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利用罕见放线菌的相互作用和内在抗菌抗性可发现不寻常的代谢抑制剂。

Harnessing Rare Actinomycete Interactions and Intrinsic Antimicrobial Resistance Enables Discovery of an Unusual Metabolic Inhibitor.

机构信息

Department of Plant and Microbial Biology, University of California, Berkeleygrid.47840.3f, California, USA.

Department of Chemical and Biomolecular Engineering, University of California, Berkeleygrid.47840.3f, California, USA.

出版信息

mBio. 2022 Jun 28;13(3):e0039322. doi: 10.1128/mbio.00393-22. Epub 2022 May 24.

Abstract

Bacterial natural products have historically been a deep source of new medicines, but their slowed discovery in recent decades has put a premium on developing strategies that enhance the likelihood of capturing novel compounds. Here, we used a straightforward approach that capitalizes on the interactive ecology of "rare" actinomycetes. Specifically, we screened for interactions that triggered the production of antimicrobials that inhibited the growth of a bacterial strain with exceptionally diverse natural antimicrobial resistance. This strategy led to the discovery of a family of antimicrobials we term the dynaplanins. Heterologous expression enabled identification of the dynaplanin biosynthetic gene cluster, which was missed by typical algorithms for natural product gene cluster detection. Genome sequencing of partially resistant mutants revealed a 2-oxo acid dehydrogenase E2 subunit as the likely molecular target of the dynaplanins, and this finding was supported by computational modeling of the dynaplanin scaffold within the active site of this enzyme. Thus, this simple strategy, which leverages microbial interactions and natural antibiotic resistance, can enable discovery of molecules with unique antimicrobial activity. In addition, these results indicate that primary metabolism may be a direct target for inhibition via chemical interference in competitive microbial interactions. Many antibiotics were originally discovered from microbes. However, in recent decades, resistance to current treatments has risen, while novel antibiotic discovery has become increasingly challenging. Thus, there is a need to develop new strategies to find novel antimicrobials. Here, we incorporated three levels of innovation into a single, simple discovery pipeline: focusing on understudied bacteria with a high potential for producing antibiotics, growing these bacteria in binary microbial interactions, and screening for activity against a multidrug-resistant bacterium. This led us to discover a family of antimicrobials that we call the dynaplanins, which are synthesized by genes that were not detected by typical prediction algorithms. We found that dynaplanins likely block the function of one of three related enzymes called 2-oxo acid dehydrogenases, which are vital to cellular metabolism. Overall, our strategy based on bacterial competition led to discovery of a novel antibiotic that inhibits the ability to metabolize nutrients.

摘要

细菌天然产物一直是新药的重要来源,但近几十年来,它们的发现速度放缓,因此开发能够提高捕获新型化合物可能性的策略变得尤为重要。在这里,我们使用了一种简单的方法,利用了“稀有”放线菌的相互作用生态。具体来说,我们筛选了能够触发产生抗生素的相互作用,这些抗生素可以抑制一种具有异常多样化天然抗微生物活性的细菌菌株的生长。这种策略导致了一类我们称之为 dynaplanins 的抗生素的发现。异源表达使我们能够识别 dynaplanin 生物合成基因簇,而典型的天然产物基因簇检测算法却错过了这个基因簇。部分耐药突变体的基因组测序揭示了 2-氧酸脱氢酶 E2 亚基可能是 dynaplanins 的分子靶标,这一发现得到了 dynaplanin 支架在该酶活性位点内的计算模型的支持。因此,这种利用微生物相互作用和天然抗生素耐药性的简单策略可以发现具有独特抗微生物活性的分子。此外,这些结果表明,通过在竞争微生物相互作用中进行化学干扰,初级代谢物可能成为直接抑制的靶标。许多抗生素最初是从微生物中发现的。然而,近几十年来,对现有治疗方法的耐药性有所上升,而新型抗生素的发现变得越来越具有挑战性。因此,需要开发新的策略来寻找新型的抗生素。在这里,我们将三个创新层面整合到一个简单的单一发现管道中:专注于具有产生抗生素高潜力的研究较少的细菌,在二元微生物相互作用中培养这些细菌,并筛选对多药耐药细菌的活性。这使我们发现了一类我们称之为 dynaplanins 的抗生素,这些抗生素是由典型预测算法无法检测到的基因合成的。我们发现 dynaplanins 可能会阻止三种称为 2-氧酸脱氢酶的相关酶中的一种的功能,而这些酶对细胞代谢至关重要。总的来说,我们基于细菌竞争的策略导致了一种新型抗生素的发现,这种抗生素可以抑制代谢营养物质的能力。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/52aa/9239090/ab7bc2ecdf2c/mbio.00393-22-f001.jpg

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