IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-62407-4.html
   My bibliography  Save this article

A broad-spectrum antibiotic targets multiple-drug-resistant bacteria with dual binding targets and no detectable resistance

Author

Listed:
  • Wenyan He

    (China Pharmaceutical University)

  • Xueting Huan

    (China Pharmaceutical University)

  • Yinchuan Li

    (China Pharmaceutical University)

  • Qisen Deng

    (China Pharmaceutical University)

  • Tao Chen

    (China Pharmaceutical University)

  • Wen Xiao

    (China Pharmaceutical University)

  • Yijun Chen

    (China Pharmaceutical University)

  • Lingman Ma

    (China Pharmaceutical University)

  • Nan Liu

    (China Pharmaceutical University)

  • Zhuo Shang

    (Shandong University)

  • Zongqiang Wang

    (China Pharmaceutical University)

Abstract

The rapid emergence of difficult-to-treat multidrug-resistant pathogens, combined with the scarcity of antibiotics possessing novel mechanisms, poses a significant threat to global public health. Here, we integrate the synthetic-bioinformatic natural product approach with peptide optimization to unveil the antibiotic-producing potential of Paenibacillaceae bacteria. Our culture-independent approach led to the discovery of paenimicin, a novel 11-mer depsi-lipopeptide featuring an unprecedented dual-binding mechanism. By sequestering the phosphate and hydroxyl groups of lipid A in Gram-negative bacteria, as well as the phosphate groups of teichoic acids in Gram-positive bacteria, paenimicin exhibits potent and broad-spectrum efficacy against MDR pathogens in vitro and in vivo models. Paenimicin demonstrates no detectable resistance, favorable pharmacokinetics and low nephrotoxicity, positioning it as a promising candidate for treating severe and urgent MDR infections.

