抗菌胜肽在各種物種的天然免疫系統中扮演重要的角色。雖然抗菌胜肽已經被廣泛性的研究而且越來越有潛力成為抵抗各種疾病的抗生素替代品，但是抗菌胜肽在癌症治療的應用上，不管是獨立用藥或是配合傳統抗癌藥物的給藥，都仍需再做進一步的設計和研究。近期，我們實驗室建立了POPC膜的分子動力(MD-POPC)模擬系統，其重現了抗菌胜肽在NMR上插入膜內深度的相對結果。另外，我們也發展了POPC/POPG膜的拉伸分子動力 (SMD-POPC/POPG)模擬系統，並藉由依序列相同排列順序不同而設計出的胜肽WLK和其同分異構物，來進行實驗和模擬系統的驗證。從生物活性實驗的結果，我們可以發現在所以WLK的同分異構物中，WLK11具有最強的抑菌和抗癌活性並擁有最低的溶血度。而利用圓二色光譜(CD)和二維NMR光譜的物性實驗，我們發現WLK11的抑菌能力與對鹽的耐受性是和胜肽包埋在膜裡的深淺程度有關。最後，從分子動力(MD)的模擬結果顯示出胜肽與膜之間的非鍵結性作用力(Non-bonded energy)與抑菌和抗癌能力有正相關性。由抑菌和抗癌的實驗結果可以來驗證我們的拉伸分子動力(SMD)模擬模式的可行性，並提供給我們更深入的觀點來探討胜肽活性和各種物理性質的關係。因此，我們的研究將分子動力(MD)模擬發展成一項利器，開啟一條新的途徑來幫助我們預測分析抗菌胜肽和抗癌胜肽。

Antimicrobial peptides (AMPs) play important roles in the innate immune system of many organisms. Although AMPs have been essentially studied and received increasing attention as potential alternatives against infectious diseases, their use as anticancer peptides (ACPs) in cancer therapy either alone or in combination with other conventional drugs has been considered to be a therapeutic strategy to explore. Recently, We have developed a MD-POPC simulation model to examine the relationship of inserting depth as well as energy statistical calculation between membranes and peptides corresponding to the NMR results. Furthermore, we also proposed a SMD-POPC/POPG simulation model to perform with antimicrobial peptide, WLK and its’ isomers, which design is dependent on the characteristics of helicity and amphipathicity. In bioactivity experiment experiments, the assays of the WLK analogues were showed that WLK11 possess strong antimicrobial, anticancer and low hemolytic activity. Additionally, the biophysical experiments, including circular dichroism and two-dimensional NMR, were used to demonstrate that the stronger antibacterial and salt resistance of WLK11 could be due to the membrane immersion depth. The results of MD simulations demonstrate that the MD statistical calculations of non-bonded energy are positively correlated to the MIC value and cancer cytotoxicity. The assay of antimicrobial and anticancer ability can verify our SMD simulation systems and provide us the in-depth view between the activity and several biophysical properties. To sum up, our work opens a new avenue to develop a potent tool to help us predict not only novel potential AMPs but promising ACPs.

中文摘要 2
Abstract 3
Acknowledgement 4
List of Tables 7
List of Figures 8
Chapter 1 Introduction 10
1.1. Antimicrobial Peptides – Promising Alternatives to Conventional Antibiotics 10
1.2. The characteristics of antimicrobial peptides 11
1.3. Rational design for antimicrobial peptide WLK. 12
1.4. Leading antimicrobial peptides into anticancer therapy 12
1.5. The aim of this research 13
Chapter 2 Materials and Methods 15
2.1　Peptide preparation 15
2.2　Bacteria culture 15
2.3 Antimicrobial activity 16
2.4　Hemolytic activity 17
2.5　MD simulation 17
2.5.1　Initial conformers of AMPs 17
2.5.2　Building the initial lipid system 18
2.5.3　The model of steered molecular dynamics in the MD-POPG simulations 18
2.5.4　Non-bounded energy 19
2.5.5　Insertion area and depth 19
2.6　Nuclear magnetic resonance (NMR) Spectroscopy 20
2.7　Cell culture 21
2.8　Cell toxicity 22
Chapter 3 Results 23
3.1　Antimicrobial activities in MIC assays 23
3.2　SMD simulation in POPC/POPG model for WLK and its other 4 isomers 23
3.2.1　The statistical result of SASAs during the insertion of peptides 24
3.2.2　The statistical result of heavy atoms between peptides and lipids 24
3.2.3　The statistical result of non-bonded energies in the SMD model 24
3.4 Anticancer activity 25
3.5 Hemolytic activity assays 26
3.6 Structure calculation and Description 26
3.7 Orientation in DPC via PRE studies 26
Chapter 4 Discussion 28
Appendix Tables and Figures 31
References 47

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