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Machushynets N, Al Ayed K, Terlouw BR, Du C, Buijs NP, Willemse J, Elsayed SS, Schill J, Trebosc V, Pieren M, Alexander FM, Cochrane SA, Liles MR, Medema MH, Martin NI, van Wezel GP. Discovery and Derivatization of Tridecaptin Antibiotics with Altered Host Specificity and Enhanced Bioactivity. ACS Chem Biol 2024; 19:1106-1115. [PMID: 38602492 PMCID: PMC11106739 DOI: 10.1021/acschembio.4c00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024]
Abstract
The prevalence of multidrug-resistant (MDR) pathogens combined with a decline in antibiotic discovery presents a major challenge for health care. To refill the discovery pipeline, we need to find new ways to uncover new chemical entities. Here, we report the global genome mining-guided discovery of new lipopeptide antibiotics tridecaptin A5 and tridecaptin D, which exhibit unusual bioactivities within their class. The change in the antibacterial spectrum of Oct-TriA5 was explained solely by a Phe to Trp substitution as compared to Oct-TriA1, while Oct-TriD contained 6 substitutions. Metabolomic analysis of producer Paenibacillus sp. JJ-21 validated the predicted amino acid sequence of tridecaptin A5. Screening of tridecaptin analogues substituted at position 9 identified Oct-His9 as a potent congener with exceptional efficacy against Pseudomonas aeruginosa and reduced hemolytic and cytotoxic properties. Our work highlights the promise of tridecaptin analogues to combat MDR pathogens.
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Affiliation(s)
- Nataliia
V. Machushynets
- Molecular
Biotechnology, Institute of Biology, Leiden
University, Leiden 2333 BE, The Netherlands
| | - Karol Al Ayed
- Biological
Chemistry Group, Institute of Biology, Leiden
University, Leiden 2333 BE, The Netherlands
| | - Barbara R. Terlouw
- Bioinformatics
Group, Wageningen University, Wageningen 6700 PB, The Netherlands
| | - Chao Du
- Molecular
Biotechnology, Institute of Biology, Leiden
University, Leiden 2333 BE, The Netherlands
| | - Ned P. Buijs
- Biological
Chemistry Group, Institute of Biology, Leiden
University, Leiden 2333 BE, The Netherlands
| | - Joost Willemse
- Molecular
Biotechnology, Institute of Biology, Leiden
University, Leiden 2333 BE, The Netherlands
| | - Somayah S. Elsayed
- Molecular
Biotechnology, Institute of Biology, Leiden
University, Leiden 2333 BE, The Netherlands
| | - Julian Schill
- BioVersys
AG, c/o Technologiepark, Basel CH-4057, Switzerland
| | - Vincent Trebosc
- BioVersys
AG, c/o Technologiepark, Basel CH-4057, Switzerland
| | - Michel Pieren
- BioVersys
AG, c/o Technologiepark, Basel CH-4057, Switzerland
| | - Francesca M. Alexander
- School of
Chemistry and Chemical Engineering, Queen’s
University of Belfast, Belfast BT9 5AG, United Kingdom
| | - Stephen A. Cochrane
- School of
Chemistry and Chemical Engineering, Queen’s
University of Belfast, Belfast BT9 5AG, United Kingdom
| | - Mark R. Liles
- Department
of Biological Sciences, Auburn University, Auburn, Alabama 36849, United States
| | - Marnix H. Medema
- Bioinformatics
Group, Wageningen University, Wageningen 6700 PB, The Netherlands
| | - Nathaniel I. Martin
- Biological
Chemistry Group, Institute of Biology, Leiden
University, Leiden 2333 BE, The Netherlands
| | - Gilles P. van Wezel
- Molecular
Biotechnology, Institute of Biology, Leiden
University, Leiden 2333 BE, The Netherlands
- Department
of Microbial Ecology, Netherlands Institute
of Ecology, Wageningen 6700 PB, The Netherlands
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2
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Sun HZ, Li Q, Shang W, Qiao B, Xu QM, Cheng JS. Combinatorial metabolic engineering of Bacillus subtilis for de novo production of polymyxin B. Metab Eng 2024; 83:123-136. [PMID: 38582143 DOI: 10.1016/j.ymben.2024.04.001] [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: 12/23/2023] [Revised: 03/07/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
Polymyxin is a lipopeptide antibiotic that is effective against multidrug-resistant Gram-negative bacteria. However, its clinical development is limited due to low titer and the presence of homologs. To address this, the polymyxin gene cluster was integrated into Bacillus subtilis, and sfp from Paenibacillus polymyxa was expressed heterologously, enabling recombinant B. subtilis to synthesize polymyxin B. Regulating NRPS domain inhibited formation of polymyxin B2 and B3. The production of polymyxin B increased to 329.7 mg/L by replacing the native promoters of pmxA, pmxB, and pmxE with PfusA, C2up, and PfusA, respectively. Further enhancement in this production, up to 616.1 mg/L, was achieved by improving the synthesis ability of 6-methyloctanoic acid compared to the original strain expressing polymyxin heterologously. Additionally, incorporating an anikasin-derived domain into the hybrid nonribosomal peptide synthase of polymyxin increased the B1 ratio in polymyxin B from 57.5% to 62.2%. Through optimization of peptone supply in the fermentation medium and fermentation in a 5.0-L bioreactor, the final polymyxin B titer reached 962.1 mg/L, with a yield of 19.24 mg/g maltodextrin and a productivity of 10.02 mg/(L·h). This study demonstrates a successful approach for enhancing polymyxin B production and increasing the B1 ratio through combinatorial metabolic engineering.
