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Australian Journal of Chemistry Australian Journal of Chemistry Society
An international journal for chemical science
REVIEW

Addressing antimicrobial resistance by using macrocyclic peptides

Samilla B. Rezende https://orcid.org/0000-0002-4820-3638 A , Elizabete S. Cândido https://orcid.org/0000-0002-3126-029X A , Ludovico Migliolo https://orcid.org/0000-0002-6606-2189 A , Marlon H. Cardoso https://orcid.org/0000-0001-6676-5362 A B * and Octávio L. Franco https://orcid.org/0000-0001-9546-0525 A C *
+ Author Affiliations
- Author Affiliations

A S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande-MS, Brazil.

B Programa de Pós-Graduação em Ciências Ambientais e Sustentabilidade Agropecuária, Universidade Católica Dom Bosco, Campo Grande-MS, Brazil.

C Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil.




Dr Samilla Beatriz de Rezende received her PhD in biotechnology from Universidade Católica Dom Bosco. She was a visiting PhD student at the Institute for Molecular Bioscience, The University of Queensland, Australia, in Prof. David Craik’s lab, and worked with Prof. Marlon H. Cardoso’s group and Prof. Octávio Franco’s lab on antimicrobial peptides and peptidomimetics. Her research focuses on rational peptide design, bioinformatics, and structural biophysics. Moreover, she has authored 12 international journal articles, contributed to book chapters and scientific conferences, and is co-inventor of a patent. She is currently a Postdoctoral Research Fellow in the MICRO Lab at the University of Alberta, Canada.



Dr Elizabete S. Cândido graduated in biological Sciences from Universidade Católica de Brasília (Brazil), obtained her Masters and PhD in genomic sciences and biotechnology, Universidade de Brasília (Brazil). As part of her doctoral training, she conducted research at the Institute for Molecular Bioscience, The University of Queensland (Australia). She is currently a visiting professor at Universidade Católica Dom Bosco (Brazil). With over 15 years of experience in plant peptide prospection and applied microbiology, her research focuses on antimicrobial peptides and biocosmetics. She has authored >30 publications in leading international journals.



Ludovico Migliolo holds a degree in Biological Sciences and a Master’s in biochemistry from UFRN, and a Ph.D. in genomic sciences and biotechnology from UCB, including a sandwich PhD at The University of Queensland under Prof. David J. Craik. His research focuses on bioactive peptides for controlling pathogenic microorganisms, integrating computational, biochemical and biophysical approaches. Currently a professor at the Universidade Católica Dom Bosco (UCDB), he works on protein purification, sequencing, molecular modelling, and peptide design. His collaborations with Prof. Craik yielded notable publications, and his studies explore antimicrobial, immunomodulatory, and toxin-inspired peptides for health and agribusiness applications.



Prof. Marlon H. Cardoso graduated in biological sciences from Universidade Católica de Brasília (Brazil) and obtained his PhD in molecular pathology from the Faculty of Medicine, Universidade de Brasília (Brazil). As part of his doctoral training, he conducted research at the Institute for Molecular Bioscience, The University of Queensland (Australia). He is currently a principal investigator, assistant professor and lecturer at Universidade Católica Dom Bosco (Brazil). With over 12 years of experience in peptide drug design, his research focuses on antimicrobial peptides and peptidomimetics, integrating computational and experimental strategies to explore their structure, function and mechanisms of action. He has received multiple awards and authored >90 publications in leading international journals.



Octávio Luiz Franco is a professor and coordinator of the Biotechnology Program at Universidade Católica Dom Bosco. He holds a PhD in biological sciences from the University of Brasília and completed postdoctoral training at Embrapa and the University of Edinburgh. A CNPq Level 1A Researcher, he has published over 550 scientific papers in leading journals and holds nearly 40 patents, including the anti-aging product OS-1. He co-founded Peptidus, Lumis, and SO Biotech, focusing on biotechnology and health. He has supervised over 120 graduate students and is actively involved in science communication through lectures, media and social media platforms.


Handling Editor: Ed Nice

Australian Journal of Chemistry 78, CH25091 https://doi.org/10.1071/CH25091
Submitted: 1 June 2025  Accepted: 9 September 2025  Published online: 14 October 2025

© 2025 The Author(s) (or their employer(s)). Published by CSIRO Publishing.

Abstract

Antimicrobial resistance (AMR) is a global health problem, therefore, anti-AMR alternatives and strategies are required to develop effective therapeutics. Bearing this in mind, macrocyclic peptides (MCPs) that present cyclic scaffolds, disulfide bonds and constrained arrangements offer a distinct structural advantage that expands their potential mechanisms of action against pathogens. By modifying and improving this class of peptides, it is possible to obtain greater stability under extreme biological conditions and extended therapeutic windows, also enabling targeted action against intracellular pathogens. These advancements are driven by integrating computational tools, including artificial intelligence, to predict optimal sequences based on amino acid motifs, patterns, and physicochemical properties. Altogether, these approaches help us to design optimised MCPs and facilitate the development of more robust, selective and effective therapeutic agents tailored to combat AMR. In this review, we will explore recent advances in the context of AMR, integrating computational approaches for MCPs design, and proposed mechanisms of action for the next generation of MCP-based therapeutics.

Keywords: antimicrobial peptides, antimicrobial resistance, cell penetrating peptides, computational tools, macrocyclic peptides, next-generation therapeutics, peptide grafting, peptide internalisation.

