HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants
HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants
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DOI：
10.1021/ja076558p
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发表时间：
2008-05-14
影响因子：
15
通讯作者：
Tidor, Bruce
中科院分区：
文献类型：
--
作者：
Altman, Michael D.;Ali, Akbar;Tidor, Bruce
感染病原体获得耐药突变仍然是一个紧迫的健康问题，制定应对这一威胁的战略是一项优先事项。在这里，我们应用了一种通用的策略，利用底物包膜进行反向设计，来开发HIV-1蛋白酶的抑制剂。基于结构的计算被用来设计预计保持在结合部位的共识底物体积内的抑制剂。经过两轮设计、合成、实验测试和结构分析，共得到51个化合物。设计方法的改进导致最佳粘结剂的野生型蛋白酶亲和力提高了约1000倍，从第一轮的K(I)为30-50 NM，到第二轮的K(I)低于100 PM。一组络合物的晶体结构显示了类似于每个设计的结合模式，几乎在所有情况下都尊重底物包膜。来自第一轮的所有四个最佳结合蛋白对临床相关的耐药HIV-1蛋白变异体表现出广泛的特异性，与野生型相比失去不超过6-13倍的亲和力。对第二轮化合物的子集与一组耐药变异体进行测试，发现了三类抑制剂：坚固结合物(最大亲和力损失14-16倍)、中等结合物(35-80倍)和敏感结合物(大于100倍)。尽管对于特别是高亲和力的抑制剂来说，额外的因素可能也很重要，但总的来说，这些结果表明，使用底物包膜设计抑制剂可能是开发对耐药敏感性低的治疗药物的有用策略。
The acquisition of drug-resistant mutations by infectious pathogens remains a pressing health concern, and the development of strategies to combat this threat is a priority. Here we have applied a general strategy, inverse design using the substrate envelope, to develop inhibitors of HIV-1 protease. Structure-based computation was used to design inhibitors predicted to stay within a consensus substrate volume in the binding site. Two rounds of design, synthesis, experimental testing, and structural analysis were carried out, resulting in a total of 51 compounds. Improvements in design methodology led to a roughly 1000-fold affinity enhancement to a wild-type protease for the best binders, from a K(i) of 30-50 nM in round one to below 100 pM in round two. Crystal structures of a subset of complexes revealed a binding mode similar to each design that respected the substrate envelope in nearly all cases. All four best binders from round one exhibited broad specificity against a clinically relevant panel of drug-resistant HIV-1 protease variants, losing no more than 6-13-fold affinity relative to wild type. Testing a subset of second-round compounds against the panel of resistant variants revealed three classes of inhibitors: robust binders (maximum affinity loss of 14-16-fold), moderate binders (35-80-fold), and susceptible binders (greater than 100-fold). Although for especially high-affinity inhibitors additional factors may also be important, overall, these results suggest that designing inhibitors using the substrate envelope may be a useful strategy in the development of therapeutics with low susceptibility to resistance.