Fragment-based screen against HIV protease.
Fragment-based screen against HIV protease.
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DOI：
10.1111/j.1747-0285.2009.00943.x
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发表时间：
2010-03
影响因子：
3
通讯作者：
Stout CD
中科院分区：
文献类型：
--
作者：
Perryman AL;Zhang Q;Soutter HH;Rosenfeld R;McRee DE;Olson AJ;Elder JE;Stout CD
我们采用了基于片段的筛选野生型（NL 4 -3）HIV蛋白酶（PR）使用Active Sight片段库和X射线晶体学。实验揭示了两个新的小分子结合位点。PR与碎片共结晶，或晶体浸泡在碎片溶液中，使用五种晶体形式，收集了378个数据集，分辨率为2.3-1.3 μ m。在共结晶过程中，片段结合诱导TL-3抑制PR的独特构象和特定晶型。一个片段，2-甲基环己醇，结合在“外位点”相邻的Gly 16 Gly 17 Gln 18环，其中Gly 17的酰胺是一个特定的氢键供体，和疏水接触发生与侧链的Lys 14和Leu 63。另一个片段，吲哚-6-羧酸，通过与Trp 42，Pro44，Met 46和Lys 55的疏水接触，与Val 56的氢键和与Arg 57的盐桥结合在“翼的外部/顶部”。2-乙酰基-苯并噻吩也结合在该位点。这项研究是第一个基于片段的针对HIV PR的晶体学筛选，也是第一次针对与靶分子结合的药物靶点筛选片段，以寻找既能与新位点结合又能稳定靶点抑制构象的化合物。
We have employed a fragment-based screen against wild-type (NL4-3) HIV protease (PR) using the Active Sight fragment library and X-ray crystallography. The experiments reveal two new binding sites for small molecules. PR was co-crystallized with fragments, or crystals were soaked in fragment solutions, using five crystal forms, and 378 data sets were collected to 2.3-1.3 Å resolution. Fragment binding induces a distinct conformation and specific crystal form of TL-3 inhibited PR during co-crystallization. One fragment, 2-methylcyclohexanol, binds in the ‘exo site’ adjacent to the Gly16Gly17Gln18 loop where the amide of Gly17 is a specific hydrogen bond donor, and hydrophobic contacts occur with the side chains of Lys14 and Leu63. Another fragment, indole-6-carboxylic acid, binds on the ‘outside/top of the flap’ via hydrophobic contacts with Trp42, Pro44, Met46, and Lys55, a hydrogen bond with Val56, and a salt-bridge with Arg57. 2-acetyl-benzothiophene also binds at this site. This study is the first fragment-based crystallographic screen against HIV PR, and the first time that fragments were screened against an inhibitor-bound drug target to search for compounds that both bind to novel sites and stabilize the inhibited conformation of the target.
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