1
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Jiang Z, Huang YH, Kaas Q, Craik DJ, Wang CK. Structure and Activity of Reconstructed Pseudo-Ancestral Cyclotides. ChemMedChem 2024:e202400124. [PMID: 38632079 DOI: 10.1002/cmdc.202400124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/19/2024]
Abstract
Cyclotides are cyclic peptides that are promising scaffolds for the design of drug candidates and chemical tools. However, despite there being hundreds of reported cyclotides, drug design studies have commonly focussed on a select few prototypic examples. Here, we explored whether ancestral sequence reconstruction could be used to generate new cyclotides for further optimization. We show that the reconstructed 'pseudo-ancestral' sequences, named Ancy-m (for the ancestral cyclotide of the Möbius sub-family) and Ancy-b (for the bracelet sub-family), have well-defined structures like their extant members, comprising the core structural feature of a cyclic cystine knot. This motif underpins efforts to re-engineer cyclotides for agrochemical and therapeutic applications. We further show that the reconstructed sequences are resistant to temperatures approaching boiling, bind to phosphatidyl-ethanolamine lipid bilayers at micromolar affinity, and inhibit the growth of insect cells at inhibitory concentrations in the micromolar range. Interestingly, the Ancy-b cyclotide had a higher oxidative folding yield than its comparator cyclotide cyO2, which belongs to the bracelet cyclotide subfamily known to be notoriously difficult to fold. Overall, this study provides new cyclotide sequences not yet found naturally that could be valuable starting points for the understanding of cyclotide evolution and for further optimization as drug leads.
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Affiliation(s)
- Zhihao Jiang
- The University of Queensland, Institute for Molecular Bioscience, 4072, Brisbane, AUSTRALIA
| | - Yen-Hua Huang
- The University of Queensland, Institute for Molecular Bioscience, 4072, Brisbane, AUSTRALIA
| | - Quentin Kaas
- The University of Queensland, Institute for Molecular Bioscience, 4072, Brisbane, AUSTRALIA
| | - David J Craik
- The University of Queensland, Institute for Molecular Bioscience, 4072, Brisbane, AUSTRALIA
| | - Conan K Wang
- The University of Queensland, Institute for Molecular Bioscience, Carmody Rd, 4072, St Lucia, AUSTRALIA
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2
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Tian S, de Veer SJ, Durek T, Wang CK, Craik DJ. Nucleation of a key beta-turn promotes cyclotide oxidative folding. J Biol Chem 2024; 300:107125. [PMID: 38432638 PMCID: PMC10999817 DOI: 10.1016/j.jbc.2024.107125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Cyclotides are plant-derived peptides characterized by a head-to-tail cyclic backbone and a cystine knot motif comprised of three disulfide bonds. Formation of this motif via in vitro oxidative folding can be challenging and can result in misfolded isomers with nonnative disulfide connectivities. Here, we investigated the effect of β-turn nucleation on cyclotide oxidative folding. Two types of β-turn mimics were grafted into kalata B1, individually replacing each of the four β-turns in the folded cyclotide. Insertion of d-Pro-Gly into loop 5 was beneficial to the folding of both cyclic kB1 and a linear form of the peptide. The linear grafted analog folded four-times faster in aqueous conditions than cyclic kB1 in optimized conditions. Additionally, the cyclic analogue folded without the need for redox agents by transitioning through a native-like intermediate that was on-pathway to product formation. Kalata B1 is from the Möbius subfamily of cyclotides. Grafting d-Pro-Gly into loop 5 of cyclotides from two other subfamilies also had a beneficial effect on folding. Our findings demonstrate the importance of a β-turn nucleation site for cyclotide oxidative folding, which could be adopted as a chemical strategy to improve the in vitro folding of diverse cystine-rich peptides.
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Affiliation(s)
- Sixin Tian
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia.
