離胺酸甲基轉移酶的結構分析與藥物發現

Abstract

離胺酸甲基轉移酶(PKMTs)催化組蛋白質上的離胺酸甲基化。離胺酸甲基轉移酶是染色質重塑複合體的一部分，參與在染色質中表象遺傳學的修飾，改變基因的表現、基因庫的穩定性、細胞的發展與細胞的分裂。有一半以上的離胺酸甲基轉移酶在癌症裡面會過度表現，因此常被做為標靶蛋白質。然而，目前PKMTs僅有不到三分之一有抑制劑。除此之外離胺酸甲基轉移和有相似的SET區域，使其很難設計有選擇性的PKMTs抑制劑。 本論文嘗試利用區域性官能基地圖來了解PKMTs的通用與專一的特性。除此之外，區域官能基地圖可以被使用在設計新的抑制劑上。為了建立區域官能基地圖，起初我們蒐集了五千個多樣化結構的化合物。然後，利用電腦將化合物嵌合在十九個PKMTs結晶結構上。以嵌合方法為基礎建立區域官能基地圖。下一步，以位點與交互作用為基礎，比對區域官能基地圖中的錨點，確立其保守與專一性。除此之外，我們設計了新的函式來促成新PKMTs抑制劑的發現。

我們分析了區域官能基地圖揭露了PKMTs的保守性與專一性。PKMTs區域官能基地圖由六個錨點組成，包括一個保守的錨點和五個專一的錨點。RA錨點位在輔因子位置在演化的過程中是高度保守的。這個錨點是輔因子上腺嘌呤的結合位置。五個專一的錨點是PKMTs專一性的位置。舉例來說，CA錨點上的殘基有16%負電、32%正電，5%的極性和47%的非極性。我們的結果顯示錨點可以改善PKMTs的命中率。除此之外，我們以現有的五個專一性錨點將PKMTs分成六群應用在設計多標靶或專一性抑制劑。我們相信區域官能基地圖和錨點的分析可以更了解PKMTs分子結合的機制，以期待將來運用於藥物的設計

Protein lysine methyltransferases (PKMTs) catalyze histone methylations at lysine residues. PKMTs are part of chromatin remodeling complex, which is involved in epigenetic modification of chromatins, determining gene expression, genomic stability, cell development, and cell division. PKMTs are considered attractive targets for drug development, because more than 50% of them are overexpressed in many cancers. However, less than 30% of PKMTs have inhibitors. In addition, PKMTs contain the SET domain, which makes it difficult to design selectively inhibitors target specific PKMTs. In this thesis, we attempts to understand common and specific characteristics of PKMTs using site-moiety maps. In addition, the site-moiety maps can be used to design new selective PKMT inhibitors. First, to establish site-moiety maps, we collected more than 5,000 compounds with diverse structures. Then, these compounds were docked into the binding sites of 19 PKMT crystal structures. Based on the docked results, the site-moiety maps of the PKMTs were established. Next, these 19 site-moiety maps were aligned to identify conserved and specific anchors based on anchor positions and interaction types. In addition, we designed a new scoring function to facilitate discovery of new PKMT inhibitors. We analyzed the site-moiety maps to reveal conserved and specific characteristics of PKMTs. The site-moiety maps of PKMTs consist of six anchors (FA-CAP6), including three conserved anchor and three specific anchors. The RA anchor is located at the cofactor binding site and is highly conserved during evolution process. This anchor is essential for the binding of adenine group of the cofactor. The other five specific anchors represent specific characteristics of PKMTs. For example, in PKMTs, 16%, 32%, 5%, and 47% of the CA anchor residues are negatively-charged, positively-charged, polar, and non-polar, respectively. Our results show that these anchors can improve the hit rate in identifying PKMT inhibitors. In addition, we classified PKMTs into six groups based on the presence of these five specific anchors, which can be applied to design common or selective PKMT inhibitors. The site-moiety maps and the anchor analysis open up the possibility in understanding molecular binding mechanisms of PKMTs and designing selective inhibitors in the future.