Mathematical Modelling of Polyamine Metabolism in Bloodstream-Form Trypanosoma brucei: An Application to Drug Target Identification

We present the first computational kinetic model of polyamine metabolism in bloodstream-form Trypanosoma brucei, the causative agent of human African trypanosomiasis. We systematically extracted the polyamine pathway from the complete metabolic network while still maintaining the predictive capability of the pathway. The kinetic model is constructed on the basis of information gleaned from the experimental biology literature and defined as a set of ordinary differential equations. We applied Michaelis-Menten kinetics featuring regulatory factors to describe enzymatic activities that are well defined. Uncharacterised enzyme kinetics were approximated and justified with available physiological properties of the system. Optimisation-based dynamic simulations were performed to train the model with experimental data and inconsistent predictions prompted an iterative procedure of model refinement. Good agreement between simulation results and measured data reported in various experimental conditions shows that the model has good applicability in spite of there being gaps in the required data. With this kinetic model, the relative importance of the individual pathway enzymes was assessed. We observed that, at low-to-moderate levels of inhibition, enzymes catalysing reactions of de novo AdoMet (MAT) and ornithine production (OrnPt) have more efficient inhibitory effect on total trypanothione content in comparison to other enzymes in the pathway. In our model, prozyme and TSHSyn (the production catalyst of total trypanothione) were also found to exhibit potent control on total trypanothione content but only when they were strongly inhibited. Different chemotherapeutic strategies against T. brucei were investigated using this model and interruption of polyamine synthesis via joint inhibition of MAT or OrnPt together with other polyamine enzymes was identified as an optimal therapeutic strategy.本研究首次构建了布氏锥虫（Trypanosoma brucei）血流型阶段的多胺代谢计算动力学模型，该病原体正是人类非洲锥虫病（human African trypanosomiasis）的致病原。本研究从完整代谢网络中系统性提取多胺代谢通路，同时保留了该通路的预测能力。本动力学模型基于实验生物学文献中获取的信息构建，并以常微分方程组（ordinary differential equations）的形式进行定义。研究采用带有调控因子的米氏动力学（Michaelis-Menten kinetics）描述已明确的酶促反应活性；对于尚未表征的酶动力学参数，则通过该系统已有的生理学特性进行近似估算并验证合理性。研究基于优化算法开展动态模拟，利用实验数据对模型进行训练，当预测结果与实验数据不符时，通过迭代流程对模型进行优化修正。尽管所需数据存在部分缺失，但在多种实验条件下，模型模拟结果与已发表的实测数据均具有良好的一致性，表明该模型具备较好的适用性。借助该动力学模型，本研究对通路中各酶的相对重要性进行了评估。研究发现，在低至中等水平的抑制条件下，催化从头合成S-腺苷甲硫氨酸的甲硫氨酸腺苷转移酶（MAT）与催化鸟氨酸生成的OrnPt，相较于通路内其他酶，对锥硫氨酸（trypanothione）总含量的抑制效果更为显著。在本模型中，前酶（prozyme）与锥硫氨酸合酶（TSHSyn，负责催化锥硫氨酸总产物的合成）同样被发现可对锥硫氨酸总含量发挥强力调控作用，但仅在其受到强抑制时生效。本研究借助该模型评估了多种针对布氏锥虫的化疗策略，结果表明，通过联合抑制MAT或OrnPt以及其他多胺通路酶来阻断多胺合成，是最优的化疗方案。