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3
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Huang YH, Jiang Z, Du Q, Yap K, Bigot A, Kaas Q, Wang CK, Craik DJ. Scanning mutagenesis identifies residues that improve the long-term stability and insecticidal activity of cyclotide kalata B1. J Biol Chem 2024; 300:105682. [PMID: 38272233 PMCID: PMC10877628 DOI: 10.1016/j.jbc.2024.105682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Cyclotides are plant-derived disulfide-rich cyclic peptides that have a natural function in plant defense and potential for use as agricultural pesticides. Because of their highly constrained topology, they are highly resistant to thermal, chemical, or enzymatic degradation. However, the stability of cyclotides at alkaline pH for incubation times of longer than a few days is poorly studied but important since these conditions could be encountered in the environment, during storage or field application as insecticides. In this study, kalata B1 (kB1), the prototypical cyclotide, was engineered to improve its long-term stability and retain its insecticidal activity via point mutations. We found that substituting either Asn29 or Gly1 to lysine or leucine increased the stability of kB1 by twofold when incubated in an alkaline buffer (pH = 9.0) for 7 days, while retaining its insecticidal activity. In addition, when Gly1 was replaced with lysine or leucine, the mutants could be cyclized using an asparaginyl endopeptidase, in vitro with a yield of ∼90% within 5 min. These results demonstrate the potential to manufacture kB1 mutants with increased stability and insecticidal activity recombinantly or in planta. Overall, the discovery of mutants of kB1 that have enhanced stability could be useful in leading to longer term activity in the field as bioinsecticides.
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Affiliation(s)
- Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Zhihao Jiang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Qingdan Du
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia.
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4
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Philippe GJB, Huang YH, Mittermeier A, Brown CJ, Kaas Q, Ramlan SR, Wang CK, Lane D, Loewer A, Troeira Henriques S, Craik DJ. Delivery to, and Reactivation of, the p53 Pathway in Cancer Cells Using a Grafted Cyclotide Conjugated with a Cell-Penetrating Peptide. J Med Chem 2024; 67:1197-1208. [PMID: 38174919 DOI: 10.1021/acs.jmedchem.3c01682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Peptides are promising drug modalities that can modulate protein-protein interactions, but their application is hampered by their limited ability to reach intracellular targets. Here, we improved the cytosolic delivery of a peptide blocking p53:MDM2/X interactions using a cyclotide as a stabilizing scaffold. We applied several design strategies to improve intracellular delivery and found that the conjugation of the lead cyclotide to the cyclic cell-penetrating peptide cR10 was the most effective. Conjugation allowed cell internalization at micromolar concentration and led to elevated intracellular p53 levels in A549, MCF7, and MCF10A cells, as well as inducing apoptosis in A549 cells without causing membrane disruption. The lead peptide had >35-fold improvement in inhibitory activity and increased cellular uptake compared to a previously reported cyclotide p53 activator. In summary, we demonstrated the delivery of a large polar cyclic peptide in the cytosol and confirmed its ability to modulate intracellular protein-protein interactions involved in cancer.
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Affiliation(s)
- Grégoire Jean-Baptiste Philippe
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
- School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Anna Mittermeier
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Christopher J Brown
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Siti Radhiah Ramlan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David Lane
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Alexander Loewer
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Sónia Troeira Henriques
- School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
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5
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Wang CK, Huang YH, Shabbir F, Pham HT, Lawrence N, Benfield AH, van der Donk W, Henriques ST, Turner MS, Craik DJ. The Circular Bacteriocin enterocin NKR-5-3B has an Improved Stability Profile over Nisin. Peptides 2023:171049. [PMID: 37390898 DOI: 10.1016/j.peptides.2023.171049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/02/2023]
Abstract
Bacteriocins are a large family of bacterial peptides that have antimicrobial activity and potential applications as clinical antibiotics or food preservatives. Circular bacteriocins are a unique class of these biomolecules distinguished by a seamless circular topology, and are widely assumed to be ultra-stable based on this constraining structural feature. However, without quantitative studies of their susceptibility to defined thermal, chemical, and enzymatic conditions, their stability characteristics remain poorly understood, limiting their translational development. Here, we produced the circular bacteriocin enterocin NKR-5-3B (Ent53B) in mg/L quantities using a heterologous Lactococcus expression system, and characterized its thermal stability by NMR, chemical stability by circular dichroism and analytical HPLC, and enzymatic stability by analytical HPLC. We demonstrate that Ent53B is ultra-stable, resistant to temperatures approaching boiling, acidic (pH 2.6) and alkaline (pH 9.0) conditions, the chaotropic agent 6M urea, and following incubation with a range of proteases (i.e., trypsin, chymotrypsin, pepsin, and papain), conditions under which most peptides and proteins degrade. Ent53B is stable across a broader range of pH conditions and proteases than nisin, the most widely used bacteriocin in food manufacturing. Antimicrobial assays showed that differences in stability correlated with differences in bactericidal activity. Overall, this study provides quantitative support for circular bacteriocins being an ultra-stable class of peptide molecules, suggesting easier handling and distribution options available to them in practical applications as antimicrobial agents.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science,.