Suggested Citation

  • Wenyan He & Xueting Huan & Yinchuan Li & Qisen Deng & Tao Chen & Wen Xiao & Yijun Chen & Lingman Ma & Nan Liu & Zhuo Shang & Zongqiang Wang, 2025. "A broad-spectrum antibiotic targets multiple-drug-resistant bacteria with dual binding targets and no detectable resistance," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-62407-4
    DOI: 10.1038/s41467-025-62407-4
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-62407-4
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-025-62407-4?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Anatol Luther & Matthias Urfer & Michael Zahn & Maik Müller & Shuang-Yan Wang & Milon Mondal & Alessandra Vitale & Jean-Baptiste Hartmann & Timothy Sharpe & Fabio Lo Monte & Harsha Kocherla & Elizabet, 2019. "Author Correction: Chimeric peptidomimetic antibiotics against Gram-negative bacteria," Nature, Nature, vol. 576(7786), pages 5-5, December.
    2. Kirstin Scherlach & Christian Hertweck, 2021. "Mining and unearthing hidden biosynthetic potential," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    3. Zongqiang Wang & Bimal Koirala & Yozen Hernandez & Matthew Zimmerman & Steven Park & David S. Perlin & Sean F. Brady, 2022. "A naturally inspired antibiotic to target multidrug-resistant pathogens," Nature, Nature, vol. 601(7894), pages 606-611, January.
    4. Ruobing Wang & Lucy Dorp & Liam P. Shaw & Phelim Bradley & Qi Wang & Xiaojuan Wang & Longyang Jin & Qing Zhang & Yuqing Liu & Adrien Rieux & Thamarai Dorai-Schneiders & Lucy Anne Weinert & Zamin Iqbal, 2018. "The global distribution and spread of the mobilized colistin resistance gene mcr-1," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
    5. Wan-Qiu Liu & Xiangyang Ji & Fang Ba & Yufei Zhang & Huiling Xu & Shuhui Huang & Xiao Zheng & Yifan Liu & Shengjie Ling & Michael C. Jewett & Jian Li, 2024. "Cell-free biosynthesis and engineering of ribosomally synthesized lanthipeptides," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    6. Selen Manioglu & Seyed Majed Modaresi & Noah Ritzmann & Johannes Thoma & Sarah A. Overall & Alexander Harms & Gregory Upert & Anatol Luther & Alexander B. Barnes & Daniel Obrecht & Daniel J. Müller & , 2022. "Antibiotic polymyxin arranges lipopolysaccharide into crystalline structures to solidify the bacterial membrane," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    7. Anatol Luther & Matthias Urfer & Michael Zahn & Maik Müller & Shuang-Yan Wang & Milon Mondal & Alessandra Vitale & Jean-Baptiste Hartmann & Timothy Sharpe & Fabio Lo Monte & Harsha Kocherla & Elizabet, 2019. "Chimeric peptidomimetic antibiotics against Gram-negative bacteria," Nature, Nature, vol. 576(7787), pages 452-458, December.
    8. Kade D. Roberts & Yan Zhu & Mohammad A. K. Azad & Mei-Ling Han & Jiping Wang & Lynn Wang & Heidi H. Yu & Andrew S. Horne & Jo-Anne Pinson & David Rudd & Nicolas H. Voelcker & Nitin A. Patil & Jinxin Z, 2022. "A synthetic lipopeptide targeting top-priority multidrug-resistant Gram-negative pathogens," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Christopher J. Barden & Fan Wu & J. Pedro Fernandez-Murray & Erhu Lu & Shengguo Sun & Marcia M. Taylor & Annette L. Rushton & Jason Williams & Mahtab Tavasoli & Autumn Meek & Alla Siva Reddy & Lisa M., 2024. "Computer-aided drug design to generate a unique antibiotic family," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    2. Runrun Wu & Jeremy W. Bakelar & Karl Lundquist & Zijian Zhang & Katie M. Kuo & David Ryoo & Yui Tik Pang & Chen Sun & Tommi White & Thomas Klose & Wen Jiang & James C. Gumbart & Nicholas Noinaj, 2021. "Plasticity within the barrel domain of BamA mediates a hybrid-barrel mechanism by BAM," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    3. Christopher Jonkergouw & Ngong Kodiah Beyeh & Ekaterina Osmekhina & Katarzyna Leskinen & S. Maryamdokht Taimoory & Dmitrii Fedorov & Eduardo Anaya-Plaza & Mauri A. Kostiainen & John F. Trant & Robin H, 2023. "Repurposing host-guest chemistry to sequester virulence and eradicate biofilms in multidrug resistant Pseudomonas aeruginosa and Acinetobacter baumannii," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    4. Parthasarathi Rath & Adrian Hermann & Ramona Schaefer & Elia Agustoni & Jean-Marie Vonach & Martin Siegrist & Christian Miscenic & Andreas Tschumi & Doris Roth & Christoph Bieniossek & Sebastian Hille, 2023. "High-throughput screening of BAM inhibitors in native membrane environment," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    5. Kerry R. Buchholz & Mike Reichelt & Matthew C. Johnson & Sarah J. Robinson & Peter A. Smith & Steven T. Rutherford & John G. Quinn, 2024. "Potent activity of polymyxin B is associated with long-lived super-stoichiometric accumulation mediated by weak-affinity binding to lipid A," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    6. Elvin Maharramov & Márton Simon Czikkely & Petra Szili & Zoltán Farkas & Gábor Grézal & Lejla Daruka & Eszter Kurkó & Léna Mészáros & Andreea Daraba & Terézia Kovács & Bence Bognár & Szilvia Juhász & , 2025. "Exploring the principles behind antibiotics with limited resistance," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
