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

Pandi, A., Adam, D., Zare, A., Trinh, V. T., Schaefer, S. L., Wiegand, M., et al. (2022). Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides. bioRxiv: the preprint server for biology, 2022.11.19.517184.

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Pandi, Amir1, Author           
Adam, David1, Author
Zare, Amir1, Author
Trinh, Van Tuan2, Author
Schaefer, Stefan L.2, Author
Wiegand, Marie2, Author
Klabunde, Björn2, Author
Bobkova, Elizaveta1, Author           
Kushwaha, Manish2, Author
Foroughijabbari, Yeganeh1, Author
Braun, Peter2, Author
Spahn, Christoph Klaus3, Author           
Preußer, Christian2, Author
von Strandmann, Elke Pogge2, Author
Bode, Helge B.3, Author                 
Buttlar, Heiner2, Author
Bertrams, Wilhelm2, Author
Jung, Anna Lena2, Author
Abendroth, Frank2, Author
Schmeck, Bernd2, Author
Hummer, Gerhard2, AuthorVázquez, Olalla2, AuthorErb, Tobias J.1, Author            more..
Affiliations:
1Understanding and Building Metabolism, Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Max Planck Society, ou_3266303              
2external, ou_persistent22              
3Natural Product Function and Engineering, Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Max Planck Society, ou_3266308              

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 Abstract: Bioactive peptides are key molecules in health and medicine. Deep learning holds a big promise for the discovery and design of bioactive peptides. Yet, suitable experimental approaches are required to validate candidates in high throughput and at low cost. Here, we established a cell- free protein synthesis (CFPS) pipeline for the rapid and inexpensive production of antimicrobial peptides (AMPs) directly from DNA templates. To validate our platform, we used deep learning to design thousands of AMPs de novo. Using computational methods, we prioritized 500 candidates that we produced and screened with our CFPS pipeline. We identified 30 functional AMPs, which we characterized further through molecular dynamics simulations, antimicrobial activity and toxicity. Notably, six de novo-AMPs feature broad-spectrum activity against multidrug-resistant pathogens and do not develop bacterial resistance. Our work demonstrates the potential of CFPS for production and testing of bioactive peptides within less than 24 hours and <10$ per screen.Competing Interest StatementThe authors have declared no competing interest.

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Language(s): eng - English
 Dates: 2022-12-23
 Publication Status: Issued
 Pages: -
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 Table of Contents: -
 Rev. Type: No review
 Degree: -

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Title: bioRxiv : the preprint server for biology
  Abbreviation : bioRxiv
Source Genre: Journal
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Pages: - Volume / Issue: - Sequence Number: 2022.11.19.517184 Start / End Page: - Identifier: ZDB: 2766415-6
CoNE: https://pure.mpg.de/cone/journals/resource/2766415-6
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