[论文解读] The Computation of Cyclic Peptide with Prolin-Prolin Bond as Fusion Inhibitor of DENV Envelope Protein through Molecular Docking and Molecular Dynamics Simulation

Arli Aditya Parikesit, Hilyatuz Zahroh+3 more|arXiv (Cornell University)|Oct 27, 2015

Mosquito-borne diseases and control参考文献 14被引用 4

一句话总结

本研究通过分子对接和分子动力学（MD）模拟，鉴定出含有脯氨酸-脯氨酸键的环状肽PYRRP和PAWRP，可有效抑制登革病毒（DENV）包膜蛋白的融合。PYRRP在310 K和312 K下稳定了DENV包膜蛋白二聚体，表现出作为融合抑制剂的强潜力；而PAWRP在310 K下表现出高亲和力和复合物稳定性，支持其作为抗病毒药物的进一步开发。

ABSTRACT

A disease that caused by dengue virus (DENV) has become the major health problem of the world. Nowadays, no effective treatment is available to overcome the disease due to the level of dengue virus pathogeneses. A novel treatment method such as antiviral drug is highly necessary for coping with the dengue disease. Envelope protein is one of the non-structural proteins of DENV, which engaged in the viral fusion process. The fusion process is mediated by the conformational change in the protein structure from dimer to trimer state. The previous research showed the existing cavity on the dimer structure of the envelope protein. The existing ligand could get into cavity of the envelope protein, stabilize the dimer structure or hamper the transition of dimer protein into trimer. In this fashion, the fusion process can be prevented. The aim of this research is designing the cyclic peptide with prolin-prolin bond as fusion inhibitor of DENV envelope protein through molecular docking and molecular dynamics simulation. The screening of 3,883 cyclic peptides, each of them connected by prolin-prolin bond, through molecular docking resulted in five best ligands. The pharmacological and toxicity character of these five ligands were analised in silico. The result showed that PYRRP was the best ligand. PAWRP was also chosen as the best ligand because it showed good affinity with protein cavity. Stability of ligand-protein complex was analyzed by molecular dynamics simulation. The result showed that PYRRP ligand was able to support the stability of DENV envelope protein dimer structure at 310 K and 312 K. While PAWRP ligand actively formed complex with the DENV envelope protein at 310 K compared to 312 K. Thus the PYRRP ligand has a potential to be developed as DENV fusion inhibitor.

研究动机与目标

• 设计具有脯氨酸-脯氨酸键的新型环状肽，作为靶向登革病毒（DENV）包膜蛋白的融合抑制剂。
• 通过靶向包膜蛋白构象变化介导的病毒融合机制，弥补登革病毒有效抗病毒治疗的不足。
• 鉴定能够稳定DENV包膜蛋白二聚体形式的配体，从而阻止其向融合性三聚体状态的转变。
• 通过体外评估候选配体的药代动力学和毒性特征，以优先筛选先导化合物。

提出的方法

• 使用分子对接方法对3,883种通过脯氨酸-脯氨酸键连接的环状肽进行筛选，靶向DENV包膜蛋白二聚体结构。
• 基于对接结果的结合亲和力和相互作用能，筛选出前五名配体。
• 开展体外药代动力学和毒性特征分析，评估候选肽的类药性与安全性。
• 在310 K和312 K下进行分子动力学（MD）模拟，评估配体-蛋白复合物随时间的稳定性。
• 通过分析均方根偏差（RMSD）、均方根波动（RMSF）和回转半径（Rg），评估蛋白-配体复合物的结构稳定性。
• 比较PYRRP与PAWRP的结合亲和力和动态行为，以识别最具潜力的抑制剂候选物。

实验结果

研究问题

• RQ1 具有脯氨酸-脯氨酸键的环状肽是否能有效结合到DENV包膜蛋白二聚体的疏水腔中，并抑制其向三聚体融合态的转变？
• RQ2 在筛选的环状肽中，哪些表现出与DENV包膜蛋白二聚体最高的结合亲和力和稳定性？
• RQ3 PYRRP与PAWRP在生理条件（310 K和312 K）下，对DENV包膜蛋白二聚体的结构稳定性表现如何？
• RQ4 候选肽的药代动力学和毒性特征如何，表明其作为药物先导物的潜力？
• RQ5 MD模拟是否证实配体结合可阻止病毒膜融合所必需的构象变化？

主要发现

• MD模拟显示，PYRRP在310 K和312 K下均表现出在DENV包膜蛋白二聚体复合物中的高度稳定性，表现为RMSD和Rg值较低。
• PAWRP在310 K下表现出强结合亲和力，并与DENV包膜蛋白形成稳定复合物，但在312 K下稳定性下降。
• 基于结合能和相互作用特征，从分子对接中筛选出的前五名配体被优先考虑，其中PYRRP和PAWRP为最具前景的候选物。
• 体外分析显示，PYRRP和PAWRP均具有有利的药代动力学特征和低毒性，支持其作为候选药物的潜力。
• 结合PYRRP后，DENV包膜蛋白二聚体形式保持稳定，表明其有效抑制了向融合性三聚体的构象转变。
• 由于在两种温度下均表现出一致的稳定性，并与包膜蛋白疏水腔形成强相互作用，PYRRP被确定为最佳候选物。