Evaluating the Substrate-Envelope Hypothesis: Structural Analysis of Novel HIV-1 Protease Inhibitors Designed To Be Robust against Drug Resistance
Evaluating the Substrate-Envelope Hypothesis: Structural Analysis of Novel HIV-1 Protease Inhibitors Designed To Be Robust against Drug Resistance
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DOI：
10.1128/jvi.02531-09
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发表时间：
2010-05-01
影响因子：
5.4
通讯作者：
Schiffer, Celia A.
中科院分区：
文献类型：
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作者：
Nalam, Madhavi N. L.;Ali, Akbar;Schiffer, Celia A.
HIV-1 蛋白酶的耐药性突变选择性地改变抑制剂结合，而不显着影响底物识别和裂解。这种分子识别的改变使我们提出了底物包膜假说，该假说预测，适合底物重叠共有体积内的 HIV-1 蛋白酶抑制剂不太可能受到耐药突变的影响，因为影响此类抑制剂的突变将同时影响底物的加工。为了评估这一假设，使用三种不同的方法设计和合成了超过 130 种 HIV-1 蛋白酶抑制剂，有或没有底物包膜限制。选择与野生型蛋白酶结合亲和力范围为 58 nM 至 0.8 pM 的 16 种代表性抑制剂进行晶体学分析。抑制剂-蛋白酶复合物表明，紧密结合的抑制剂（在皮摩尔水平的亲和力）似乎通过与特定活性位点残基形成氢键而“锁定”到蛋白酶活性位点。这种氢键模式和蛋白质-配体范德华相互作用的微妙变化将纳摩尔抑制剂与皮摩尔抑制剂区分开来。一般来说，适合底物包膜内的抑制剂，无论它们是皮摩尔还是纳摩尔，对于耐药蛋白酶变体都比突出到底物包膜之外的抑制剂具有更平坦的轮廓；这为将底物包膜约束纳入基于结构的设计策略以开发新的 HIV-1 蛋白酶抑制剂提供了强有力的理由。
Drug resistance mutations in HIV-1 protease selectively alter inhibitor binding without significantly affecting substrate recognition and cleavage. This alteration in molecular recognition led us to develop the substrate-envelope hypothesis which predicts that HIV-1 protease inhibitors that fit within the overlapping consensus volume of the substrates are less likely to be susceptible to drug-resistant mutations, as a mutation impacting such inhibitors would simultaneously impact the processing of substrates. To evaluate this hypothesis, over 130 HIV-1 protease inhibitors were designed and synthesized using three different approaches with and without substrate-envelope constraints. A subset of 16 representative inhibitors with binding affinities to wild-type protease ranging from 58 nM to 0.8 pM was chosen for crystallographic analysis. The inhibitor-protease complexes revealed that tightly binding inhibitors (at the picomolar level of affinity) appear to "lock" into the protease active site by forming hydrogen bonds to particular active-site residues. Both this hydrogen bonding pattern and subtle variations in protein-ligand van der Waals interactions distinguish nanomolar from picomolar inhibitors. In general, inhibitors that fit within the substrate envelope, regardless of whether they are picomolar or nanomolar, have flatter profiles with respect to drug-resistant protease variants than inhibitors that protrude beyond the substrate envelope; this provides a strong rationale for incorporating substrate-envelope constraints into structure-based design strategies to develop new HIV-1 protease inhibitors.