利用核心區域官能基地圖開發組蛋白去甲基化酶家族之多標靶抑制劑及探討結合機制

Abstract

「單一藥物針對單一標靶，治療單一疾病」是過去數十年藥物發展的主要概念，這個概念促使研究者發展具有高專一性的藥物，然而這個概念常常不適用於治療複雜疾病上，如癌症、後天免疫缺乏症候群和動脈粥狀硬化等疾病。許多複雜疾病是由多個不同蛋白質過量表現所引起的，針對單一蛋白質進行抑制並無法達到有效的治療效果，因此同時使用數個藥物的策略經常用於治療複雜疾病上(如雞尾酒療法)。然而，合併數種藥物治療，常常抑制了其他非標靶之蛋白質，而造成未預期的副作用。所以如何同時針對多標靶設計單一抑制劑，在藥物設計上已成為了一個刻不容緩的議題。 許多蛋白質的序列和結構的相似度很低，但卻會對相同的受質進行催化，如組蛋白去甲基化化酶家族皆會對組蛋白上的賴氨酸催化，顯示了這些能進行相似反應之蛋白質擁有相似的結合環境。本研究根據此特性提出了一個策略:利用本實驗室先前發展的核心區域官能基地圖對組蛋白去甲基化酶家族開發抑制劑及探討其結合機制。首先對數個組蛋白去甲基化酶建構區域官能基地圖，包含了JMJD2A、JMJD3、JMJD5和JHDM1A；接著藉著疊合這些蛋白質的區域官能基地圖定義出核心結合環境和數個核心錨點；再利用核心結合環境對化合物資料庫進行虛擬藥物篩選，最後篩選出能同時符合這些蛋白質核心結合環境的化合物，透過這個策略，我們與清華大學王雯靜教授合作篩選出組蛋白去甲基化酶2A (JMJD2A)小分子抑制劑WY01，抑制能力是目前JMJD2A抑制劑中療效最佳的，IC50 值為1.5μM，日後會再將此化合物受測於JMJD3上，以達到多標靶抑制劑的目標。另外，統計結果說明了核心錨點能夠定義出在演化過程中呈現高度保留性且執行生物功能的重要殘基，對許多尚不明瞭其生物機制的蛋白質而言，定義蛋白質核心錨點將會對於瞭解蛋白質有很大的幫助。這些實驗結果顯示，核心區域官能基地圖的藥物篩選概念將有助於開發多標靶抑制劑及瞭解結合機制。

The concept of "one-drug, one-target, one-disease" has been dominant to drug development strategy. The concept induces researchers to develop single-target inhibitors. However, the concept is inappropriate for treating complex diseases (e.g., cancers) because the complex diseases caused by a group of aberrantly expressed proteins. Although combinations of multiple drugs are often used to treat the complex diseases by inhibiting the aberrantly expressed proteins, these treatments often inhibit unexpected proteins, resulting in unexpected side effects. Therefore, a new method that discovers multiple-target inhibitors that simultaneously inhibit the aberrantly expressed proteins provides a great value for drug development. Many proteins interact with similar substrates to perform their functions despite the low sequence and structure similarity, such as histone demethylases and protein kinases. This suggests that these proteins may have similar binding environments to interact with the similar substrates. Here, we propose a new method to multiple-target inhibitors of the proteins binding similar substrates by using core site-moiety maps. The method firstly established the site-moiety maps of the histone demethylases, including JMJD2A、JMJD5、JMJD3 and JHDM1A and. Then, the core binding environments (core anchors) were identified by aligning the site-moiety maps of the proteins. Subsequently, we screen public compound databases to discover compounds that match simultaneously the core anchors of the demethylases. Finally, we identified a new inhibitor (WY01) that inhibits histone demethylase (JMJD2A) with an IC50 of 1.5 μM. To our knowledge, this inhibitor is the most potent inhibitor for JMJD2A. We believe the core site-moiety maps are very useful to discovery multi-target inhibitors and understand binding mechanism.