Kamata K, Kawamoto H, Honma T, Iwama T, Kim S H
Department of Chemistry and Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720-5230, USA.
Proc Natl Acad Sci U S A. 1998 Jun 9;95(12):6630-5. doi: 10.1073/pnas.95.12.6630.
Factor Xa, the converting enzyme of prothrombin to thrombin, has emerged as an alternative (to thrombin) target for drug discovery for thromboembolic diseases. An inhibitor has been synthesized and the crystal structure of the complex between Des[1-44] factor Xa and the inhibitor has been determined by crystallographic methods in two different crystal forms to 2.3- and 2.4-A resolution. The racemic mixture of inhibitor FX-2212, (2RS)-(3'-amidino-3-biphenylyl)-5-(4-pyridylamino)pentanoic acid, inhibits factor Xa activity by 50% at 272 nM in vitro. The S-isomer of FX-2212 (FX-2212a) was found to bind to the active site of factor Xa in both crystal forms. The biphenylamidine of FX-2212a occupies the S1-pocket, and the pyridine ring makes hydrophobic interactions with the factor Xa aryl-binding site. Several water molecules meditate inhibitor binding to residues in the active site. In contrast to the earlier crystal structures of factor Xa, such as those of apo-Des[1-45] factor Xa and Des[1-44] factor Xa in complex with a naphthyl inhibitor DX-9065a, two epidermal growth factor-like domains of factor Xa are well ordered in both our crystal forms as well as the region between the two domains, which recently was found to be the binding site of the effector cell protease receptor-1. This structure provides a basis for designing next generation inhibitors of factor Xa.
凝血因子Xa是将凝血酶原转化为凝血酶的转换酶，已成为血栓栓塞性疾病药物研发的另一个（相对于凝血酶）靶点。已合成了一种抑制剂，并通过晶体学方法以两种不同晶体形式确定了去[1-44]凝血因子Xa与该抑制剂复合物的晶体结构，分辨率分别为2.3 Å和2.4 Å。抑制剂FX-2212，即(2RS)-(3'-脒基-3-联苯基)-5-(4-吡啶基氨基)戊酸的外消旋混合物，在体外272 nM时可抑制凝血因子Xa活性50%。发现FX-2212的S-异构体（FX-2212a）在两种晶体形式中均与凝血因子Xa的活性位点结合。FX-2212a的联苯脒占据S1口袋，吡啶环与凝血因子Xa的芳基结合位点形成疏水相互作用。几个水分子介导抑制剂与活性位点中的残基结合。与早期凝血因子Xa的晶体结构不同，如脱辅基去[1-45]凝血因子Xa和与萘基抑制剂DX-9065a形成复合物的去[1-44]凝血因子Xa的晶体结构，在我们的两种晶体形式以及两个结构域之间的区域中，凝血因子Xa的两个表皮生长因子样结构域排列良好，最近发现该区域是效应细胞蛋白酶受体-1的结合位点。该结构为设计下一代凝血因子Xa抑制剂提供了基础。