Biographies

CH25091_B1.gif

Dr Samilla Beatriz de Rezende received her PhD in biotechnology from Universidade Católica Dom Bosco. She was a visiting PhD student at the Institute for Molecular Bioscience, The University of Queensland, Australia, in Prof. David Craik’s lab, and worked with Prof. Marlon H. Cardoso’s group and Prof. Octávio Franco’s lab on antimicrobial peptides and peptidomimetics. Her research focuses on rational peptide design, bioinformatics, and structural biophysics. Moreover, she has authored 12 international journal articles, contributed to book chapters and scientific conferences, and is co-inventor of a patent. She is currently a Postdoctoral Research Fellow in the MICRO Lab at the University of Alberta, Canada.

CH25091_B2.gif

Dr Elizabete S. Cândido graduated in biological Sciences from Universidade Católica de Brasília (Brazil), obtained her Masters and PhD in genomic sciences and biotechnology, Universidade de Brasília (Brazil). As part of her doctoral training, she conducted research at the Institute for Molecular Bioscience, The University of Queensland (Australia). She is currently a visiting professor at Universidade Católica Dom Bosco (Brazil). With over 15 years of experience in plant peptide prospection and applied microbiology, her research focuses on antimicrobial peptides and biocosmetics. She has authored >30 publications in leading international journals.

CH25091_B3.gif

Ludovico Migliolo holds a degree in Biological Sciences and a Master’s in biochemistry from UFRN, and a Ph.D. in genomic sciences and biotechnology from UCB, including a sandwich PhD at The University of Queensland under Prof. David J. Craik. His research focuses on bioactive peptides for controlling pathogenic microorganisms, integrating computational, biochemical and biophysical approaches. Currently a professor at the Universidade Católica Dom Bosco (UCDB), he works on protein purification, sequencing, molecular modelling, and peptide design. His collaborations with Prof. Craik yielded notable publications, and his studies explore antimicrobial, immunomodulatory, and toxin-inspired peptides for health and agribusiness applications.

CH25091_B4.gif

Prof. Marlon H. Cardoso graduated in biological sciences from Universidade Católica de Brasília (Brazil) and obtained his PhD in molecular pathology from the Faculty of Medicine, Universidade de Brasília (Brazil). As part of his doctoral training, he conducted research at the Institute for Molecular Bioscience, The University of Queensland (Australia). He is currently a principal investigator, assistant professor and lecturer at Universidade Católica Dom Bosco (Brazil). With over 12 years of experience in peptide drug design, his research focuses on antimicrobial peptides and peptidomimetics, integrating computational and experimental strategies to explore their structure, function and mechanisms of action. He has received multiple awards and authored >90 publications in leading international journals.

CH25091_B5.gif

Octávio Luiz Franco is a professor and coordinator of the Biotechnology Program at Universidade Católica Dom Bosco. He holds a PhD in biological sciences from the University of Brasília and completed postdoctoral training at Embrapa and the University of Edinburgh. A CNPq Level 1A Researcher, he has published over 550 scientific papers in leading journals and holds nearly 40 patents, including the anti-aging product OS-1. He co-founded Peptidus, Lumis, and SO Biotech, focusing on biotechnology and health. He has supervised over 120 graduate students and is actively involved in science communication through lectures, media and social media platforms.

References

Zampaloni C, Mattei P, Bleicher K, Winther L, Thäte C, Bucher C, et al. A novel antibiotic class targeting the lipopolysaccharide transporter. Nature 2024; 625: 566-571.
| Crossref | Google Scholar | PubMed |

Craik DJ, Fairlie DP, Liras S, Price D. The future of peptide‐based drugs. Chem Biol Drug Des 2013; 81: 136-147.
| Crossref | Google Scholar | PubMed |

Wang CK, Craik DJ. Designing macrocyclic disulfide-rich peptides for biotechnological applications. Nat Chem Biol 2018; 14: 417-427.
| Crossref | Google Scholar | PubMed |

Bechtler C, Lamers C. Macrocyclization strategies for cyclic peptides and peptidomimetics. RSC Med Chem 2021; 12: 1325-1351.
| Crossref | Google Scholar | PubMed |

Wang W-J, Dong X-M, Li G-B. Macrocyclic peptides: up-and-coming weapons to combat antimicrobial resistance. Signal Transduct Target Ther 2024; 9: 81.
| Crossref | Google Scholar | PubMed |

Luther A, Bisang C, Obrecht D. Advances in macrocyclic peptide-based antibiotics. Bioorg Med Chem 2018; 26: 2850-2858.
| Crossref | Google Scholar | PubMed |

Walsh CT, Wencewicz TA. Prospects for new antibiotics: a molecule-centered perspective. J Antibiot 2014; 67: 7-22.
| Crossref | Google Scholar | PubMed |

Cochrane SA, Vederas JC. Lipopeptides from Bacillus and Paenibacillus spp.: a gold mine of antibiotic candidates. Med Res Rev 2016; 36: 4-31.
| Crossref | Google Scholar | PubMed |

Brown DG. Drug discovery strategies to outer membrane targets in Gram-negative pathogens. Bioorg Med Chem 2016; 24: 6320-6331.
| Crossref | Google Scholar | PubMed |

10  Velkov T, Thompson PE, Nation RL, Li J. Structure–activity relationships of polymyxin antibiotics. J Med Chem 2010; 53: 1898-1916.
| Crossref | Google Scholar | PubMed |

