而补偿由于与年龄相关的 NAD+ 下降而导致的 SIRT3 活性损失，它们可能被开发用于治疗应用以对抗多种类型的年龄相关疾病。这些发现为一类新型药物的开发奠定了基础，这些药物通过调节局部构象集合来激活酶来发挥作用。美国物理学会 2024 年出版