<i>In silico</i> prediction of drug resistance due to S247R mutation of Influenza H1N1 neuraminidase protein

We present here <i>in silico</i> studies on antiviral drug resistance due to a novel mutation of influenza A/H1N1 neuraminidase (NA) protein. Influenza A/H1N1 virus was responsible for a recent pandemic and is currently circulating among the seasonal influenza strains. M2 and NA are the two major viral proteins related to pathogenesis in humans and have been targeted for drug designing. Among them, NA is preferred because the ligand-binding site of NA is highly conserved between different strains of influenza virus. Different mutations of the NA active site residues leading to drug resistance or susceptibility of the virus were studied earlier. We report here a novel mutation (S247R) in the NA protein that was sequenced earlier from the nasopharyngeal swab from Sri Lanka and Thailand in the year 2009 and 2011, respectively. Another mutation (S247N) was already known to confer resistance to oseltamivir. We did a comparative study of these two mutations vis-a-vis the drug-sensitive wild type NA to understand the mechanism of drug resistance of S247N and to predict the probability of the novel S247R mutation to become resistant to the currently available drugs, oseltamivir and zanamivir. We performed molecular docking- and molecular dynamics-based analysis of both the mutant proteins and showed that mutation of S247R affects drug binding to the protein by positional displacement due to altered active site cavity architecture, which in turn reduces the affinity of the drug molecules to the NA active site. Our analysis shows that S247R may have high probability of being resistant.本研究针对甲型流感病毒A/H1N1神经氨酸酶（neuraminidase, NA）蛋白的新型突变引发的抗病毒药物耐药性开展计算机模拟（in silico）研究。甲型流感病毒A/H1N1曾引发近期全球大流行，目前仍在季节性流感毒株中传播流行。M2蛋白与NA是与人类流感致病机制相关的两大主要病毒蛋白，均为抗病毒药物研发的核心靶点。其中NA更受青睐，原因在于不同流感毒株的NA配体结合位点高度保守。此前已有研究针对NA活性位点残基的各类突变展开分析，此类突变可导致病毒产生耐药性或药物敏感性改变。本研究报道了NA蛋白上的一处新型突变（S247R），该突变此前分别于2009年和2011年在斯里兰卡与泰国的鼻咽拭子样本中被测序检出。另一处已知突变（S247N）可使病毒对奥司他韦（oseltamivir）产生耐药性。本研究以药物敏感性野生型NA为对照，对上述两种突变开展对比研究，旨在阐明S247N突变的耐药机制，并预测新型S247R突变对当前临床可用药物奥司他韦与扎那米韦（zanamivir）的耐药可能性。本研究对两种突变蛋白开展了基于分子对接（molecular docking）与分子动力学（molecular dynamics）的分析，结果显示S247R突变通过改变NA活性位点的空腔结构，引发关键残基的位置位移，进而干扰药物与蛋白的结合，最终降低药物分子与NA活性位点的结合亲和力。本研究分析结果表明，S247R突变存在较高的耐药可能性。