| | - Yen-Hua Huang
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science
| | - Fatima Shabbir
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science
| | - Huong T Pham
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science
| | - Aurélie H Benfield
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Wilfred van der Donk
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sónia T Henriques
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Mark S Turner
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science
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6
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Morin M, Jönsson M, Wang CK, Craik DJ, Degnan SM, Degnan BM. Captivity induces a sweeping and sustained genomic response in a starfish. Mol Ecol 2023. [PMID: 37009965 DOI: 10.1111/mec.16947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 03/03/2023] [Accepted: 03/29/2023] [Indexed: 04/04/2023]
Abstract
Marine animals in the wild are often difficult to access, so they are studied in captivity. However, the implicit assumption that physiological processes of animals in artificial environments are not different from those in the wild has rarely been tested. Here we investigate the extent to which an animal is impacted by captivity by comparing global gene expression in wild and captive crown-of-thorns starfish (COTS). In a preliminary analysis, we compared transcriptomes of three external tissues obtained from multiple wild COTS with a single captive COTS maintained in aquaria for at least one week. On average, an astonishingly large 24% of the coding sequences in the genome were differentially expressed. This led us to conduct a replicated experiment to test more comprehensively the impact of captivity on gene expression. Specifically, a comparison of 13 wild with 8 captive COTS coelomocyte transcriptomes revealed significant differences in the expression of 20% of coding sequences. Coelomocyte transcriptomes in captive COTS remain different from those in wild COTS for more than 30 days and show no indication of reverting back to a wild state (i.e. no evidence of acclimation). Genes upregulated in captivity include those involved in oxidative stress and energy metabolism, whereas genes downregulated are involved in cell signalling. These changes in gene expression indicate that being translocated and maintained in captivity has a marked impact on the physiology and health of these echinoderms. This study suggests that caution should be exercised when extrapolating results from captive aquatic invertebrates to their wild counterparts.
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Affiliation(s)
- Marie Morin
- Centre for Marine Science, School of Biological Sciences, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Mathias Jönsson
- Centre for Marine Science, School of Biological Sciences, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Sandie M Degnan
- Centre for Marine Science, School of Biological Sciences, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Bernard M Degnan
- Centre for Marine Science, School of Biological Sciences, University of Queensland, Brisbane, Queensland, 4072, Australia
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7
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Wang CK. The 2022 Kazuhiko Tatemoto Prize: ACE2-derived peptides for COVID-19 treatment. Peptides 2023; 162:170964. [PMID: 36738828 DOI: 10.1016/j.peptides.2023.170964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Conan K Wang
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane 4069, Qld, Australia.