11  Robinson JA, Shankaramma SC, Jetter P, Kienzl U, Schwendener RA, Vrijbloed JW, et al. Properties and structure–activity studies of cyclic beta-hairpin peptidomimetics based on the cationic antimicrobial peptide protegrin I. Bioorg Med Chem 2005; 13: 2055-2064.
| Crossref | Google Scholar | PubMed |

12  Martin-Loeches I, Dale GE, Torres A. Murepavadin: a new antibiotic class in the pipeline. Expert Rev Anti Infect Ther 2018; 16: 259-268.
| Crossref | Google Scholar | PubMed |

13  de la Fuente-Nunez C. Toward autonomous antibiotic discovery. mSystems 2019; 4: e00151-19.
| Crossref | Google Scholar | PubMed |

14  Durrant JD, Amaro RE. Machine‐learning techniques applied to antibacterial drug discovery. Chem Biol Drug Des 2015; 85: 14-21.
| Crossref | Google Scholar | PubMed |

15  Zorzi A, Deyle K, Heinis C. Cyclic peptide therapeutics: past, present and future. Curr Opin Chem Biol 2017; 38: 24-29.
| Crossref | Google Scholar | PubMed |

16  Muttenthaler M, King GF, Adams DJ, Alewood PF. Trends in peptide drug discovery. Nat Rev Drug Discov 2021; 20: 309-325.
| Crossref | Google Scholar | PubMed |

17  Lohan S, Konshina AG, Tiwari RK, Efremov RG, Maslennikov I, Parang K. Broad-spectrum activity of membranolytic cationic macrocyclic peptides against multi-drug resistant bacteria and fungi. Eur J Pharm Sci 2024; 197: 106776.
| Crossref | Google Scholar | PubMed |

18  Miller WR, Arias CA. ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics. Nat Rev Microbiol 2024; 22: 598-616.
| Crossref | Google Scholar | PubMed |

19  Weidmann J, Craik DJ. Discovery, structure, function, and applications of cyclotides: circular proteins from plants. J Exp Bot 2016; 67: 4801-4812.
| Crossref | Google Scholar | PubMed |

20  Butler MS, Blaskovich MA, Cooper MA. Antibiotics in the clinical pipeline at the end of 2015. J Antibiot 2017; 70: 3-24.
| Crossref | Google Scholar | PubMed |

21  Obrecht D, Robinson JA, Bernardini F, Bisang C, DeMarco SJ, Moehle K, et al. Recent progress in the discovery of macrocyclic compounds as potential anti-infective therapeutics. Curr Med Chem 2009; 16: 42-65.
| Crossref | Google Scholar | PubMed |

22  Ghosh M, Miller PA, Möllmann U, Claypool WD, Schroeder VA, Wolter WR, et al. Targeted antibiotic delivery: selective siderophore conjugation with daptomycin confers potent activity against multidrug resistant Acinetobacter baumannii both in vitro and in vivo. J Med Chem 2017; 60: 4577-4583.
| Crossref | Google Scholar | PubMed |

23  Baquero F, Beis K, Craik DJ, Li Y, Link AJ, Rebuffat S, et al. The pearl jubilee of microcin J25: thirty years of research on an exceptional lasso peptide. Nat Prod Rep 2024; 41: 469-511.
| Crossref | Google Scholar | PubMed |

24  Smith PA, Romesberg FE. Mechanism of action of the arylomycin antibiotics and effects of signal peptidase I inhibition. Antimicrob Agents Chemother 2012; 56: 5054-5060.
| Crossref | Google Scholar | PubMed |

25  Brown DG, Lister T, May-Dracka TL. New natural products as new leads for antibacterial drug discovery. Bioorg Med Chem Lett 2014; 24: 413-418.
| Crossref | Google Scholar | PubMed |

26  Kiho T, Nakayama M, Yasuda K, Miyakoshi S, Inukai M, Kogen H. Synthesis and antimicrobial activity of novel globomycin analogues. Bioorg Med Chem Lett 2003; 13: 2315-2318.
| Crossref | Google Scholar | PubMed |

27  Hancock RE. Cationic antimicrobial peptides: towards clinical applications. Expert Opin Investig Drugs 2000; 9: 1723-1729.
| Crossref | Google Scholar | PubMed |

28  Wang CK, Craik DJ. Cyclic peptide oral bioavailability: lessons from the past. Biopolymers 2016; 106: 901-909.
| Crossref | Google Scholar | PubMed |

29  De Veer SJ, Kan M-W, Craik DJ. Cyclotides: from structure to function. Chem Rev 2019; 119: 12375-12421.
| Crossref | Google Scholar | PubMed |

30  Luckett S, Garcia RS, Barker JJ, Konarev AV, Shewry PR, Clarke A, et al. High-resolution structure of a potent, cyclic proteinase inhibitor from sunflower seeds. J Mol Biol 1999; 290: 525-533.
| Crossref | Google Scholar | PubMed |

31  Wang C, Shao C, Fang Y, Wang J, Dong N, Shan A. Binding loop of sunflower trypsin inhibitor 1 serves as a design motif for proteolysis-resistant antimicrobial peptides. Acta Biomater 2021; 124: 254-269.
| Crossref | Google Scholar | PubMed |

