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Lopatniuk M, Riedel F, Wildfeuer J, Stierhof M, Dahlem C, Kiemer AK, Luzhetskyy A. Development of a Streptomyces-based system for facile thioholgamide library generation and analysis. Metab Eng 2023; 78:48-60. [PMID: 37142115 DOI: 10.1016/j.ymben.2023.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/06/2023]
Abstract
Derivatizing natural products (NPs) is essential in structure-activity relationship (SAR) studies, compound optimization, and drug development. Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent one of the major classes of natural products. Thioholgamide represents thioamitide - a recently emerged family of RiPPs with unique structures and great potential in anticancer drug development. Although the method for generating the RiPP library by codon substitutions in the precursor peptide gene is straightforward, the techniques to perform RiPP derivatization in Actinobacteria remain limited and time-consuming. Here, we report a facile system for producing a library of randomized thioholgamide derivatives utilizing an optimized Streptomyces host. This technique enabled us to access all possible amino acid substitutions of the thioholgamide molecule, one position at a time. Out of 152 potential derivatives, 85 were successfully detected, revealing the impact of amino acid substitutions on thioholgamide post-translational modifications (PTMs). Moreover, new PTMs were observed among thioholgamide derivatives: thiazoline heterocycles, which have not yet been reported for thioamitides, and S-methylmethionine, which is very rare in nature. The obtained library was subsequently used for thioholgamide SAR studies and stability assays.
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Affiliation(s)
- Maria Lopatniuk
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Florian Riedel
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Julia Wildfeuer
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany; Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Marc Stierhof
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Charlotte Dahlem
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.
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Thokkadam A, Do T, Ran X, Brynildsen MP, Yang ZJ, Link AJ. High-Throughput Screen Reveals the Structure-Activity Relationship of the Antimicrobial Lasso Peptide Ubonodin. ACS CENTRAL SCIENCE 2023; 9:540-550. [PMID: 36968541 PMCID: PMC10037499 DOI: 10.1021/acscentsci.2c01487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Indexed: 06/16/2023]
Abstract
The Burkholderia cepacia complex (Bcc) is a group of bacteria including opportunistic human pathogens. Immunocompromised individuals and cystic fibrosis patients are especially vulnerable to serious infections by these bacteria, motivating the search for compounds with antimicrobial activity against the Bcc. Ubonodin is a lasso peptide with promising activity against Bcc species, working by inhibiting RNA polymerase in susceptible bacteria. We constructed a library of over 90 000 ubonodin variants with 2 amino acid substitutions and used a high-throughput screen and next-generation sequencing to examine the fitness of the entire library, generating the most comprehensive data set on lasso peptide activity so far. This screen revealed information regarding the structure-activity relationship of ubonodin over a large sequence space. Remarkably, the screen identified one variant with not only improved activity compared to wild-type ubonodin but also a submicromolar minimum inhibitory concentration (MIC) against a clinical isolate of the Bcc member Burkholderia cenocepacia. Ubonodin and several of the variants identified in this study had lower MICs against certain Bcc strains than those of many clinically approved antibiotics. Finally, the large library size enabled us to develop DeepLasso, a deep learning model that can predict the RNAP inhibitory activity of an ubonodin variant.
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Affiliation(s)
- Alina Thokkadam
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Truc Do
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Xinchun Ran
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Mark P. Brynildsen
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Zhongyue J. Yang
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data
Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - A. James Link
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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Striving for sustainable biosynthesis: discovery, diversification, and production of antimicrobial drugs in Escherichia coli. Biochem Soc Trans 2022; 50:1315-1328. [PMID: 36196987 DOI: 10.1042/bst20220218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/07/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022]
Abstract
New antimicrobials need to be discovered to fight the advance of multidrug-resistant pathogens. A promising approach is the screening for antimicrobial agents naturally produced by living organisms. As an alternative to studying the native producer, it is possible to use genetically tractable microbes as heterologous hosts to aid the discovery process, facilitate product diversification through genetic engineering, and ultimately enable environmentally friendly production. In this mini-review, we summarize the literature from 2017 to 2022 on the application of Escherichia coli and E. coli-based platforms as versatile and powerful systems for the discovery, characterization, and sustainable production of antimicrobials. We highlight recent developments in high-throughput screening methods and genetic engineering approaches that build on the strengths of E. coli as an expression host and that led to the production of antimicrobial compounds. In the last section, we briefly discuss new techniques that have not been applied to discover or engineer antimicrobials yet, but that may be useful for this application in the future.
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