Center for Peptide-Based Antibiotics

Center for Peptide-Based Antibiotics (CEPAN) existed from 2017-2022

CEPAN was a research center at the University of Copenhagen dedicated to developing new antibiotic solutions to combat antibiotic-resistant bacteria. The aim of the center was to establish a discovery platform focused on peptide-based antibiotics, exploiting the unique properties of peptides that interact with the bacterial envelope. The discovery of leads, therapeutic strategies, and antibiotic targets useful for treating multidrug-resistant Gram-negative infections, as well as elucidation of their mechanisms of action, were core activities.

In particular, the center explored antisense antibacterial concepts using the peptide-like DNA mimic PNA (Peptide Nucleic Acid) to target essential genes at the translational level, by simply designing a short PNA with a sequence complementary to the mRNA translation initiation site, thereby blocking the access of the ribosome to this crucial mRNA translation start site. In addition, the center explored novel peptide carriers for efficient delivery of potential antibacterial compounds with inherently poor bacterial uptake. Peptide-based adjuvant antibiotics were investigated as a means to circumvent resistance to existing antibiotics and to sensitize bacteria to drugs they were inherently resistant to. Additionally, synergistic combinations representing multimodal treatment regimens were examined to reduce the risk of resistance development.

 

Across biology, antimicrobial peptides (AMPs) constitute a central part of the innate immune systems, and most intriguingly both last-resort antibiotics and more recently discovered leads were peptide-based. Thus, AMPs and mimics therefore reappeared as attractive sources of novel antibiotics, not least due to their alternative mode of action, structural diversity, and potential for rapid optimization.

The research objectives were to:

  1. Discover narrow-spectrum antisense PNA (peptide nucleic acid) antibiotics targeting resistance, virulence or essential bacterial gene expression at the translational level.
  2. Identify and characterize novel antibiotic targets using innovative biological expression methodologies and advanced molecular biology tools
  3. Develop membrane-permeabilizing peptidomimetics as adjunct antibiotics, capable of potentiating efficacy of clinically approved antibiotics on resistant clinical isolates
  4. Discover bacteria-penetrating peptides that could act as bacterial delivery agents
  1. Elucidate the molecular mechanisms responsible for membrane permeabilization and transport across the bacterial envelope
  2. Investigate the pharmacodynamics and pharmacokinetics of AMPs, antibacterial peptidomimetics and peptide nucleic acid (PNA) antibiotics in vivo.
  3. Develop an intracellular release peptide display technology for in bacteria selection of antimicrobial peptides with high potency and low probability for resistance development.

Center for Peptide-Based Antibiotics (Cepan) was established in 2017 at the University of Copenhagen headed by Peter E. Nielsen, with funding from the Novo Nordisk Foundation Challenge Programme. The center includes research groups from both the Faculty of Health and Medical Sciences and Faculty of Science as well as from Statens Serum Institut:

  • Professor,  Dr. scient.  Peter E. Nielsen, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences
  • Professor Anders Løbner-Olesen, Department of Biology, Faculty of Science
  • Associate Professor Henrik Franzyk, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences
  • Dr. Anette M. Hammerum, Statens Serum Institut

 

 

