Using quantum chemistry, molecular simulation and machine learning techniques to study the enzymatic mechanism for several enzymes

• Main Authors: Fu, chien wei, 傅建維
• Other Authors: Lin, Thy-Hou
• Format: Others
• Language: en_US
• Published: 2015
• Online Access: http://ndltd.ncl.edu.tw/handle/j556k8

博士 === 國立清華大學 === 分子醫學研究所 === 103 === Chapter I: Site of metabolism prediction for FMO enzymes via machine learning and condensed Fukui function The flavin-containing monooxygenase (FMO) catalyzes xenobiotics with soft nucleophiles and also plays an important role in drug metabolism in Phase I enzymes. The site of metabolism (SOM) refers to the place where the reaction of metabolism occurs in a molecule. Identification of SOMs of a compound is not usually a low-cost task in drug discovery. Thus, a silico method to predict site of metabolism (SOMs) of FMOs would provide medical chemists information of SOMs before experiments. In this work, we developed a machine learning model combining quantum features (condensed Fukui function) and circular fingerprints to predict potential SOMs in a molecule. The final model via SVM was easily interpreted with only five features. In the training set with 10 CV showed an area under curve (AUC) value of ROC curve, 0.889, and the value of MCC,0.767. In the external validation, AUC value of the model was 0.801 and the accuracy (MCC) was 0.611. These showed the predictive power of our model and we wish such a research to assist medical chemists in the assessment of FMO metabolism at the preclinical stage of drug discovery. Chapter II: Interaction between Trehalose and MTHase from Sulfolobus solfataricus studied by theoretical computation and site-directed mutagenesis Maltooligosyltrehalose trehalohydrolase (MTHase) catalyzes the release of trehalose by cleaving the α-1,4-glucosidic linkage next to the α-1,1-linked terminal disaccharide of maltooligosyltrehalose. Computer simulation using the hydrogen bond analysis, free energy decomposition, and computational alanine scanning were employed to investigate the interaction between maltooligosyltrehalose and the enzyme. The same residues that were chosen for theoretical investigation were also studied by site-directed mutagenesis and enzyme kinetic analysis. The importance of residues determined either experimentally or computed theoretically were in good accord with each other. It was found that residues Y155, D156, and W218 of subsites -2 and -3 of the enzyme might play an important role in interacting with the ligand. The theoretically constructed structure of the enzyme-ligand complex was further validated through an ab initio quantum chemical calculation using the Gaussian09 package. The activation energy computed from this latter study was very similar to those reported in literatures for the same type of hydrolysis reactions. Chapter III: A Theoretical Study on the Alkaline Hydrolysis of Methyl Thioacetate in Aqueous Solution A base catalyzed hydrolysis reaction of thiolester has been studied in both gas and solution phases using two ab initio quantum mechanics calculations such as Gaussian09 and CPMD. The free energy surface along the reaction path is also constructed using a configuration sampling technique namely the metadynamics method. While there are two different reaction paths obtained for the potential profile of the base-catalyzed hydrolysis reaction for thiolester in gas phase, a triple-well reaction path is computed for the reaction in solution phase by both two quantum mechanics calculations. Unlike a SN2 mechanism (a concerted mechanism) found for the gas-phase reaction, a nucleophilic attack from the hydroxide ion on the carbonyl carbon to yield a tetrahedral intermediate (a stepwise mechanism) is observed for the solution phase reaction. Moreover, the energy profiles computed by these two theoretical calculations are found to be well comparable with those determined experimentally.