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8
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Chen Z, Cui Y, Yao Y, Liu B, Yunis J, Gao X, Wang N, Cañete PF, Tuong ZK, Sun H, Wang H, Yang S, Wang R, Leong YA, Simon Davis D, Qin J, Liang K, Deng J, Wang CK, Huang YH, Roco JA, Nettelfield S, Zhu H, Xu H, Yu Z, Craik D, Liu Z, Qi H, Parish C, Yu D. Heparan sulfate regulates IL-21 bioavailability and signal strength that control germinal center B cell selection and differentiation. Sci Immunol 2023; 8:eadd1728. [PMID: 36800411 DOI: 10.1126/sciimmunol.add1728] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
In antibody responses, mutated germinal center B (BGC) cells are positively selected for reentry or differentiation. As the products from GCs, memory B cells and antibody-secreting cells (ASCs) support high-affinity and long-lasting immunity. Positive selection of BGC cells is controlled by signals received through the B cell receptor (BCR) and follicular helper T (TFH) cell-derived signals, in particular costimulation through CD40. Here, we demonstrate that the TFH cell effector cytokine interleukin-21 (IL-21) joins BCR and CD40 in supporting BGC selection and reveal that strong IL-21 signaling prioritizes ASC differentiation in vivo. BGC cells, compared with non-BGC cells, show significantly reduced IL-21 binding and attenuated signaling, which is mediated by low cellular heparan sulfate (HS) sulfation. Mechanistically, N-deacetylase and N-sulfotransferase 1 (Ndst1)-mediated N-sulfation of HS in B cells promotes IL-21 binding and signal strength. Ndst1 is down-regulated in BGC cells and up-regulated in ASC precursors, suggesting selective desensitization to IL-21 in BGC cells. Thus, specialized biochemical regulation of IL-21 bioavailability and signal strength sets a balance between the stringency and efficiency of GC selection.
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Affiliation(s)
- Zhian Chen
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Yanfang Cui
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, China
| | - Yin Yao
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia.,Department of Otolaryngology-Head and Neck Surgery, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Liu
- Tsinghua-Peking Center for Life Sciences, Laboratory of Dynamic Immunobiology, School of Medicine, Tsinghua University, Beijing, China
| | - Joseph Yunis
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Xin Gao
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Naiqi Wang
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Pablo F Cañete
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Hongjian Sun
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Hao Wang
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Siling Yang
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Runli Wang
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Yew Ann Leong
- Centre for Inflammatory Diseases, Department of Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, VIC, Australia
| | - David Simon Davis
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Jiahuan Qin
- China-Australia Centre for Personalised Immunology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kaili Liang
- China-Australia Centre for Personalised Immunology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Deng
- China-Australia Centre for Personalised Immunology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Conan K Wang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Queensland, Brisbane, QLD, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Jonathan A Roco
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Sam Nettelfield
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Huaming Zhu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
| | - Huajun Xu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
| | - Zhijia Yu
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - David Craik
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Queensland, Brisbane, QLD, Australia
| | - Zheng Liu
- Department of Otolaryngology-Head and Neck Surgery, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Hai Qi
- Tsinghua-Peking Center for Life Sciences, Laboratory of Dynamic Immunobiology, School of Medicine, Tsinghua University, Beijing, China
| | - Christopher Parish
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Di Yu
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia.,Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
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9
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Jönsson M, Morin M, Wang CK, Craik DJ, Degnan SM, Degnan BM. Sex-specific expression of pheromones and other signals in gravid starfish. BMC Biol 2022; 20:288. [PMID: 36528687 PMCID: PMC9759900 DOI: 10.1186/s12915-022-01491-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Many echinoderms form seasonal aggregations prior to spawning. In some fecund species, a spawning event can lead to population outbreaks with detrimental ecosystem impacts. For instance, outbreaks of crown-of-thorns starfish (COTS), a corallivore, can destroy coral reefs. Here, we examine the gene expression in gravid male and female COTS prior to spawning in the wild, to identify genome-encoded factors that may regulate aggregation and spawning. This study is informed by a previously identified exoproteome that attracts conspecifics. To capture the natural gene expression profiles, we isolated RNAs from gravid female and male COTS immediately after they were removed from the Great Barrier Reef. RESULTS: Sexually dimorphic gene expression is present in all seven somatic tissues and organs that we surveyed and in the gonads. Approximately 40% of the exoproteome transcripts are differentially expressed between sexes. Males uniquely upregulate an additional 68 secreted factors in their testes. A suite of neuropeptides in sensory organs, coelomocytes and gonads is differentially expressed between sexes, including the relaxin-like gonad-stimulating peptide and gonadotropin-releasing hormones. Female sensory tentacles-chemosensory organs at the distal tips of the starfish arms-uniquely upregulate diverse receptors and signalling molecules, including chemosensory G-protein-coupled receptors and several neuropeptides, including kisspeptin, SALMFamide and orexin. CONCLUSIONS Analysis of 103 tissue/organ transcriptomes from 13 wild COTS has revealed genes that are consistently differentially expressed between gravid females and males and that all tissues surveyed are sexually dimorphic at the molecular level. This finding is consistent with female and male COTS using sex-specific pheromones to regulate reproductive aggregations and synchronised spawning events. These pheromones appear to be received primarily by the sensory tentacles, which express a range of receptors and signalling molecules in a sex-specific manner. Furthermore, coelomocytes and gonads differentially express signalling and regulatory factors that control gametogenesis and spawning in other echinoderms.