32  Chan LY, Zhang VM, Huang Yh, Waters NC, Bansal PS, Craik DJ, et al. Cyclization of the antimicrobial peptide gomesin with native chemical ligation: influences on stability and bioactivity. ChemBioChem 2013; 14: 617-624.
| Crossref | Google Scholar | PubMed |

33  Troeira Henriques S, Lawrence N, Chaousis S, Ravipati AS, Cheneval O, Benfield AH, et al. Redesigned spider peptide with improved antimicrobial and anticancer properties. ACS Chem Biol 2017; 12: 2324-2334.
| Crossref | Google Scholar | PubMed |

34  Tang Y-Q, Yuan J, Osapay G, Osapay K, Tran D, Miller CJ, et al. A cyclic antimicrobial peptide produced in primate leukocytes by the ligation of two truncated α-defensins. Science 1999; 286: 498-502.
| Crossref | Google Scholar | PubMed |

35  Basso V, Tran DQ, Schaal JB, Tran P, Eriguchi Y, Ngole D, et al. Rhesus theta defensin 1 promotes long term survival in systemic candidiasis by host directed mechanisms. Sci Rep 2019; 9: 16905.
| Crossref | Google Scholar | PubMed |

36  Dughbaj MA, Jayne JG, Park AYJ, Bensman TJ, Algorri M, Ouellette AJ, et al. Anti-inflammatory effects of RTD-1 in a murine model of chronic pseudomonas aeruginosa lung infection: inhibition of NF-κB, inflammasome gene expression, and Pro-IL-1β biosynthesis. Antibiotics 2021; 10: 1043.
| Crossref | Google Scholar | PubMed |

37  Li Y, Gould A, Aboye T, Bi T, Breindel L, Shekhtman A, et al. Full sequence amino acid scanning of θ-defensin RTD-1 yields a potent anthrax lethal factor protease inhibitor. J Med Chem 2017; 60: 1916-1927.
| Crossref | Google Scholar | PubMed |

38  Morales Duque H, Campos Dias S, Franco OL. Structural and functional analyses of cone snail toxins. Mar Drugs 2019; 17: 370.
| Crossref | Google Scholar | PubMed |

39  Akondi KB, Muttenthaler M, Dutertre S, Kaas Q, Craik DJ, Lewis RJ, et al. Discovery, synthesis, and structure–activity relationships of conotoxins. Chem Rev 2014; 114: 5815-5847.
| Crossref | Google Scholar | PubMed |

40  Hemu X, Tam JP. Macrocyclic antimicrobial peptides engineered from ω-conotoxin. Curr Pharm Des 2017; 23: 2131-2138.
| Crossref | Google Scholar | PubMed |

41  Cascales L, Henriques ST, Kerr MC, Huang Y-H, Sweet MJ, Daly NL, et al. Identification and characterization of a new family of cell-penetrating peptides: cyclic cell-penetrating peptides. J Biol Chem 2011; 286: 36932-36943.
| Crossref | Google Scholar | PubMed |

42  Greenwood KP, Daly NL, Brown DL, Stow JL, Craik DJ. The cyclic cystine knot miniprotein MCoTI-II is internalized into cells by macropinocytosis. Int J Biochem Cell Biol 2007; 39: 2252-2264.
| Crossref | Google Scholar | PubMed |

43  Contreras J, Elnagar AY, Hamm-Alvarez SF, Camarero JA. Cellular uptake of cyclotide MCoTI-I follows multiple endocytic pathways. J Control Release 2011; 155: 134-143.
| Crossref | Google Scholar | PubMed |

44  Henriques ST, Huang Y-H, Rosengren KJ, Franquelim HG, Carvalho FA, Johnson A, et al. Decoding the membrane activity of the cyclotide kalata B1: the importance of phosphatidylethanolamine phospholipids and lipid organization on hemolytic and anti-HIV activities. J Biol Chem 2011; 286: 24231-24241.
| Crossref | Google Scholar | PubMed |

45  D’Souza C, Henriques ST, Wang CK, Craik DJ. Structural parameters modulating the cellular uptake of disulfide-rich cyclic cell-penetrating peptides: MCoTI-II and SFTI-1. Eur J Med Chem 2014; 88: 10-18.
| Crossref | Google Scholar | PubMed |

46  Troeira Henriques S, Craik DJ. Cyclotide structure and function: the role of membrane binding and permeation. Biochemistry 2017; 56: 669-682.
| Crossref | Google Scholar | PubMed |

47  Lättig-Tünnemann G, Prinz M, Hoffmann D, Behlke J, Palm-Apergi C, Morano I, et al. Backbone rigidity and static presentation of guanidinium groups increases cellular uptake of arginine-rich cell-penetrating peptides. Nat Commun 2011; 2: 453.
| Crossref | Google Scholar | PubMed |

48  Mandal D, Nasrolahi Shirazi A, Parang K. Cell‐penetrating homochiral cyclic peptides as nuclear‐targeting molecular transporters. Angew Chem Int Ed 2011; 50: 9633-9637.
| Crossref | Google Scholar | PubMed |

49  Qian Z, Liu T, Liu Y-Y, Briesewitz R, Barrios AM, Jhiang SM, et al. Efficient delivery of cyclic peptides into mammalian cells with short sequence motifs. ACS Chem Biol 2013; 8: 423-431.
| Crossref | Google Scholar | PubMed |

