合成生物学是实现化工绿色化、可持续发展的有效方法之一。代谢途径重构是合成生物学中工业菌种开发与化学品生物催化合成的关键步骤,目的在于确定宿主内合成目标化合物的反应路径与底物,是酶定向进化、实现目标物质生物合成的基础。考虑到生物代谢网络的复杂性,代谢途径重构一般会得到较为庞大的路径结果。为了提高效率、减少无效的实验尝试,合理、有效的路径评估与筛选是重要与必须的。针对已有路径评估方法存在的问题,该文构建了一种生物合成路径评估与排序方法,设计了6个反映路径理论可行性的评估指标,结合层次分析法实现了合理、可解释的路径推荐。通过实例测试,证明了所提出的路径评估方法的有效性。该路径评估方法可降低实验的试错成本,为增加生物逆合成工具的实用性提供了基础。

Synthetic biology employs cells and enzymes to produce high-value-added chemicals through biocatalytic processes. Synthetic biology uses renewable biomass as the substrate as well as the energy source, thus meeting the requirements of green and sustainable chemical engineering. In synthetic biology, metabolic pathway reconstruction is a key step in the development of industrial strains and the biocatalytic synthesis of chemicals, which aims to determine the reaction pathways and substrates for the synthesis of target compounds in the host; and metabolic pathway reconstruction is the basis for the directed evolution of enzymes and the biosynthesis of target substances. Considering the complexity of the biological metabolic network, a metabolic pathway reconstruction typically results in numerous pathway results. To improve efficiency and reduce invalid experimental attempts, reasonable and effective pathway evaluation and screening are highly important. Current evaluation methods of relevant pathway reconstruction tools are relatively simple, using a few indicators without prioritizing any of them. To solve this problem, this paper proposes a biosynthetic pathway evaluation method. Metabolic path reconstruction generally includes path acquisition and evaluation. The path evaluation process can score and rank the most optimal candidate paths and make recommendations based on the ranking results to obtain several candidate paths to synthesize the target product. This study achieved path acquisition based on the Rhea database. The proposed path evaluation method designed six path evaluation indicators and calculated different path characteristics of several candidate paths, which indicated the path theoretical feasibility, including the path length score, the proportion of real reactions from the database, the path molecular similarity score, the path feasibility score, the proportion of reactions with enzyme information, and the reaction rules feasibility score. These characteristics reflected the theoretical feasibility of biosynthetic pathways from different aspects. To realize the scientific-weighted summation of the indicators, their individual weights were determined using the analytic hierarchy process. Three experts were invited to give the judgment matrices based on their subjective judgments of the relative importance of the indicators. Using these matrices, the respective indicator weights were calculated. Combined with the consistency index, the indicator weights determined by different experts were fused to obtain the final composite index weight, which was subsequently used to calculate the final path score for each path. The effectiveness of the biosynthetic path evaluation method established in this study is demonstrated by an actual test of conversion between benzoate and 2, 3-dihydroxybenzoate. The evaluation score for each path is calculated and used to provide reasonable and interpretable path recommendations. Paths with higher evaluation scores offer advantages in terms of theoretical feasibility. The proposed path evaluation method achieves the expected results, which can be used to deal with the contradiction between the richness of data and difficulty of practice in synthetic biology, reduce the trial-and-error cost of experiments, and provide a basis for increasing the practicability of biological retrosynthesis tools.