Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore, Madhya Pradesh 453552, India.
J Chem Inf Model. 2022 Aug 22;62(16):3800-3813. doi: 10.1021/acs.jcim.2c00461. Epub 2022 Aug 11.
Dengue virus, a flavivirus that causes dengue shock syndrome and dengue hemorrhagic fever, is currently prevalent worldwide. A two-component protease (NS2B-NS3) is essential for maturation, representing an important target for designing anti-flavivirus drugs. Previously, consideration has been centered on developing active-site inhibitors of NS2B-NS3pro. However, the flat and charged nature of its active site renders difficulties in developing inhibitors, suggesting an alternative strategy for identifying allosteric inhibitors. The allosterically sensitive site of the dengue protease is located near Ala125, between the 120s loop and 150s loop. Using atomistic molecular dynamics simulations, we have explored the protease's conformational dynamics upon binding of an allosteric inhibitor. Furthermore, characterization of the inherent flexible loops (71-75s loop, 120s loop, and 150s loop) is carried out for allosteric-inhibitor-bound wild-type and mutant A125C variants and a comparison is performed with its unbound state to extract the structural changes describing the inactive state of the protease. Our study reveals that compared to the unliganded system, the inhibitor-bound system shows large structural changes in the 120s loop and 150s loop in contrast to the rigid 71-75s loop. The unliganded system shows a closed-state pocket in contrast to the open state for the wild-type complex that locks the protease into the open and inactive-state conformations. However, the mutant complex fluctuates between open and closed states. Also, we tried to see how mutation and binding of an allosteric inhibitor perturb the connectivity in a protein structure network (PSN) at contact levels. Altogether, our study reveals the mechanism of conformational rearrangements of loops at the molecular level, locking the protein in an inactive conformation, which may be useful for developing allosteric inhibitors.
登革热病毒是一种黄病毒，可引起登革热休克综合征和登革出血热，目前在全球广泛流行。二组分蛋白酶（NS2B-NS3）是成熟所必需的，是设计抗黄病毒药物的重要靶点。以前，研究重点集中在开发 NS2B-NS3pro 的活性位点抑制剂上。然而，其活性位点的平坦和带电性质使得开发抑制剂变得困难，这表明寻找别构抑制剂是一种替代策略。登革热蛋白酶的别构敏感位点位于 Ala125 附近，在 120s 环和 150s 环之间。我们使用原子分子动力学模拟，研究了蛋白酶与别构抑制剂结合时的构象动力学。此外，对别构抑制剂结合的野生型和突变体 A125C 变体的固有柔性环（71-75s 环、120s 环和 150s 环）进行了特征描述，并与未结合状态进行了比较，以提取描述蛋白酶无活性状态的结构变化。我们的研究表明，与未结合系统相比，抑制剂结合系统在 120s 环和 150s 环中显示出较大的结构变化，而在刚性 71-75s 环中则没有。与野生型复合物的闭口袋相比，未结合系统显示出开放状态，这将蛋白酶锁定在开放和无活性构象中。然而，突变体复合物在开放和关闭状态之间波动。此外，我们还试图观察突变和别构抑制剂的结合如何在接触水平上扰乱蛋白质结构网络（PSN）中的连接。总的来说，我们的研究揭示了分子水平上环构象重排的机制，将蛋白质锁定在无活性构象中，这可能有助于开发别构抑制剂。