50  Qian Z, Martyna A, Hard RL, Wang J, Appiah-Kubi G, Coss C, et al. Discovery and mechanism of highly efficient cyclic cell-penetrating peptides. Biochemistry 2016; 55: 2601-2612.
| Crossref | Google Scholar | PubMed |

51  Huang Y-H, Chaousis S, Cheneval O, Craik DJ, Henriques ST. Optimization of the cyclotide framework to improve cell penetration properties. Front Pharmacol 2015; 6: 17.
| Crossref | Google Scholar | PubMed |

52  Kamimori H, Hall K, Craik DJ, Aguilar M-I. Studies on the membrane interactions of the cyclotides kalata B1 and kalata B6 on model membrane systems by surface plasmon resonance. Anal Biochem 2005; 337: 149-153.
| Crossref | Google Scholar | PubMed |

53  Muratspahić E, Koehbach J, Gruber CW, Craik DJ. Harnessing cyclotides to design and develop novel peptide GPCR ligands. RSC Chem Biol 2020; 1: 177-191.
| Crossref | Google Scholar | PubMed |

54  Shenkarev ZO, Nadezhdin KD, Sobol VA, Sobol AG, Skjeldal L, Arseniev AS. Conformation and mode of membrane interaction in cyclotides: spatial structure of kalata B1 bound to a dodecylphosphocholine micelle. FEBS J 2006; 273: 2658-2672.
| Crossref | Google Scholar | PubMed |

55  Randall JR, Wang X, Groover KE, O’Donnell AC, Davies BW. Using display technologies to identify macrocyclic peptide antibiotics. Biochim Biophys Acta Mol Cell Res 2023; 1870: 119473.
| Crossref | Google Scholar | PubMed |

56  World Health Organization. Global research agenda for antimicrobial resistance in human health. WHO; 2024. Available at https://www.who.int/publications/m/item/global-research-agenda-for-antimicrobial-resistance-in-human-health

57  Li J, Koh J-J, Liu S, Lakshminarayanan R, Verma CS, Beuerman RW. Membrane active antimicrobial peptides: translating mechanistic insights to design. Front Neurosci 2017; 11: 73.
| Crossref | Google Scholar | PubMed |

58  Sabnis A, Hagart KL, Klöckner A, Becce M, Evans LE, Furniss RCD, et al. Colistin kills bacteria by targeting lipopolysaccharide in the cytoplasmic membrane. elife 2021; 10: e65836.
| Crossref | Google Scholar | PubMed |

59  Lee T-H, Hall KN, Aguilar M-I. Antimicrobial peptide structure and mechanism of action: a focus on the role of membrane structure. Curr Top Med Chem 2016; 16: 25-39.
| Crossref | Google Scholar | PubMed |

60  Avci FG, Akbulut BS, Ozkirimli E. Membrane active peptides and their biophysical characterization. Biomolecules 2018; 8: 77.
| Crossref | Google Scholar | PubMed |

61  Wang CK, Wacklin HP, Craik DJ. Cyclotides insert into lipid bilayers to form membrane pores and destabilize the membrane through hydrophobic and phosphoethanolamine-specific interactions. J Biol Chem 2012; 287: 43884-43898.
| Crossref | Google Scholar | PubMed |

62  Huang Y-H, Colgrave ML, Clark RJ, Kotze AC, Craik DJ. Lysine-scanning mutagenesis reveals an amendable face of the cyclotide kalata B1 for the optimization of nematocidal activity. J Biol Chem 2010; 285: 10797-10805.
| Crossref | Google Scholar | PubMed |

63  Henriques ST, Huang Y-H, Castanho MA, Bagatolli LA, Sonza S, Tachedjian G, et al. Phosphatidylethanolamine binding is a conserved feature of cyclotide-membrane interactions. J Biol Chem 2012; 287: 33629-33643.
| Crossref | Google Scholar | PubMed |

64  Panteleev PV, Balandin SV, Ivanov VT, Ovchinnikova TV. A therapeutic potential of animal β-hairpin antimicrobial peptides. Curr Med Chem 2017; 24: 1724-1746.
| Crossref | Google Scholar |

65  Burman R, Strömstedt AA, Malmsten M, Göransson U. Cyclotide–membrane interactions: defining factors of membrane binding, depletion and disruption. Biochim Biophys Acta Biomembr 2011; 1808: 2665-2673.
| Crossref | Google Scholar | PubMed |

66  Makino A, Baba T, Fujimoto K, Iwamoto K, Yano Y, Terada N, et al. Cinnamycin (Ro 09-0198) promotes cell binding and toxicity by inducing transbilayer lipid movement. J Biol Chem 2003; 278: 3204-3209.
| Crossref | Google Scholar | PubMed |

67  Strömstedt AA, Park S, Burman R, Göransson U. Bactericidal activity of cyclotides where phosphatidylethanolamine–lipid selectivity determines antimicrobial spectra. Biochim Biophys Acta Biomembr 2017; 1859: 1986-2000.
| Crossref | Google Scholar | PubMed |

68  Strömstedt AA, Kristiansen PE, Gunasekera S, Grob N, Skjeldal L, Göransson U. Selective membrane disruption by the cyclotide kalata B7: complex ions and essential functional groups in the phosphatidylethanolamine binding pocket. Biochim Biophys Acta Biomembr 2016; 1858: 1317-1327.
| Crossref | Google Scholar | PubMed |