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Affiliation(s)
- Mathias Jönsson
- grid.1003.20000 0000 9320 7537Centre for Marine Science, School of Biological Sciences, University of Queensland, Brisbane, QLD 4072 Australia
| | - Marie Morin
- grid.1003.20000 0000 9320 7537Centre for Marine Science, School of Biological Sciences, University of Queensland, Brisbane, QLD 4072 Australia
| | - Conan K. Wang
- grid.1003.20000 0000 9320 7537Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072 Australia
| | - David J. Craik
- grid.1003.20000 0000 9320 7537Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Sandie M. Degnan
- grid.1003.20000 0000 9320 7537Centre for Marine Science, School of Biological Sciences, University of Queensland, Brisbane, QLD 4072 Australia
| | - Bernard M. Degnan
- grid.1003.20000 0000 9320 7537Centre for Marine Science, School of Biological Sciences, University of Queensland, Brisbane, QLD 4072 Australia
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10
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Tian S, Durek T, Wang CK, Zdenek CN, Fry BG, Craik DJ, de Veer SJ. Engineering the Cyclization Loop of MCoTI-II Generates Targeted Cyclotides that Potently Inhibit Factor XIIa. J Med Chem 2022; 65:15698-15709. [PMID: 36383928 DOI: 10.1021/acs.jmedchem.2c01080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Factor XIIa (FXIIa) is a promising target for developing new drugs that prevent thrombosis without causing bleeding complications. A native cyclotide (MCoTI-II) is gaining interest for engineering FXIIa-targeted anticoagulants as this peptide inhibits FXIIa but not other coagulation proteases. Here, we engineered the native biosynthetic cyclization loop of MCoTI-II (loop 6) to generate improved FXIIa inhibitors. Decreasing the loop length led to gains in potency up to 7.7-fold, with the most potent variant having five residues in loop 6 (Ki = 25 nM). We subsequently examined sequence changes within loop 6 and an adjacent loop, with substitutions at P4 and P2' producing a potent FXIIa inhibitor (Ki = 2 nM) that displayed more than 700-fold selectivity, was stable in human serum, and blocked the intrinsic coagulation pathway in human plasma. These findings demonstrate that engineering the biosynthetic cyclization loop can generate improved cyclotide variants, expanding their potential for drug discovery.
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Affiliation(s)
- Sixin Tian
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Christina N Zdenek
- Venom Evolution Lab, School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Bryan G Fry
- Venom Evolution Lab, School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
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11
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Zhang Y, Wang L, Tombling BJ, Lammi C, Huang YH, Li Y, Bartolomei M, Hong B, Craik DJ, Wang CK. Improving Stability Enhances In Vivo Efficacy of a PCSK9 Inhibitory Peptide. J Am Chem Soc 2022; 144:19485-19498. [DOI: 10.1021/jacs.2c08029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuhui Zhang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD4072, Australia
| | - Li Wang
- NHC Key Laboratory of Biotechnology Antibiotics and CAMS Key Laboratory of Synthetic Biology for Drug Innovation, & Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing100050, China
| | - Benjamin J. Tombling
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD4072, Australia
| | - Carmen Lammi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milan, Via L. Mangiagalli 25, 20133Milan, Italy
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD4072, Australia
| | - Yue Li
- NHC Key Laboratory of Biotechnology Antibiotics and CAMS Key Laboratory of Synthetic Biology for Drug Innovation, & Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing100050, China
| | - Martina Bartolomei
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milan, Via L. Mangiagalli 25, 20133Milan, Italy
| | - Bin Hong
- NHC Key Laboratory of Biotechnology Antibiotics and CAMS Key Laboratory of Synthetic Biology for Drug Innovation, & Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing100050, China
| | - David J. Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD4072, Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD4072, Australia
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12
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Wang CK, Craik DJ. CIPPS, an Australian Centre for Peptide and Protein Research, goes live! Peptides 2022; 155:170835. [PMID: 35753503 DOI: 10.1016/j.peptides.2022.170835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia.
