Structure-based phenotyping predicts HIV-1 protease inhibitor resistance
Structure-based phenotyping predicts HIV-1 protease inhibitor resistance
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DOI：
10.1110/ps.0301103
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发表时间：
2003-08-01
期刊：
影响因子：
8
通讯作者：
Ramnarayan, K
中科院分区：
文献类型：
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作者：
Shenderovich, MD;Kagan, RM;Ramnarayan, K
HIV-1药物靶点的突变会导致抗逆转录病毒药物的耐药性，从而导致治疗失败。表型耐药性分析既耗时又昂贵，基于基因规则的解释可能无法预测多个突变的影响。我们已经开发了一种计算程序，可以快速评估抑制剂与HIV-1 PR突变株结合能的变化。根据晶体结构建立了WT络合物的模型。在WT络合物中通过氨基酸取代和随后的配体和PR结合部位残基的能量最小化来构建突变络合物。通过与现有晶体结构的比较和对已知抗药性相关突变的预测，证实了模型的准确性。来自临床分离株的PR变异体被模拟在FDA批准的6个PI的复合体中，突变和WT复合体结合能(DeltaE(Bind))的变化与表型50%抑制浓度(IC50)值的比率相关。5个PI的增量E(BIND)与Virco抗病毒试验的IC50呈显著相关(R2=0.7~0.8)，6个PI的DeltaE(BIND)与病毒学表观分析的IC50呈良好的相关性(R-2=0.76~0.85)。与IC50增加四倍相对应的DeltaE(BIND)阈值被用来定义基于结构的表型为易感、耐药或不明确。对78个PR变异体的盲法预测与表现型和抗病毒谱表型的总体符合率分别为92%(kappa=0.756)和86%(kappa=0.666)。结构表型分析预测了临床HIV-1PR变异体的耐药性，其准确性接近常用的基于细胞的表型分析。
Mutations in HIV-1 drug targets lead to resistance and consequent therapeutic failure of antiretroviral drugs. Phenotypic resistance assays are time-consuming and costly, and genotypic rules-based interpretations may fail to predict the effects of multiple mutations. We have developed a computational procedure that rapidly evaluates changes in the binding energy of inhibitors to mutant HIV-1 PR variants. Models of WT complexes were produced from crystal structures. Mutant complexes were built by amino acid substitutions in the WT complexes with subsequent energy minimization of the ligand and PR binding site residues. Accuracy of the models was confirmed by comparison with available crystal structures and by prediction of known resistance-related mutations. PR variants from clinical isolates were modeled in complex with six FDA-approved PIs, and changes in the binding energy (DeltaE(bind)) of mutant versus WT complexes were correlated with the ratios of phenotypic 50% inhibitory concentration (IC50) values. The calculated DeltaE(bind) of five PIs showed significant correlations (R-2 = 0.7-0.8) with IC50 ratios from the Virco Antivirogram assay, and the DeltaE(bind) of six PIs showed good correlation (R-2 = 0.76-0.85) with IC50 ratios from the Virologic PhenoSense assay. DeltaE(bind) cutoffs corresponding to a four-fold increase in IC50 were used to define the structure-based phenotype as susceptible, resistant, or equivocal. Blind predictions for 78 PR variants gave overall agreement of 92% (kappa = 0.756) and 86% (kappa = 0.666) with PhenoSense and Antivirogram phenotypes, respectively. The structural phenotyping predicted drug resistance of clinical HIV-1 PR variants with an accuracy approaching that of frequently used cell-based phenotypic assays.