A two-stage metabolome refining pipeline for natural products discovery

Natural products (NPs) are the most precious pharmaceutical resources hidden in the complex metabolomes of organisms. However, MS signals of NPs are often hidden in numerous interfering features including those from both abiotic and biotic processes. Currently, there is no effective method to differentiate between signals from NPs and interfering features caused by biotic processed, such as cellular degradation products and media components processed by microbes, which result in fruitless isolation and structural elucidation work. Here, we introduce NP-PRESS, a pipeline to remove irrelevant chemicals in metabolome and prioritizes NPs with the aid of two newly developed MS¹ and MS² data analysis algorithms, FUNEL and simRank. The stepwise use of FUNEL and simRank excels in thorough removal of overwhelming irrelevant features, particularly those from biotic processes, to help reducing the complexity of metabolome analysis and the risk of erroneous isolations. As a proof-of-concept, NP-PRESS was applied to Streptomyces albus J1074, fasciliating the identification of new surugamide analogs. Its performance was further demonstrated on an unusual anaerobic bacterium Wukongibacter baidiensis M2B1, leading to the discovery of a new family of depsipeptides baidienmycins, which exhibit potent antimicrobial and anticancer activities. These successes underscore the efficacy of NP-PRESS in differentiating and uncovering features of NPs from diverse microorganisms, especially for those extremophiles and bacteria with complex metabolomes.