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13
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Du Q, Huang YH, Wang CK, Kaas Q, Craik DJ. Mutagenesis of bracelet cyclotide hyen D reveals functionally and structurally critical residues for membrane binding and cytotoxicity. J Biol Chem 2022; 298:101822. [PMID: 35283188 PMCID: PMC9006653 DOI: 10.1016/j.jbc.2022.101822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 11/05/2022] Open
Abstract
Cyclotides have a wide range of bioactivities relevant for agricultural and pharmaceutical applications. This large family of naturally occurring macrocyclic peptides is divided into three subfamilies, with the bracelet subfamily being the largest and comprising the most potent cyclotides reported to date. However, attempts to harness the natural bioactivities of bracelet cyclotides and engineer-optimized analogs have been hindered by a lack of understanding of the structural and functional role of their constituent residues, which has been challenging because bracelet cyclotides are difficult to produce synthetically. We recently established a facile strategy to make the I11L mutant of cyclotide hyen D that is as active as the parent peptide, enabling the subsequent production of a series of variants. In the current study, we report an alanine mutagenesis structure-activity study of [I11L] hyen D to probe the role of individual residues on peptide folding using analytical chromatography, on molecular function using surface plasmon resonance, and on therapeutic potential using cytotoxicity assays. We found that Glu-6 and Thr-15 are critical for maintaining the structure of bracelet cyclotides and that hydrophobic residues in loops 2 and 3 are essential for membrane binding and cytotoxic activity, findings that are distinct from the structural and functional characteristics determined for other cyclotide subfamilies. In conclusion, this is the first report of a mutagenesis scan conducted on a bracelet cyclotide, offering insights into their function and supporting future efforts to engineer bracelet cyclotides for biotechnological applications.
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Affiliation(s)
- Qingdan Du
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, Australia.
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, Australia.
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14
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Yin H, Zhou X, Huang YH, King GJ, Collins BM, Gao Y, Craik DJ, Wang CK. Rational Design of Potent Peptide Inhibitors of the PD-1:PD-L1 Interaction for Cancer Immunotherapy. J Am Chem Soc 2021; 143:18536-18547. [PMID: 34661406 DOI: 10.1021/jacs.1c08132] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Peptides have potential to be developed into immune checkpoint inhibitors, but the target interfaces are difficult to inhibit. Here, we explored an approach to mimic the binding surface of PD-1 to design inhibitors. Mimicking native PD-1 resulted in a mimetic with no activity. However, mimicking an affinity-optimized PD-1 resulted in the peptide mimetic MOPD-1 that displayed nanomolar affinity to PD-L1 and could inhibit PD-1:PD-L1 interactions in both protein- and cell-based assays. Mutagenesis and structural characterization using NMR spectroscopy and X-ray crystallography revealed that binding residues from the high affinity PD-1 are crucial for the bioactivity of MOPD-1. Furthermore, MOPD-1 was extremely stable in human serum and inhibited tumor growth in vivo, suggesting it has potential for use in cancer immunotherapy. The successful design of an inhibitor of PD-1:PD-L1 using the mimicry approach described herein illustrates the value of placing greater emphasis on optimizing the target interface before inhibitor design and is an approach that could have broader utility for the design of peptide inhibitors for other complex protein-protein interactions.