69  Han L, Zheng J, Wang Y, Yang X, Liu Y, Sun C, et al. Structure of the BAM complex and its implications for biogenesis of outer-membrane proteins. Nat Struct Mol Biol 2016; 23: 192-196.
| Crossref | Google Scholar | PubMed |

70  Kaur H, Jakob RP, Marzinek JK, Green R, Imai Y, Bolla JR, et al. The antibiotic darobactin mimics a β-strand to inhibit outer membrane insertase. Nature 2021; 593: 125-129.
| Crossref | Google Scholar | PubMed |

71  Imai Y, Meyer KJ, Iinishi A, Favre-Godal Q, Green R, Manuse S, et al. A new antibiotic selectively kills Gram-negative pathogens. Nature 2019; 576: 459-464.
| Crossref | Google Scholar | PubMed |

72  Sperandeo P, Martorana AM, Polissi A. The lipopolysaccharide transport (Lpt) machinery: a nonconventional transporter for lipopolysaccharide assembly at the outer membrane of Gram-negative bacteria. J Biol Chem 2017; 292: 17981-17990.
| Crossref | Google Scholar | PubMed |

73  Vetterli SU, Zerbe K, Müller M, Urfer M, Mondal M, Wang S-Y, et al. Thanatin targets the intermembrane protein complex required for lipopolysaccharide transport in Escherichia coli. Sci Adv 2018; 4: eaau2634.
| Crossref | Google Scholar | PubMed |

74  Dougherty PG, Sahni A, Pei D. Understanding cell penetration of cyclic peptides. Chem Rev 2019; 119: 10241-10287.
| Crossref | Google Scholar | PubMed |

75  Kauffman WB, Fuselier T, He J, Wimley WC. Mechanism matters: a taxonomy of cell penetrating peptides. Trends Biochem Sci 2015; 40: 749-764.
| Crossref | Google Scholar | PubMed |

76  Kaplan IM, Wadia JS, Dowdy SF. Cationic TAT peptide transduction domain enters cells by macropinocytosis. J Control Release 2005; 102: 247-253.
| Crossref | Google Scholar | PubMed |

77  Qian Z, LaRochelle JR, Jiang B, Lian W, Hard RL, Selner NG, et al. Early endosomal escape of a cyclic cell-penetrating peptide allows effective cytosolic cargo delivery. Biochemistry 2014; 53: 4034-4046.
| Crossref | Google Scholar | PubMed |

78  Dinca A, Chien W-M, Chin MT. Intracellular delivery of proteins with cell-penetrating peptides for therapeutic uses in human disease. Int J Mol Sci 2016; 17: 263.
| Crossref | Google Scholar | PubMed |

79  Karpurapu M, Lee YG, Qian Z, Wen J, Ballinger MN, Rusu L, et al. Inhibition of nuclear factor of activated T cells (NFAT) c3 activation attenuates acute lung injury and pulmonary edema in murine models of sepsis. Oncotarget 2018; 9: 10606-10620.
| Crossref | Google Scholar | PubMed |

80  Hadjicharalambous A, Newman H, Lewis N, Rowland C, Bournakas N, Stanway SJ, et al. Investigating penetration and antimicrobial activity of vector-bicycle conjugates. ACS Infect Dis 2024; 10: 2381-2389.
| Crossref | Google Scholar | PubMed |

81  Vinogradov AA, Yin Y, Suga H. Macrocyclic peptides as drug candidates: recent progress and remaining challenges. J Am Chem Soc 2019; 141: 4167-4181.
| Crossref | Google Scholar | PubMed |

82  Fang P, Pang W-K, Xuan S, Chan W-L, Leung KC-F. Recent advances in peptide macrocyclization strategies. Chem Soc Rev 2024; 53: 11725-11771.
| Crossref | Google Scholar | PubMed |

83  Wu J, Tang J, Chen H, He Y, Wang H, Yao H. Recent developments in peptide macrocyclization. Tetrahedron Lett 2018; 59: 325-333.
| Crossref | Google Scholar |

84  Morioka T, Loik ND, Hipolito CJ, Goto Y, Suga H. Selection-based discovery of macrocyclic peptides for the next generation therapeutics. Curr Opin Chem Biol 2015; 26: 34-41.
| Crossref | Google Scholar | PubMed |

85  Colgrave ML, Craik DJ. Thermal, chemical, and enzymatic stability of the cyclotide kalata B1: the importance of the cyclic cystine knot. Biochemistry 2004; 43: 5965-5975.
| Crossref | Google Scholar | PubMed |

86  Conibear AC, Bochen A, Rosengren KJ, Stupar P, Wang C, Kessler H, et al. The cyclic cystine ladder of theta‐defensins as a stable, bifunctional scaffold: a proof‐of‐concept study using the integrin‐binding RGD motif. ChemBioChem 2014; 15: 451-459.
| Crossref | Google Scholar | PubMed |

87  Clark RJ, Jensen J, Nevin ST, Callaghan BP, Adams DJ, Craik DJ. The engineering of an orally active conotoxin for the treatment of neuropathic pain. Angew Chem Int Ed Engl 2010; 49: 6545-6548.
| Crossref | Google Scholar | PubMed |

88  Akcan M, Stroud MR, Hansen SJ, Clark RJ, Daly NL, Craik DJ, et al. Chemical re-engineering of chlorotoxin improves bioconjugation properties for tumor imaging and targeted therapy. J Med Chem 2011; 54: 782-787.
| Crossref | Google Scholar | PubMed |