  1. Peptide nucleic acid-zirconium coordination nanoparticles. Öztürk Ö, Lessl AL, Höhn M, Wuttke S, Nielsen PE, Wagner E, Lächelt U. Sci Rep. 2023 Aug 30;13(1):14222. doi: 10.1038/s41598-023-40916-w.PMID: 37648689 
  2. Polymyxins with Potent Antibacterial Activity against Colistin-Resistant Pathogens: Fine-Tuning Hydrophobicity with Unnatural Amino Acids. Jørgensen JS, Mood EH, Knap ASH, Nielsen SE, Nielsen PE, Żabicka D, Matias C, Domraceva I, Björkling F, Franzyk H.J Med Chem. 2024 Jan 25;67(2):1370-1383. doi: 10.1021/acs.jmedchem.3c01908. Epub 2024 Jan 3.PMID: 38169430 
  3. An intracellular release peptide display technology unveils an antimicrobial peptide with low probability for resistance development. Ebbensgaard A, Olivera C, Bentin T, Franzyk H, Charbon G, Nielsen PE, Løbner-Olesen A. 2025 May 9;28(6):112619.
  4. Antisense Peptide Nucleic Acid-Diaminobutanoic Acid Dendron Conjugates with SbmA-Independent Antimicrobial Activity against Gram-Negative Bacteria. Iubatti M, Gabas IM, Cavaco LM, Mood EH, Lim E, Bonanno F, Yavari N, Brolin C, Nielsen PE. ACS Infect Dis. 2022 May 13;8(5):1098-1106. doi: 10.1021/acsinfecdis.2c00089.
  5. Targeting of the Essential acpP, ftsZ, and rneGenes in Carbapenem-   resistant Acinetobacter baumannii by Antisense PNA Precision Antibacterials. Nejad AJ, Shahrokhi N, Nielsen PE. Biomedicines. 2021 Apr 15;9(4):429   doi: 10.3390/biomedicines9040429.PMID: 33921011 
  6. Targeting synthesis of the Chromosome Replication Initiator Protein DnaA by antisense PNA-peptide conjugates in Escherichia coli.  Campion C, Charbon G, Nielsen PE, Løbner-Olesen A. Front Antibiot. 2024 Apr 8;3:1384390. doi: 10.3389/frabi.2024.1384390. eCollection 2024.PMID: 39816250 
  7.    Effects of LPS Composition in Escherichia coli on Antibacterial Activity and Bacterial Uptake of Antisense Peptide-PNA Conjugates. Goltermann L, Zhang M, Ebbensgaard AE, Fiodorovaite M, Yavari N, Løbner-Olesen A, Nielsen PE. Front Microbiol. 2022 Jun 20;13:877377. doi: 10.3389/fmicb.2022.877377. eCollection 2022.
  8. Uptake, Stability, and Activity of Antisense Anti-acpP PNA-Peptide Conjugates in Escherichia coli and the Role of SbmA. Yavari N, Goltermann L, Nielsen PE. ACS Chem Biol. 2021 Mar 19;16(3):471-479. doi: 10.1021/acschembio.0c00822.
  9. Bactericidal antisense effects of peptide-PNA conjugates. Good L, Awasthi SK, Dryselius R, Larsson O, Nielsen PE. Nat Biotechnol. 2001 Apr;19(4):360-4. doi: 10.1038/86753.
  10. Uptake, Stability, and Activity of Antisense Anti-acpP PNA-Peptide Conjugates in Escherichia coli and the Role of SbmA. Yavari N, Goltermann L, Nielsen PE.ACS Chem Biol. 2021 Mar 19;16(3):471-479. doi: 10.1021/acschembio.0c00822. Epub 2021 Mar 8
  11. Translocation of non-lytic antimicrobial peptides and bacteria penetrating peptides across the inner membrane of the bacterial envelope. Frimodt-Møller J, Campion C, Nielsen PE, Løbner-Olesen A.  Curr Genet. 2022 Feb;68(1):83-90. doi: 10.1007/s00294-021-01217-9. Epub 2021 Nov 8. PMID: 34750687  Review.
  12. Antibiotic Potentiation in Multidrug-Resistant Gram-Negative Pathogenic   Bacteria by a Synthetic Peptidomimetic. Mood EH, Goltermann L, Brolin C, Cavaco LM, Nejad AJ, Yavari N, Frederiksen N, Franzyk H, Nielsen PE.  ACS Infect Dis. 2021 Aug 13;7(8):2152-2163. doi: 10.1021/acsinfecdis.1c00147. Epub 2021 Jul6.PMID: 34227804

 

 

  1. Novel antisense PNA-peptide conjugate antibiotic lead compounds targeting the essential acpP gene have been developed. These compounds are bactericidal against multi-resistant coli and Klebsiella pneumoniae, and show potent in vivo activity in mouse infection models (sepsis, peritoneal and urinary tract infection) via systemic, subcutaneous delivery. An analogous compound targeting the essential rne gene in multi-resistant Acinitobacter baumannii is bactericidal against this bacterium and also shows potent in vivo activity in a soft tissue mouse infection model upon subcutaneous delivery.
  2. In a structure/activity study on polymyxins, new derivatives with potent antibacterial activity against Colistin-resistant pathogenic bacteria have been identified.
  3. The antisense PNA-peptide conjugate antibiotics constitute a technology platform allowing the easy development of novel designer antibiotics, by simply choosing the PNA sequence according to the bacterial gene, and optimizing the carrier for effective bacterial uptake in the targeted species.
  4. In the quest for identifying novel, effective peptide based antibiotics, a bacterium based peptide library screening assay has been developed, and a small series of antibacterial hit compounds have been identified and partially characterized.
  5. New peptide based enhancer of bacterial uptake of antibiotics has been identified.   

 

 

 

 

It has long been realized that due to the increasing spread of multi-resistance amongst pathogenic bacteria (in particular gram negatives), novel types of antibiotics are urgently needed.

The CEPAN project has contributed to this by providing novel, effective solutions. Obviously, there is still a long and very expensive road to clinical applications, and financing the necessary clinical development towards obtaining an IND (indication of new drug, e.g. from the FDA) is extremely difficult. This is due to the fact that the market for such new antibiotics is very small as they should only be used for infections that are caused by resistant bacteria.  Therefore, the (potential) market is limited (but rising) and the profit cannot cover the drug development costs. Thus, the commercial pharmaceutical industry in general has no interest in developing such new narrow indication antibiotic drugs. The world community is aware of this, but progress towards solutions is slow.           

 

 

Securing the intellectual property rights (IPR) is the first and mandatory step towards drug development. Within Copenhagen University, this is typically taken care of by UCPH Lighthouse (https://lighthouse.ku.dk/en/researchers/commercialization-of-inventions/). Thus, UCPH Lighthouse was approached with the project, and a patent search showed that the specific technology had inventive steps which could be IPR protected by patenting. However, highly disappointingly, UCPH Lighthouse declined to support patenting, with the argument that a commercial partner to support the project could not be found, and without patent protection, pursuing drug development is futile. Therefore, other strategies must be considered.

 

Professor Peter E. Nielsen
Center Director
ptrn@sund.ku.dk

Novo Nordisk Foundation

Center for Peptide-Based Antibiotics was funded by a grant from the Novo Nordisk Foundation Challenge Programme.