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Affiliation(s)
- Huawu Yin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Xiuman Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Gordon J King
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Brett M Collins
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yanfeng Gao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China.,School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
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15
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Huang YH, Du Q, Jiang Z, King GJ, Collins BM, Wang CK, Craik DJ. Enabling Efficient Folding and High-Resolution Crystallographic Analysis of Bracelet Cyclotides. Molecules 2021; 26:molecules26185554. [PMID: 34577034 PMCID: PMC8467136 DOI: 10.3390/molecules26185554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/05/2021] [Accepted: 09/09/2021] [Indexed: 11/23/2022] Open
Abstract
Cyclotides have attracted great interest as drug design scaffolds because of their unique cyclic cystine knotted topology. They are classified into three subfamilies, among which the bracelet subfamily represents the majority and comprises the most bioactive cyclotides, but are the most poorly utilized in drug design applications. A long-standing challenge has been the very low in vitro folding yields of bracelets, hampering efforts to characterize their structures and activities. Herein, we report substantial increases in bracelet folding yields enabled by a single point mutation of residue Ile-11 to Leu or Gly. We applied this discovery to synthesize mirror image enantiomers and used quasi-racemic crystallography to elucidate the first crystal structures of bracelet cyclotides. This study provides a facile strategy to produce bracelet cyclotides, leading to a general method to easily access their atomic resolution structures and providing a basis for development of biotechnological applications.
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Affiliation(s)
- Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Qingdan Du
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Zhihao Jiang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Gordon J. King
- The Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Brett M. Collins
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
| | - Conan K. Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence: ; Tel.: +61-7-3346-2019
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16
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Yin H, Huang YH, Best SA, Sutherland KD, Craik DJ, Wang CK. An Integrated Molecular Grafting Approach for the Design of Keap1-Targeted Peptide Inhibitors. ACS Chem Biol 2021; 16:1276-1287. [PMID: 34152716 DOI: 10.1021/acschembio.1c00388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Inhibiting the Nrf2:Keap1 interaction to trigger cytoprotective gene expression is a promising treatment strategy for oxidative stress-related diseases. A short linear motif from Nrf2 has the potential to directly inhibit this protein-protein interaction, but poor stability and limited cellular uptake impede its therapeutic development. To address these limitations, we utilized an integrated molecular grafting strategy to re-engineer the Nrf2 motif. We combined the motif with an engineered non-native disulfide bond and a cell-penetrating peptide onto a single multifunctionalizable and ultrastable molecular scaffold, namely, the cyclotide MCoTI-II, resulting in the grafted peptide MCNr-2c. The engineered disulfide bond enhanced the conformational rigidity of the motif, resulting in a nanomolar affinity of MCNr-2c for Keap1. The cell-penetrating peptide led to an improved cellular uptake and increased ability to enhance the intracellular expression of two well-described Nrf2-target genes NQO1 and TALDO1. Furthermore, the stability of the scaffold was inherited by the grafted peptide, which became resistant to proteolysis in serum. Overall, we have provided proof-of-concept for a strategy that enables the encapsulation of multiple desired and complementary activities into a single molecular entity to design a Keap1-targeted inhibitor. We propose that this integrated approach could have broad utility for the design of peptide drug leads that require multiple functions and/or biopharmaceutical properties to elicit a therapeutic activity.
