The diphenyl-pyrazole compound anle138b is a known inhibitor of oligomeric aggregate formation in vitro and in vivo. Therefore, anle138b is considered a promising drug candidate to beneficially interfere with neurodegenerative processes causing devastating pathologies in humans. The atomistic details of the aggregation inhibition mechanism, however, are to date unknown since the ensemble of small nonfibrillar aggregates is structurally heterogeneous and inaccessible to direct structural characterization. Here, we set out to elucidate anle138b’s mode of action using all-atom molecular dynamics simulations on the multi-microsecond time scale. By comparing simulations of dimeric to tetrameric aggregates from fragments of four amyloidogenic proteins (Aβ, hTau40, hIAPP, and Sup35N) in the presence and absence of anle138b, we show that the compound reduces the overall number of intermolecular hydrogen bonds, disfavors the sampling of the aggregated state, and remodels the conformational distributions within the small oligomeric peptide aggregates. Most notably, anle138b preferentially interacts with the disordered structure ensemble via its pyrazole moiety, thereby effectively blocking interpeptide main chain interactions and impeding the spontaneous formation of ordered β-sheet structures, in particular those with out-of-register antiparallel β-strands. The structurally very similar compound anle234b was previously identified as inactive by in vitro experiments. Here, we show that anle234b has no significant effect on the aggregation process in terms of reducing the β-structure content. Moreover, we demonstrate that the hydrogen bonding capabilities are autoinhibited due to steric effects imposed by the molecular geometry of anle234b and thereby indirectly confirm the proposed inhibitory mechanism of anle138b. We anticipate that the prominent binding of anle138b to partially disordered and dynamical aggregate structures is a generic basis for anle138b’s ability to suppress toxic oligomer formation in a wide range of amyloidogenic peptides and proteins.

中文翻译：

---

解决Anle138b对肽寡聚物形成的抑制作用的原子模式

二苯基吡唑化合物anle138b是已知的体外和体内寡聚聚集体形成的抑制剂。因此，anle138b被认为是一种有前途的候选药物，可以有益地干扰导致人类毁灭性病理的神经退行性过程。然而，迄今为止，聚集抑制机制的原子细节尚不清楚，因为小的非原纤维聚集体在结构上是异质的，无法直接进行结构表征。在这里，我们着手使用多微秒级的全原子分子动力学模拟来阐明anle138b的作用方式。在存在和不存在anle138b的情况下，通过比较来自四种淀粉样蛋白（Aβ，hTau40，hIAPP和Sup35N）片段的二聚体到四聚体聚集体的模拟，我们表明该化合物减少了分子间氢键的总数，不利于聚集状态的采样，并重塑了小寡聚肽聚集体中的构象分布。最值得注意的是，anle138b优先通过其吡唑部分与无序结构体相互作用，从而有效地阻断肽间主链相互作用并阻碍自发形成有序的β-折叠结构，特别是那些具有失配的反平行β链的结构。结构上非常相似的化合物anle234b先前已通过体外实验鉴定为无活性。在这里，我们显示anle234b在降低β结构含量方面对聚集过程没有显着影响。而且，我们证明氢键结合能力由于anle234b分子几何结构所施加的空间效应而被自动抑制，从而间接证实了anle138b的拟议抑制机制。我们预期anle138b与部分无序和动态聚集结构的突出结合是anle138b抑制多种淀粉样蛋白生成肽和蛋白质中毒性低聚物形成的能力的通用基础。