Fig. 2: Cell-free production of de novo-generated and prioritized AMPs and activity screening against B. subtilis and E. coli. | Nature Communications

Fig. 2: Cell-free production of de novo-generated and prioritized AMPs and activity screening against B. subtilis and E. coli.

From: Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides

Fig. 2: Cell-free production of de novo-generated and prioritized AMPs and activity screening against B. subtilis and E. coli.

a We used different generative and regressor models (Supplementary Table 4) to design and prioritize AMPs in five rounds, produced and screened a total number of 500 AMPs from synthetic DNA fragments and found 30 functional candidates. b Charge and AlphaFold-predicted structure of the functional AMPs with associated slowed/stopped growth curves for B. subtilis and E. coli. All (including control) AMPs were produced using CFPS and no peptide purification was carried out prior to the activity test. Growth curves (OD600 0–0.45 over time 4–20 h for all) are the average of n = 3 independent experiments. Growth curves with error bars as standard deviation are provided in Supplementary Fig. 1. c 2D-projections of the 50-dimensional latent space were obtained by principal component analysis (PCA) for the two variational autoencoders (VAEs, without and with the KL-term annealing, VAE_v1 and VAE_v2, respectively, see Methods) that were used for de novo-design of AMPs. Blue color intensity represents the frequency of training AMPs in the latent space. Functional AMPs (red), BP100 and Cecropin B (black) annotated back into the latent space. Source data for b are provided as a Source Data file. Created with BioRender.com.

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