Départment de physique, Université de Montréal, Case postale 6128, succursale Centre-ville, Montréal, QC, H3C 3J7 Canada.
Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC, H7V 1B7 Canada.
Phys Chem Chem Phys. 2021 Jul 14;23(27):14873-14888. doi: 10.1039/d1cp01790j.
The COVID-19 disease caused by the virus SARS-CoV-2, first detected in December 2019, is still emerging through virus mutations. Although almost under control in some countries due to effective vaccines that are mitigating the worldwide pandemic, the urgency to develop additional vaccines and therapeutic treatments is imperative. In this work, the natural polyphenols corilagin and 1,3,6-tri-O-galloy-β-d-glucose (TGG) are investigated to determine the structural basis of inhibitor interactions as potential candidates to inhibit SARS-CoV-2 viral entry into target cells. First, the therapeutic potential of the ligands are assessed on the ACE2/wild-type RBD. We first use molecular docking followed by molecular dynamics, to take into account the conformational flexibility that plays a significant role in ligand binding and that cannot be captured using only docking, and then analyze more precisely the affinity of these ligands using MMPBSA binding free energy. We show that both ligands bind to the ACE2/wild-type RBD interface with good affinities which might prevent the ACE2/RBD association. Second, we confirm the potency of these ligands to block the ACE2/RBD association using a combination of surface plasmon resonance and biochemical inhibition assays. These experiments confirm that TGG and, to a lesser extent, corilagin, inhibit the binding of RBD to ACE2. Both experiments and simulations show that the ligands interact preferentially with RBD, while weak binding is observed with ACE2, hence, avoiding potential physiological side-effects induced by the inhibition of ACE2. In addition to the wild-type RBD, we also study numerically three RBD mutations (E484K, N501Y and E484K/N501Y) found in the main SARS-CoV-2 variants of concerns. We find that corilagin could be as effective for RBD/E484K but less effective for the RBD/N501Y and RBD/E484K-N501Y mutants, while TGG strongly binds at relevant locations to all three mutants, demonstrating the significant interest of these molecules as potential inhibitors for variants of SARS-CoV-2.
由病毒 SARS-CoV-2 引起的 COVID-19 疾病于 2019 年 12 月首次被发现，目前仍在通过病毒突变不断出现。尽管由于具有减轻全球大流行的有效疫苗，在一些国家已基本得到控制，但开发额外疫苗和治疗方法的紧迫性是至关重要的。在这项工作中，研究了天然多酚柯里拉京和 1,3,6-三-O-没食子酰基-β-D-葡萄糖（TGG），以确定抑制剂相互作用的结构基础，作为抑制 SARS-CoV-2 病毒进入靶细胞的潜在候选物。首先，评估配体在 ACE2/野生型 RBD 上的治疗潜力。我们首先使用分子对接，然后是分子动力学，以考虑构象灵活性，构象灵活性在配体结合中起着重要作用，仅使用对接无法捕捉到这种灵活性，然后使用 MMPBSA 结合自由能更精确地分析这些配体的亲和力。我们表明，两种配体都与 ACE2/野生型 RBD 界面具有良好的亲和力，这可能阻止 ACE2/RBD 结合。其次，我们使用表面等离子体共振和生化抑制测定的组合，证实了这些配体阻断 ACE2/RBD 结合的能力。这些实验证实，TGG 并且在较小程度上，柯里拉京，抑制 RBD 与 ACE2 的结合。实验和模拟都表明，配体优先与 RBD 相互作用，而与 ACE2 的结合较弱，因此避免了 ACE2 抑制引起的潜在生理副作用。除了野生型 RBD 外，我们还数值研究了在主要 SARS-CoV-2 关注变体中发现的三个 RBD 突变（E484K、N501Y 和 E484K/N501Y）。我们发现，柯里拉京对 RBD/E484K 同样有效，但对 RBD/N501Y 和 RBD/E484K-N501Y 突变体的效果较差，而 TGG 则强烈结合到所有三个突变体的相关位置，证明这些分子作为 SARS-CoV-2 变体的潜在抑制剂具有重要意义。