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Affiliation(s)
- Hui-Zhong Sun
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Qing Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Wei Shang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Bin Qiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Qiu-Man Xu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Binshuixi Road 393, Xiqing District, Tianjin 300387, China.
| | - Jing-Sheng Cheng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China.
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3
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Couturier C, Ronzon Q, Lattanzi G, Lingard I, Coyne S, Cazals V, Dubarry N, Yvon S, Leroi-Geissler C, Gracia OR, Teague J, Sordello S, Corbett D, Bauch C, Monlong C, Payne L, Taillier T, Fuchs H, Broenstrup M, Harrison PH, Moynié L, Lakshminarayanan A, Gianga TM, Hussain R, Naismith JH, Mourez M, Bacqué E, Björkling F, Sabuco JF, Franzyk H. Studies of antibacterial activity (in vitro and in vivo) and mode of action for des-acyl tridecaptins (DATs). Eur J Med Chem 2024; 265:116097. [PMID: 38157595 DOI: 10.1016/j.ejmech.2023.116097] [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: 11/09/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Tridecaptins comprise a class of linear cationic lipopeptides with an N-terminal fatty acyl moiety. These 13-mer antimicrobial peptides consist of a combination of d- and l-amino acids, conferring increased proteolytic stability. Intriguingly, they are biosynthesized by non-ribosomal peptide synthetases in the same bacterial species that also produce the cyclic polymyxins displaying similar fatty acid tails. Previously, the des-acyl analog of TriA1 (termed H-TriA1) was found to possess very weak antibacterial activity, albeit it potentiated the effect of several antibiotics. In the present study, two series of des-acyl tridecaptins were explored with the aim of improving the direct antibacterial effect. At the same time, overall physico-chemical properties were modulated by amino acid substitution(s) to diminish the risk of undesired levels of hemolysis and to avoid an impairment of mammalian cell viability, since these properties are typically associated with highly hydrophobic cationic peptides. Microbiology and biophysics tools were used to determine bacterial uptake, while circular dichroism and isothermal calorimetry were used to probe the mode of action. Several analogs had improved antibacterial activity (as compared to that of H-TriA1) against Enterobacteriaceae. Optimization enabled identification of the lead compound 29 that showed a good ADMET profile as well as in vivo efficacy in a variety of mouse models of infection.
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Affiliation(s)
- Cédric Couturier
- Evotec, 1541, Avenue Marcel Mérieux, 69280, Marcy L'Etoile, France.
