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BioNavi-NP: Biosynthesis Navigator for Natural Products
arXiv - CS - Computational Engineering, Finance, and Science Pub Date : 2021-05-26 , DOI: arxiv-2105.13121
Shuangjia Zheng, Tao Zeng, Chengtao Li, Binghong Chen, Connor W. Coley, Yuedong Yang, Ruibo Wu

Nature, a synthetic master, creates more than 300,000 natural products (NPs) which are the major constituents of FDA-proved drugs owing to the vast chemical space of NPs. To date, there are fewer than 30,000 validated NPs compounds involved in about 33,000 known enzyme catalytic reactions, and even fewer biosynthetic pathways are known with complete cascade-connected enzyme catalysis. Therefore, it is valuable to make computer-aided bio-retrosynthesis predictions. Here, we develop BioNavi-NP, a navigable and user-friendly toolkit, which is capable of predicting the biosynthetic pathways for NPs and NP-like compounds through a novel (AND-OR Tree)-based planning algorithm, an enhanced molecular Transformer neural network, and a training set that combines general organic transformations and biosynthetic steps. Extensive evaluations reveal that BioNavi-NP generalizes well to identifying the reported biosynthetic pathways for 90% of test compounds and recovering the verified building blocks for 73%, significantly outperforming conventional rule-based approaches. Moreover, BioNavi-NP also shows an outstanding capacity of biologically plausible pathways enumeration. In this sense, BioNavi-NP is a leading-edge toolkit to redesign complex biosynthetic pathways of natural products with applications to total or semi-synthesis and pathway elucidation or reconstruction.

中文翻译:

BioNavi-NP:天然产物的生物合成导航器

Nature 作为合成大师,创造了超过 300,000 种天然产物 (NPs),由于 NPs 的巨大化学空间,它们是 FDA 证明药物的主要成分。迄今为止,只有不到 30,000 种经过验证的 NPs 化合物参与了大约 33,000 种已知的酶催化反应,而已知的具有完整级联酶催化作用的生物合成途径甚至更少。因此,进行计算机辅助的生物逆合成预测是很有价值的。在这里,我们开发了 BioNavi-NP,这是一种可导航且用户友好的工具包,能够通过基于(AND-OR 树)的新型规划算法(一种增强的分子 Transformer 神经网络)预测 NP 和 NP 类化合物的生物合成途径。网络,以及结合一般有机转化和生物合成步骤的训练集。广泛的评估表明,BioNavi-NP能够很好地概括出所报告的90%测试化合物的生物合成途径,并回收了73%的已验证构建基块,大大优于传统的基于规则的方法。此外,BioNavi-NP 还显示出生物学上合理的途径枚举的出色能力。从这个意义上说,BioNavi-NP 是一个前沿工具包,用于重新设计天然产物的复杂生物合成途径,应用于全合成或半合成以及途径阐明或重建。BioNavi-NP 还显示出生物学上合理的途径枚举的出色能力。从这个意义上说,BioNavi-NP 是一个前沿工具包,用于重新设计天然产物的复杂生物合成途径,应用于全合成或半合成以及途径阐明或重建。BioNavi-NP 还显示出生物学上合理的途径枚举的出色能力。从这个意义上说,BioNavi-NP 是一个前沿工具包,用于重新设计天然产物的复杂生物合成途径,应用于全合成或半合成以及途径阐明或重建。
更新日期:2021-05-28
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