Structure based drug design of peroxisome proliferator-activated receptor (PPAR) agonists

結構為主的藥物設計輔助抗糖尿病藥物的設計與發展

彭懿慧(Yi-Hui Peng)

指導教授 ： 呂平江 ； 伍素瑩

國立清華大學/生命科學院/生物資訊與結構生物研究所/博士(2010年)

摘要

Peroxisome proliferator-activated receptors (PPARs) were the drug targets with different activation mechanism. Activation of PPARγ would improve the insulin sensitivity and thus was the action site of antidiabetes TZD drugs. To develop safer and effective antidiabetic drug in our study, structure based drug design (SBDD) was applied to help to design the antidiabetic drugs.

We subcloned different fragments of PPARγ ligand binding domain (LBD) for co-crystallization with different agonists. The fragments: amino acids 252-477, 175 - 477, and 207 - 477 were expressed and purified. The clone of amino acids 252 - 477 produced insoluble form mostly and was difficult to purify. The other two clones produced large amount of soluble proteins and were able to crystallization. In X-ray data collection, the co-crystals of fragment 207 - 477 a. a. complexing with different agonists diffracted to 1.9 - 2.5 Å of resolution that was better than that of the fragment of 175 - 477 a. a diffracted to 2.8 - 3.0 Å.

A potent PPARα/γ/δ pan agonist BPR1H036 (PPARα/γ/δ EC50 = 14/230/10 nM), a novel series of indole based compound with a benzisoxazole tail, was the lead in this study. X-ray structure biology showed that the carboxylic acid head of BPR1H036 formed four conserved H-bonds and the indole ring contributed to strong hydrophobic interactions with PPARγ. Thus, the indole head moiety played an important role in binding to the protein.

Followed, the diverse tail parts of indole-based agonists were studied. Compound BPR1H172 (PPARα/γ/δ EC50 = 8/70/500 nM), with the n-propyl substituted naphthophenone tail part attaching to 5-position of indole through a linker, showed more potent PPAR pan activity than lead. The structure biology showed that the naphthophenone tail makes intensive hydrophobic interactions with PPARγ; the distance between the acidic group and linker were also important for the potency.

In addition, we also explained the structure-activity relationships (SAR) of the series of indole based compounds with different selectivity and potency by structure biology. When the indole ring of head was reversed from the orientation of BPR1H172 to BPR1H201 (PPARα/γ/δ EC50 = 32/2210/>10000 nM), the activity of PPARγ was decreased due to the lose of H-binds. By adding the fibrate moiety to the head of BPR1H201, BPR1H183 (PPARα/γ/δ EC50 = 123/650/>10000 nM) recovered PPARγ activity by reforming four conserved H-bonds.

Further modifications of hydrophobic tail parts of BPR1H183 to improve PPARγ potency, we found that compound BPR1H378 (PPARα/γ/δ EC50 = 1920/120/>10000 nM) contained the most potent and selective 4-phenyl-benzophenone tail with the lowest binding energy, which contributed to the improved PPARγ potency. Ring expansion of the indole head resulted in compound BPR1H385 (PPARα/γ/δ EC50 = 3990/50/>10000 nM) forming more extensive hydrophobic interactions with protein and thus increased the PPARγ activity.

Based on the SAR and structure biology analysis, we suggested that the indole head part would play an important role in improved PPARγ potency. Therefore, while the potent and selective 4-phenly-benzophenone tail was attached to the indole head, compound BPR1H382 (PPARα/γ/δ EC50 = 120/10/>10000 nM), the most potent PPARγ agonist in our study, made stronger H-bonds and hydrophobic interactions with PPARγ than compound BPR1H172 and BPR1H385. The improved activity (EC50) of BPR1H382 was 22-fold potent than the TZD drug, rosiglitazone.

In summary, through SBDD, the detailed interactions of indole based compounds with protein were elucidated, and guide lead to optimization to obtain the potent PPAR agonists.

關鍵字

結構為主的藥物設計 ； 過氧化酶增生子活化接受器 ； 結構生物學 ； X -ray 結晶學

並列摘要

無資料

並列關鍵字

structure based drug design ； peroxisome proliferator-activated receptors ； structure biology ； X-ray crystallography

參考文獻

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