Structural determinants of inhibition of Porphyromonas gingivalis gingipain K by KYT-36, a potent, selective, and bioavailable peptidase inhibitor
Structural determinants of inhibition of Porphyromonas gingivalis gingipain K by KYT-36, a potent, selective, and bioavailable peptidase inhibitor
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DOI：
10.1038/s41598-019-41354-3
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发表时间：
2019-03-20
影响因子：
4.6
通讯作者：
Xavier Gomis-Ruth, F.
中科院分区：
文献类型：
--
作者：
Guevara, Tibisay;Rodriguez-Banqueri, Arturo;Xavier Gomis-Ruth, F.
牙龈卟啉单胞菌是生态失调的口腔微生物组的成员，也是导致严重牙周病的“关键病原体”，而严重牙周病是最普遍的传染病之一。牙龈卟啉单胞菌分泌的部分毒力因子是必需的半胱氨酸肽酶牙龈菌蛋白酶K（Kgp）和R（RgpA和RgpB），其占病原体的细胞外蛋白水解活性的85%，因此是抑制的主要靶标。我们报告了Kgp与KYT-36的高分辨率（1.20埃）复合物结构，KYT-36是一种肽衍生的、有效的、生物可利用的和高选择性的抑制剂，广泛用于体外、细胞和体内的研究。Kgp的亚纳摩尔抑制是通过与活性位点裂隙紧密结合实现的，在建立9个疏水相互作用、14个氢键和1个盐桥的情况下，活性位点裂隙被其子位点S-3至S-1'覆盖。此外，模拟底物的易裂羰基的抑制剂羰基碳被还原，并且距离Kgp的催化亲核试剂（CS）-S-477 γ仅2.02埃。因此，晶体结构模拟半胱氨酸肽酶催化期间第一亲核攻击的反应中间体。目前的研究为开发定制的下一代药物以解决牙龈卟啉单胞菌奠定了基础。
Porphyromonas gingivalis is a member of the dysbiotic oral microbiome and a "keystone pathogen" that causes severe periodontal disease, which is among the most prevalent infectious diseases. Part of the virulence factors secreted by P. gingivalis are the essential cysteine peptidases gingipain K (Kgp) and R (RgpA and RgpB), which account for 85% of the extracellular proteolytic activity of the pathogen and are thus prime targets for inhibition. We report the high-resolution (1.20 angstrom) complex structure of Kgp with KYT-36, a peptide-derived, potent, bioavailable and highly selective inhibitor, which is widely used for studies in vitro, in cells and in vivo. Sub-nanomolar inhibition of Kgp is achieved by tight binding to the active-site cleft, which is covered for its sub-sites S-3 through S-1' under establishment of nine hydrophobic interactions, 14 hydrogen bonds and one salt bridge. In addition, an inhibitor carbonyl carbon that mimics the scissile carbonyl of substrates is pyramidalized and just 2.02 angstrom away from the catalytic nucleophile of Kgp, (CS)-S-477 gamma. Thus, the crystal structure emulates a reaction intermediate of the first nucleophilic attack during catalysis of cysteine peptidases. The present study sets the pace for the development of tailored next-generation drugs to tackle P. gingivalis.