89  Wang CK, Gruber CW, Cemazar M, Siatskas C, Tagore P, Payne N, et al. Molecular grafting onto a stable framework yields novel cyclic peptides for the treatment of multiple sclerosis. ACS Chem Biol 2014; 9: 156-163.
| Crossref | Google Scholar | PubMed |

90  Chan LY, Gunasekera S, Henriques ST, Worth NF, Le S-J, Clark RJ, et al. Engineering pro-angiogenic peptides using stable, disulfide-rich cyclic scaffolds. Blood 2011; 118: 6709-6717.
| Crossref | Google Scholar | PubMed |

91  Ganesan R, Dughbaj MA, Ramirez L, Beringer S, Aboye TL, Shekhtman A, et al. Engineered cyclotides with potent broad in vitro and in vivo antimicrobial activity. Chem Eur J 2021; 27: 12702-12708.
| Crossref | Google Scholar | PubMed |

92  Cândido ES, Gasparetto LS, Luchi LV, Pimentel J, Cardoso MH, Macedo MLR, et al. Small and versatile cyclotides as anti-infective agents. ACS Infect Dis 2025; 11: 386-397.
| Crossref | Google Scholar | PubMed |

93  Rajendran S, Slazak B, Mohotti S, Muhammad T, Strömstedt AA, Kapusta M, et al. Screening for cyclotides in Sri Lankan medicinal plants: discovery, characterization, and bioactivity screening of cyclotides from Geophila repens. J Nat Prod 2023; 86: 52-65.
| Crossref | Google Scholar | PubMed |

94  Claveria-Gimeno R, Vega S, Abian O, Velazquez-Campoy A. A look at ligand binding thermodynamics in drug discovery. Expert Opin Drug Discov 2017; 12: 363-377.
| Crossref | Google Scholar | PubMed |

95  Martin SF, Clements JH. Correlating structure and energetics in protein–ligand interactions: paradigms and paradoxes. Annu Rev Biochem 2013; 82: 267-293.
| Crossref | Google Scholar | PubMed |

96  Walensky LD, Bird GH. Hydrocarbon-stapled peptides: principles, practice, and progress. J Med Chem 2014; 57: 6275-6288.
| Crossref | Google Scholar | PubMed |

97  Kawamoto SA, Coleska A, Ran X, Yi H, Yang C-Y, Wang S. Design of triazole-stapled BCL9 α-helical peptides to target the β-catenin/B-cell CLL/lymphoma 9 (BCL9) protein–protein interaction. J Med Chem 2012; 55: 1137-1146.
| Crossref | Google Scholar | PubMed |

98  Edwards AL, Wachter F, Lammert M, Huhn AJ, Luccarelli J, Bird GH, et al. Cellular uptake and ultrastructural localization underlie the pro-apoptotic activity of a hydrocarbon-stapled BIM BH3 peptide. ACS Chem Biol 2015; 10: 2149-2157.
| Crossref | Google Scholar | PubMed |

99  Zhang H, Zhao Q, Bhattacharya S, Waheed AA, Tong X, Hong A, et al. A cell-penetrating helical peptide as a potential HIV-1 inhibitor. J Mol Biol 2008; 378: 565-580.
| Crossref | Google Scholar | PubMed |

100  Crawford MA, Ward AE, Gray V, Bailer P, Fisher DJ, Kubicka E, et al. Disparate regions of the human chemokine CXCL10 exhibit broad-spectrum antimicrobial activity against biodefense and antibiotic-resistant bacterial pathogens. ACS Infect Dis 2023; 9: 122-139.
| Crossref | Google Scholar | PubMed |

101  Kang S-M, Moon H, Han S-W, Kim BW, Kim D-H, Kim BM, et al. Toxin-activating stapled peptides discovered by structural analysis were identified as new therapeutic candidates that trigger antibacterial activity against Mycobacterium tuberculosis in the Mycobacterium smegmatis model. Microorganisms 2021; 9: 568.
| Crossref | Google Scholar | PubMed |

102  Lourenço ALP, Rios TB, da Silva ÁP, Franco OL, Ramada MHS. Peptide stapling applied to antimicrobial peptides. Antibiotics 2023; 12: 1400.
| Crossref | Google Scholar | PubMed |

103  Badaczewska-Dawid A, Wróblewski K, Kurcinski M, Kmiecik S. Structure prediction of linear and cyclic peptides using CABS-flex. Brief Bioinform 2024; 25: bbae003.
| Crossref | Google Scholar | PubMed |

104  Rezende SB, Lima LR, Macedo ML, Franco OL, Cardoso MH. Advances in peptide/protein structure prediction tools and their relevance for structural biology in the last decade. Curr Bioinform 2023; 18: 559-575.
| Crossref | Google Scholar |

105  Bhardwaj G, O’Connor J, Rettie S, Huang Y-H, Ramelot TA, Mulligan VK, et al. Accurate de novo design of membrane-traversing macrocycles. Cell 2022; 185: 3520-3532.
| Crossref | Google Scholar | PubMed |

106  Fiser A, Šali A. Modeller: generation and refinement of homology-based protein structure models. In: Carter DW Jr, Sweet RM, editors. Methods in Enzymology. Volume 374: Macromolecular Crystallography, Part D. Elsevier; 2003. pp. 461–491. doi:10.1016/S0076-6879(03)74020-8

