In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain)

The N terminal domain (NTD) of Nucleocapsid protein (N protein) of coronavirus (CoV) binds to the viral (+) sense RNA and results in CoV ribonucleoprotien (CoV RNP) complex, essential for the virus replication. In this study, the RNA-binding N terminal domain (NTD) of the N protein was targeted for the identification of possible inhibitors of RNA binding. Two NTD structures of N proteins were selected (2OFZ and 1SSK, 92% homology) for virtual screening of 56,079 compounds from Asinex and Maybridge library to identify top 15 hits for each of the targets based on ‘docking score’. These top-hits were further screened for MM-GBSA binding free energy, pharmacokinetic properties (QikProp) and drug-likeness (SwissADME) and subjected to molecular dynamics (MD) studies. Two suitable binders (ZINC00003118440 and ZINC0000146942) against the target 2OFZ were identified. ZINC00003118440 is a theophylline derivative under the drug class ‘bronchodilators’ and further screening with approved bronchodilators was also studied to identify their ability to bind to the RNA binding region on the N protein. The other identified top hit is ZINC0000146942, which is a 3,4dihydropyrimidone class molecule. Hence this study suggests two important class of compounds, theophylline and pyrimidone derivaties as possible inhibitors of RNA binding to the N terminal domain of N protein of coronavirus, thus opening new avenues for in vitro validations. Communicated by Ramaswamy H. Sarma

冠状病毒（coronavirus, CoV）核衣壳蛋白（nucleocapsid protein, N蛋白）的N端结构域（N terminal domain, NTD）可结合病毒正义链RNA（(+) sense RNA），并形成冠状病毒核糖核蛋白复合物（CoV ribonucleoprotein, CoV RNP），该复合物对病毒复制至关重要。本研究以N蛋白的RNA结合型N端结构域为靶点，旨在筛选可阻断其RNA结合功能的潜在抑制剂。研究选取了两种N蛋白的NTD结构（PDB编号2OFZ与1SSK，序列同源性达92%），对来自Asinex和Maybridge化合物库的56079个化合物进行虚拟筛选，基于“对接评分（docking score）”分别为两个靶点筛选出排名前15的命中化合物。随后，对这些命中化合物进一步开展MM-GBSA结合自由能、药代动力学性质（QikProp）及药物相似性（SwissADME）分析，并进行分子动力学（molecular dynamics, MD）模拟研究。最终针对靶点2OFZ，筛选得到两种合适的结合配体：ZINC00003118440与ZINC0000146942。其中ZINC00003118440属于支气管扩张剂类的茶碱衍生物，研究还进一步对已获批的支气管扩张剂开展筛选，以验证其结合N蛋白RNA结合区域的能力。另一个命中化合物ZINC0000146942则属于3,4-二氢嘧啶酮类分子。综上，本研究表明茶碱类与嘧啶酮类两类化合物可作为冠状病毒N蛋白N端结构域RNA结合功能的潜在抑制剂，为后续体外验证实验开辟了新的研究方向。本文由Ramaswamy H. Sarma供稿。