Helicobacter pylori 近年來已發現與胃炎、十二指腸潰瘍甚至胃癌有密切之關聯。在治療上仍以消化性潰瘍用藥加抗生素治療，但治療失敗與菌株產生抗藥性的機率日漸升高，所以找出適合去除H. pylori 的抑制藥物是未來對於此菌的治療上的重要工作。Shikimate 路徑存在於原核生物、真核生物、植物中，但在哺乳細
胞卻沒有，在原核生物主要反應是由七個步驟所組成，其功能是將D-Erythrose-4-phosphate 和Phosphoenoylpyruvate 經酵素轉變成最終產物chorismate，而chorismate則為合成許多aromatic 化合物重要的中間代謝物，因此路徑中的酵素便成為發展抑菌藥物的標靶。而Dehydroquinate synthase 是路徑中第二步驟的酵素，能將
7-deoxy-D-arabino-heptulosoe-7-phosphate 轉成3-dehydroquinate ， 我們利用molecular replacement 的方法， 發表了解析度達到2.4Å 的H. pylori 的3-dehydroquinate synthase 的蛋白質結構。接下來，以循理性藥物設計方法結合蛋白質結構與電腦模擬的方法，加上電腦輔助的快速篩選則可以將藥物發展的時程
縮短。本論文則以HpDHQS 的蛋白質結構為基礎，深入研究其受質結合後與結構之間的關係，並配合以電腦模擬輔助篩選資料庫中的化合物，找出較有可能的candidate 化合物，再進一步測量其酵素活性的方法來印證其化合物的抑制能力。經由以上方法，我們以GOLD 程式以電腦模擬的方法快速大量篩選Maybridge 資料庫中約60000 筆的化合物，挑中的化合物中有7 組化合物對HpDHQS 有抑制活性，其中有2 組candidate 化合物其IC50 的值分別到達61 與84μM，透過循理性藥物設計方法分析，將會輔助前導化合物最佳化過程(lead optimization)以獲得最具潛力之抗菌藥物。

Helicobacter pylori is a gram-negative gastric pathogen that colonizes
approximately half of the human population and may persist in its presence for a
lifetime. Enduring infection of this peculiar microbe leads to the chronic inflammation
of gastric epithelial cells, which may further progress into peptic ulcers, gastric atrophy,
and gastric adenocarcinoma. The treatment of H. pylori infection using high-dosage
antibiotics, however, has resulted in decreased efficacy and resistance of antibiotics.
The need for new antibacterial therapies to overcome the problems of the drug
resistance is therefore a major concern of healthcare professionals. One potential
approach towards discovering new classes of inhibitors is to target crucial proteins in
bacterial but not in mammals. The shikimate pathway which involves seven sequential
enzymatic steps in the conversion of erythrose 4-phosphate (E4P) and
phosphoenolpyruvate (PEP) into chorismate for subsequent synthesis of aromatic
compounds is unique to microbial. Enzymes of this pathway are attractive targets for
the development of nontoxic antimicrobial compounds.Dehydroquinate synthase
(DHQS) is a nicotinamide adenine dinucleotide (NAD)-dependent enzyme that
converts 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) into 3-dehydroquinate
(DHQ). Since it catalyzes the second key step in the shikimate pathway, which is
crucial for the aromatic amino acid metabolism in bacteria, fungi and plants, but not in
mammals, DHQS is a potential target for new antimicrobial agents, antiparasitic agents
and herbicides. The crystal structure of H. pylori DHQS complexed with NAD has
been determined at 2.4-Å resolution and was found to possess an N-terminal
Rossmann-fold domain and a C-terminal α-helical domain. Structural comparison
reveals that the binary complex adopts an open-state conformation and shares
conserved residues in the binding pocket. Virtual docking of compounds into the active
site of the HpDHQS structure using the GOLD docking program led to the
identification of several inhibitors. The most active compound had an IC50 value of 61
μM, which may serve as a lead for potent inhibitors.

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