利用分子動態模擬探討抑制劑PCMPS對核酸外切酶的動態影響

Molecular Simulation Studies for the Effects of Inhibitor PCMPS on the Conformational Dynamics of Exonuclease

褚煜瑜(Yu-Yu Chu)

指導教授 ： 朱智瑋

國立交通大學/生物科技學院/生物資訊及系統生物研究所/碩士(2019年)

摘要

拉薩病毒 (Lassa virus)侵入人體後會使人感染俗稱拉薩出血熱的疾病，其主要肆虐於非洲地區並有著高死亡率，文獻指出拉薩病毒中有一種核酸外切酶 (LVNP，Lassa fever virus nucleoprotein)，拉薩病毒會藉由LVNP來降解宿主細胞內的核酸類之PAMP (Pattern Associated Molecular Pattern)信號，而PAMP信號是啟動人體先天性免疫的重要因子，拉薩病毒因此透過LVNP的降解機制避開免疫系統的毒殺，並潛伏於人體內。若LVNP受到抑制，病毒將失去降解機制而難存活於人體內，但歷經漫長的藥物測試下，至今尚未找到合適於人體的藥物去抑制拉薩病毒中的LVNP。其中我們發現一項具有抑制LVNP能力的抑制劑PCMPS，它雖然有效的抑制LVNP，但因為結構含有汞而不適合用於人體，然而我們欲從PCMPS如何抑制LVNP的機制來作為我們設計藥物的策略，從結晶結構上發現，PCMPS會接合於LVNP上的CYS，並與其產生共價鍵，但接合抑制劑與未接合的LVNP之結晶結構差異甚小，我們並無法利用結晶結構的差異了解PCMPS抑制LVNP的機制，故我們推測PCMPS應為干擾LVNP的動態，致使LVNP的活性受到影響。在此論文的研究中，我們利用分子動態模擬計算LVNP於水溶液中應有的動態變化，以及接合抑制劑後的LVNP之動態變化，並比較兩者之間的差異，我們從動態模擬的分析中發現了兩項特徵，而這兩項特徵與PCMPS的抑制機制息息相關，一為抑制劑將導致LVNP傾向於閉合其活性位H528，另一特徵則為LVNP在活性位的自由度受到PCMPS的間接影響而改變。我們連結兩項特徵與抑制機制的相關性，並藉由了解此抑制機制獲得我們設計藥物的策略。

關鍵字

核酸外切酶 ； 拉薩病毒 ； 分子動態模擬

並列摘要

Lassa fever virus nucleoprotein (LVNP) is a kind of exonuclease within the DEDDh family. When a certain strand of double-­stranded RNA in the host cell is digested by LVNP, Lassa fever virus is able to prevent itself from recognized by the host cytosolic RNA sensors and in turn escape from the immune system. The disease, Lassa fever, spreads out in Africa causing high mortality rate. Thus, it is urgent to find drugs to inhibit the LVNP in Lassa fever virus. However, no drugs have been found to efficiently target the LVNP up to the present. We develop a strategy by finding the dynamic mechanisms of potential testing compounds by doing MD simulation and inspecting the corresponding networks of force constants via “Fluctmatch”, followed by designing the drugs that satisfy the dynamic features similar to the previous found dynamic features. In the biochemical essays, we found the inhibitor, PCMPS, among the testing compounds has the prominent inhibition effect toward the activity of LVNP. Subsequently, we examine the dynamic behaviors of PCMPS due to its obscure differences between apo and ligand­binding form of LVNP’s X-ray crystal structure. We found PCMPS inhibits LVNP in an indirect way by causing the H528 in LVNP being closed, and the change of force constants around the active site. In the future, we will link the change patterns of force constants toward the closing phenomena of H528, and design the drug that satisfy these inhibition features.

並列關鍵字

exonuclease ； Lassa virus ； dynamic simulation

參考文獻

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