| | - Quentin Ronzon
- Evotec, 1541, Avenue Marcel Mérieux, 69280, Marcy L'Etoile, France
| | - Giulia Lattanzi
- Evotec-Aptuit (Verona) Srl, Via Alessandro Fleming 4, 37135, Verona, Italy
| | - Iain Lingard
- Evotec-Aptuit (Verona) Srl, Via Alessandro Fleming 4, 37135, Verona, Italy
| | | | | | | | | | | | | | - Joanne Teague
- Evotec, No. 23F, Mereside, Alderley Park, Cheshire, SK10 4TG, United Kingdom
| | | | - David Corbett
- Evotec, No. 23F, Mereside, Alderley Park, Cheshire, SK10 4TG, United Kingdom
| | - Caroline Bauch
- Evotec-Cyprotex, No. 24, Mereside, Alderley Park, Cheshire, SK10 4TG, United Kingdom
| | | | - Lloyd Payne
- Evotec, No. 23F, Mereside, Alderley Park, Cheshire, SK10 4TG, United Kingdom
| | | | - Hazel Fuchs
- Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Mark Broenstrup
- Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Peter H Harrison
- Division of Structural Biology, Wellcome Trust Centre of Human Genomics, 7 Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Lucile Moynié
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | - Abirami Lakshminarayanan
- Division of Structural Biology, Wellcome Trust Centre of Human Genomics, 7 Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Tiberiu-Marius Gianga
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - James H Naismith
- Division of Structural Biology, Wellcome Trust Centre of Human Genomics, 7 Roosevelt Drive, Oxford, OX3 7BN, United Kingdom; Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | | | - Eric Bacqué
- Evotec, 1541, Avenue Marcel Mérieux, 69280, Marcy L'Etoile, France
| | - Fredrik Björkling
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
| | | | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
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Pilz M, Cavelius P, Qoura F, Awad D, Brück T. Lipopeptides development in cosmetics and pharmaceutical applications: A comprehensive review. Biotechnol Adv 2023; 67:108210. [PMID: 37460047 DOI: 10.1016/j.biotechadv.2023.108210] [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: 01/26/2023] [Revised: 07/05/2023] [Accepted: 07/09/2023] [Indexed: 07/25/2023]
Abstract
Lipopeptides are surface active, natural products of bacteria, fungi and green-blue algae origin, having diverse structures and functionalities. In analogy, a number of chemical synthesis techniques generated new designer lipopeptides with desirable features and functions. Lipopetides are self-assembly guided, supramolecular compounds which have the capacity of high-density presentation of the functional epitopes at the surface of the nanostructures. This feature contributes to their successful application in several industry sectors, including food, feed, personal care, and pharmaceutics. In this comprehensive review, the novel class of ribosomally synthesized lipopeptides is introduced alongside the more commonly occuring non-ribosomal lipopeptides. We highlight key representatives of the most researched as well as recently described lipopeptide families, with emphasis on structural features, self-assembly and associated functions. The common biological, chemical and hybrid production routes of lipopeptides, including prominent analogues and derivatives are also discussed. Furthermore, genetic engineering strategies aimed at increasing lipopeptide yields, diversity and biological activity are summarized and exemplified. With respect to application, this work mainly details the potential of lipopeptides in personal care and cosmetics industry as cleansing agents, moisturizer, anti-aging/anti-wrinkling, skin whitening and preservative agents as well as the pharmaceutical industry as anitimicrobial agents, vaccines, immunotherapy, and cancer drugs. Given that this review addresses human applications, we conclude on the topic of safety of lipopeptide formulations and their sustainable production.
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Affiliation(s)
- Melania Pilz
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Philipp Cavelius
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Farah Qoura
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Dania Awad
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany.
| | - Thomas Brück
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany.
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Krusong W, La China S, Pothimon R, Gullo M. Defining Paenibacillus azoreducens (P8) and Acetobacter pasteurianus (UMCC 2951) strains performances in producing acetic acid. Front Microbiol 2022; 13:991688. [DOI: 10.3389/fmicb.2022.991688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/19/2022] [Indexed: 11/18/2022] Open
Abstract
In this study, spore-forming bacteria isolated from saccharified rice were selected for producing acetic acid. From the screening of 15 strains, P8 strain was chosen as a candidate. The strain was identified as Paenibacillus azoreducens by 16S rRNA analysis (99.85% similarity with P. azoreducens CM1T). Acetic acid is the main component of vinegar but also an industrial commodity produced by chemical synthesis. Sustainable routes for obtaining acetic acid are of great interest for decreasing the environmental impact generated by chemical syntheses. Biological acetic acid production is effective for vinegar production by acetic acid bacteria, but it cannot economically compete with the chemical synthesis for producing it as a pure commodity. Considering the need to improve the yield of pure acetic acid produced by microbial conversions, in this study, P8 strain was chosen for designing processes in different fermentation conditions. Tests were conducted in single and semi-continuous systems, using rice wine as substrate. Acetic acid produced by P8 strain was compared with that of Acetobacter pasteurianus (UMCC 2951), a strain known for producing acetic acid from rice wine. Even though the fermentation performances of P. azoreducens P8 were slightly lower than those of acetic acid bacteria usually used for vinegar production, results highlight its suitability for producing acetic acid. The final acetic acid produced by P. azoreducens P8 was 73 g/L, in a single stage fermentation, without losses. In nine cycles of semi-continuous regime the average of acetification rate was 0.814 (g/L/days). Two main attributes of P. azoreducens P8 are of relevance for producing acetic acid, namely the ability to grow at temperature higher (+ 37°C), than mesophilic acetic acid bacteria, and the absence of cytoplasmic assimilation of acetic acid. These features allow to design multiple strains cultures, in which P. azoreducens can acts as a helper strain. Based on our results, the new isolate P. azoreducens P8 can be propagated in fermenting broths for boosting acetic acid production, under the selected conditions, and used in combination with acetic acid bacteria to produce biological acetic acid, as a non-food grade commodity.
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