Université de Paris, BFA, UMR 8521, CNRS, ERL U1133, Inserm, F-75013 Paris, France.
Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France.
Viruses. 2020 May 14;12(5):537. doi: 10.3390/v12050537.
The non-structural protein NS1 of influenza A viruses is considered to be the major antagonist of the interferon system and antiviral defenses of the cell. It could therefore represent a suitable target for novel antiviral strategies. As a first step towards the identification of small compounds targeting NS1, we here investigated the druggable potential of its RNA-binding domain since this domain is essential to the biological activities of NS1. We explored the flexibility of the full-length protein by running molecular dynamics simulations on one of its published crystal structures. While the RNA-binding domain structure was remarkably stable along the simulations, we identified a flexible site at the two extremities of the "groove" that is delimited by the antiparallel α-helices that make up its RNA-binding interface. This groove region is able to form potential binding pockets, which, in 60% of the conformations, meet the druggability criteria. We characterized these pockets and identified the residues that contribute to their druggability. All the residues involved in the druggable pockets are essential at the same time to the stability of the RNA-binding domain and to the biological activities of NS1. They are also strictly conserved across the large sequence diversity of NS1, emphasizing the robustness of this search towards the identification of broadly active NS1-targeting compounds.
甲型流感病毒的非结构蛋白 NS1 被认为是干扰素系统和细胞抗病毒防御的主要拮抗剂。因此，它可能是新型抗病毒策略的合适靶点。作为鉴定靶向 NS1 的小分子的第一步，我们在此研究了其 RNA 结合域的可成药性潜力，因为该结构域对 NS1 的生物学活性至关重要。我们通过对其已发表晶体结构之一进行分子动力学模拟来探索全长蛋白的柔韧性。虽然 RNA 结合域结构在模拟过程中非常稳定，但我们在由构成其 RNA 结合界面的反平行α-螺旋限定的“沟槽”的两个末端处鉴定了一个柔性位点。该沟槽区域能够形成潜在的结合口袋，其中 60%的构象符合成药性标准。我们对这些口袋进行了表征，并确定了对其成药性有贡献的残基。所有参与成药性口袋的残基同时对 RNA 结合域的稳定性和 NS1 的生物学活性至关重要。它们在 NS1 的大序列多样性中也是严格保守的，这强调了这种搜索方法在鉴定广泛有效的 NS1 靶向化合物方面的稳健性。