    7. Dawei Sun & Kelly M. Storek & Dimitry Tegunov & Ying Yang & Christopher P. Arthur & Matthew Johnson & John G. Quinn & Weijing Liu & Guanghui Han & Hany S. Girgis & Mary Kate Alexander & Austin K. Murc, 2024. "The discovery and structural basis of two distinct state-dependent inhibitors of BamA," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    8. Morgan E. Walker & Wei Zhu & Janine H. Peterson & Hao Wang & Jon Patteson & Aileen Soriano & Han Zhang & Todd Mayhood & Yan Hou & Samaneh Mesbahi-Vasey & Meigang Gu & John Frost & Jun Lu & Jennifer Jo, 2025. "Antibacterial macrocyclic peptides reveal a distinct mode of BamA inhibition," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
    9. Mathieu Botte & Dongchun Ni & Stephan Schenck & Iwan Zimmermann & Mohamed Chami & Nicolas Bocquet & Pascal Egloff & Denis Bucher & Matilde Trabuco & Robert K. Y. Cheng & Janine D. Brunner & Markus A. , 2022. "Cryo-EM structures of a LptDE transporter in complex with Pro-macrobodies offer insight into lipopolysaccharide translocation," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    10. Telmo O. Paiva & Albertus Viljoen & Yves F. Dufrêne, 2022. "Seeing the unseen: High-resolution AFM imaging captures antibiotic action in bacterial membranes," Nature Communications, Nature, vol. 13(1), pages 1-3, December.
    11. Xudong Li & Huifeng Hu & Yongwei Zhu & Taiquan Wang & Youlan Lu & Xiangru Wang & Zhong Peng & Ming Sun & Huanchun Chen & Jinshui Zheng & Chen Tan, 2024. "Population structure and antibiotic resistance of swine extraintestinal pathogenic Escherichia coli from China," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    12. Georges P. Schmartz & Jacqueline Rehner & Miriam J. Schuff & Leidy-Alejandra G. Molano & Sören L. Becker & Marcin Krawczyk & Azat Tagirdzhanov & Alexey Gurevich & Richard Francke & Rolf Müller & Veren, 2024. "Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    13. Selen Manioglu & Seyed Majed Modaresi & Johannes Thoma & Sarah A. Overall & Gregory Upert & Anatol Luther & Alexander B. Barnes & Daniel Obrecht & Daniel J. Müller & Sebastian Hiller, 2023. "Reply to: Antibiotics and hexagonal order in the bacterial outer membrane," Nature Communications, Nature, vol. 14(1), pages 1-4, December.
    14. Hanna Chen & Lin Zhong & Haibo Zhou & Xianping Bai & Tao Sun & Xingyan Wang & Yiming Zhao & Xiaoqi Ji & Qiang Tu & Youming Zhang & Xiaoying Bian, 2023. "Biosynthesis and engineering of the nonribosomal peptides with a C-terminal putrescine," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    15. Adéla Melcrová & Sourav Maity & Josef Melcr & Niels A. W. Kok & Mariella Gabler & Jonne Eyden & Wenche Stensen & John S. M. Svendsen & Arnold J. M. Driessen & Siewert J. Marrink & Wouter H. Roos, 2023. "Lateral membrane organization as target of an antimicrobial peptidomimetic compound," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    16. David Geller-McGrath & Paraskevi Mara & Gordon T. Taylor & Elizabeth Suter & Virginia Edgcomb & Maria Pachiadaki, 2023. "Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    17. Clare I. R. Chandler, 2019. "Current accounts of antimicrobial resistance: stabilisation, individualisation and antibiotics as infrastructure," Humanities and Social Sciences Communications, Palgrave Macmillan, vol. 5(1), pages 1-13, December.
    18. Swapnil Prakash Doijad & Nicolas Gisch & Renate Frantz & Bajarang Vasant Kumbhar & Jane Falgenhauer & Can Imirzalioglu & Linda Falgenhauer & Alexander Mischnik & Jan Rupp & Michael Behnke & Michael Bu, 2023. "Resolving colistin resistance and heteroresistance in Enterobacter species," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    19. Seth W. Dickey & Dylan J. Burgin & Ama N. Antwi & Amer Villaruz & Madeline R. Galac & Gordon Y. C. Cheung & Tatiana K. Rostovtseva & Liam J. Worrall & Aleksander C. Lazarski & Elio A. Cino & D. Peter , 2025. "Antimicrobial peptide class that forms discrete β-barrel stable pores anchored by transmembrane helices," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    20. Jinfeng Li & Bao Chen & Zunyun Fu & Jingjing Mao & Lijun Liu & Xiaochen Chen & Mingyue Zheng & Chang-Yun Wang & Chengyuan Wang & Yue-Wei Guo & Baofu Xu, 2024. "Discovery of a terpene synthase synthesizing a nearly non-flexible eunicellane reveals the basis of flexibility," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-62407-4. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.