107  Maximiano MR, Rezende SB, Rios TB, Leite ML, Boas LCPV, da Cunha NB, et al. Chapter Four – Screening for cysteine-stabilized scaffolds for developing proteolytic-resistant AMPs. In: Hicks LM, editor. Antimicrobial Peptides. Methods in enzymology. Elsevier; 2022. pp. 67–98. doi:10.1016/bs.mie.2021.11.001

108  Huang P-S, Ban Y-EA, Richter F, Andre I, Vernon R, Schief WR, et al. RosettaRemodel: a generalized framework for flexible backbone protein design. PLoS One 2011; 6: e24109.
| Crossref | Google Scholar | PubMed |

109  Zhang C, Zhang C, Shang T, Zhu N, Wu X, Duan H. HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints. Brief Bioinform 2024; 25: bbae215.
| Crossref | Google Scholar | PubMed |

110  Rettie SA, Campbell KV, Bera AK, Kang A, Kozlov S, De La Cruz J, et al. Cyclic peptide structure prediction and design using AlphaFold2. Nat Commun 2025; 16(1): 4730.
| Crossref | Google Scholar | PubMed |

111  Grambow CA, Weir H, Diamant NL, Tseng AM, Biancalani T, Scalia G, et al. RINGER: rapid conformer generation for macrocycles with sequence-conditioned internal coordinate diffusion. arXiv 2024; 2024: arXiv:2305.19800 [Preprint, published 13 August 2024].
| Crossref | Google Scholar |

112  Li J, Yanagisawa K, Sugita M, Fujie T, Ohue M, Akiyama Y. CycPeptMPDB: a comprehensive database of membrane permeability of cyclic peptides. J Chem Inf Model 2023; 63: 2240-2250.
| Crossref | Google Scholar | PubMed |

113  Xu X, Xu C, He W, Wei L, Li H, Zhou J, et al. HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer. Bioinformatics 2024; 40: btae364.
| Crossref | Google Scholar | PubMed |

114  Mendez D, Gaulton A, Bento AP, Chambers J, De Veij M, Félix E, et al. ChEMBL: towards direct deposition of bioassay data. Nucleic Acids Res 2019; 47: D930-D940.
| Crossref | Google Scholar | PubMed |

115  Yan Y, Zhang D, Huang S-Y. Efficient conformational ensemble generation of protein-bound peptides. J Cheminform 2017; 9: 59.
| Crossref | Google Scholar | PubMed |

116  Tao H, Wu Q, Zhao X, Lin P, Huang S-Y. Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond. J Cheminform 2022; 14: 26.
| Crossref | Google Scholar | PubMed |

117  Thévenet P, Shen Y, Maupetit J, Guyon F, Derreumaux P, Tufféry P. PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. Nucleic Acids Res 2012; 40: 288-293.
| Crossref | Google Scholar | PubMed |

118  Riniker S, Landrum GA. Better informed distance geometry: using what we know to improve conformation generation. J Chem Inf Model 2015; 55: 2562-2574.
| Crossref | Google Scholar | PubMed |

119  Wang S, Witek J, Landrum GA, Riniker S. Improving conformer generation for small rings and macrocycles based on distance geometry and experimental torsional-angle preferences. J Chem Inf Model 2020; 60: 2044-2058.
| Crossref | Google Scholar | PubMed |

120  Grambow CA, Weir H, Cunningham CN, Biancalani T, Chuang KV. CREMP: conformer-rotamer ensembles of macrocyclic peptides for machine learning. Sci Data 2024; 11: 859.
| Crossref | Google Scholar | PubMed |

121  Mao Q, Shang T, Xu W, Zhai S, Zhang C, Su A, et al. NCPepFold: accurate prediction of non-canonical cyclic peptide structures via cyclization optimization with multigranular representation. J Chem Theory Comput 2024; 21: 4979-4991.
| Crossref | Google Scholar |

122  Cardoso MH, Orozco RQ, Rezende SB, Rodrigues G, Oshiro K, Cândido ES, et al. Computer-aided design of antimicrobial peptides: are we generating effective drug candidates? Front Microbiol 2019; 10: 3097.
| Crossref | Google Scholar | PubMed |

123  Randall JR, DuPai CD, Cole TJ, Davidson G, Groover KE, Slater SL, et al. Designing and identifying β-hairpin peptide macrocycles with antibiotic potential. Sci Adv 2023; 9: eade0008.
| Crossref | Google Scholar | PubMed |

124  Cheng Z, He B-B, Lei K, Gao Y, Shi Y, Zhong Z, et al. Rule-based omics mining reveals antimicrobial macrocyclic peptides against drug-resistant clinical isolates. Nat Commun 2024; 15: 4901.
| Crossref | Google Scholar | PubMed |

125  Miao J, Descoteaux ML, Lin Y-S. Structure prediction of cyclic peptides by molecular dynamics + machine learning. Chem Sci 2021; 12: 14927-14936.
| Crossref | Google Scholar | PubMed |

126  Roseli RB, Huang Y-H, Henriques ST, Kaas Q, Craik DJ. Molecular dynamics simulations support a preference of cyclotide kalata B1 for phosphatidylethanolamine phospholipids. Biochim Biophys Acta Biomembr 2024; 1866: 184268.
| Crossref | Google Scholar | PubMed |