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Affiliation(s)
- Huawu Yin
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sarah A. Best
- ACRF Cancer Biology and Stem Cells Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Kate D. Sutherland
- ACRF Cancer Biology and Stem Cells Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
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17
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Tombling BJ, Zhang Y, Huang YH, Craik DJ, Wang CK. The emerging landscape of peptide-based inhibitors of PCSK9. Atherosclerosis 2021; 330:52-60. [PMID: 34246818 DOI: 10.1016/j.atherosclerosis.2021.06.903] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/18/2021] [Accepted: 06/23/2021] [Indexed: 12/13/2022]
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a clinically validated target for treating cardiovascular disease (CVD) due to its involvement in cholesterol metabolism. Although approved monoclonal antibodies (alirocumab and evolocumab) that inhibit PCSK9 function are very effective in lowering cholesterol, their limitations, including high treatment costs, have so far prohibited widespread use. Accordingly, there is great interest in alternative drug modalities to antibodies. Like antibodies, peptides are valuable therapeutics due to their high target potency and specificity. Furthermore, being smaller than antibodies means they have access to more drug administration options, are less likely to induce adverse immunogenic responses, and are better suited to affordable production. This review surveys the current peptide-based landscape aimed towards PCSK9 inhibition, covering pre-clinical to patented drug candidates and comparing them to current cholesterol lowering therapeutics. Classes of peptides reported to be inhibitors include nature-inspired disulfide-rich peptides, combinatorially derived cyclic peptides, and peptidomimetics. Their functional activities have been validated in biophysical and cellular assays, and in some cases pre-clinical mouse models. Recent efforts report peptides with potent sub-nanomolar binding affinities to PCSK9, which highlights their potential to achieve antibody-like potency. Studies are beginning to address pharmacokinetic properties of PCSK9-targeting peptides in more detail. We conclude by highlighting opportunities to investigate their biological effects in pre-clinical models of cardiovascular disease. The anticipation concerning the PCSK9-targeting peptide landscape is accelerating and it seems likely that a peptide-based therapeutic for treating PCSK9-mediated hypercholesterolemia may be clinically available in the near future.
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Affiliation(s)
- Benjamin J Tombling
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Yuhui Zhang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia.
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18
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Tombling BJ, Lammi C, Bollati C, Anoldi A, Craik DJ, Wang CK. Increased Valency Improves Inhibitory Activity of Peptides Targeting Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9). Chembiochem 2021; 22:2154-2160. [PMID: 33755275 DOI: 10.1002/cbic.202100103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/23/2021] [Indexed: 12/18/2022]
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a clinically validated target for treating hypercholesterolemia. Peptide-based PCSK9 inhibitors have attracted pharmaceutical interest, but the effect of multivalency on bioactivity is poorly understood. Here we designed bivalent and tetravalent dendrimers, decorated with the PCSK9 inhibitory peptides Pep2-8[RRG] or P9-38, to study relationships between peptide binding affinity, peptide valency, and PCSK9 inhibition. Increased valency resulted in improved PCSK9 inhibition for both peptides, with activity improvements of up to 100-fold achieved for the P9-38-decorated dendrimers compared to monomeric P9-38 in in vitro competition binding assays. Furthermore, the P9-38-decorated dendrimers showed improved potency at restoring functional low-density lipoprotein (LDL) receptor levels and internalizing LDL in the presence of PCSK9, demonstrating significant cell-based activity at picomolar concentrations. This study demonstrates the potential of increasing valency as a strategy for increasing the efficacy of peptide-based PCSK9 therapeutics.
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Affiliation(s)
- Benjamin J Tombling
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Carmen Lammi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milan, Italy
| | - Carlotta Bollati
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milan, Italy
| | - Anna Anoldi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milan, Italy
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
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19
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Tombling BJ, Lammi C, Lawrence N, Li J, Arnoldi A, Craik DJ, Wang CK. Engineered EGF-A Peptides with Improved Affinity for Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9). ACS Chem Biol 2021; 16:429-439. [PMID: 33512150 DOI: 10.1021/acschembio.0c00991] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The epidermal growth-factor-like domain A (EGF-A) of the low-density lipoprotein (LDL) receptor is a promising lead for therapeutic inhibition of proprotein convertase subtilisin/kexin type 9 (PCSK9). However, the clinical potential of EGF-A is limited by its suboptimal affinity for PCSK9. Here, we use phage display to identify EGF-A analogues with extended bioactive segments that have improved affinity for PCSK9. The most potent analogue, TEX-S2_03, demonstrated ∼130-fold improved affinity over the parent domain and had a reduced calcium dependency for efficient PCSK9 binding. Thermodynamic binding analysis suggests the improved affinity of TEX-S2_03 is enthalpically driven, indicating favorable interactions are formed between the extended segment of TEX-S2_03 and the PCSK9 surface. The improved affinity of TEX-S2_03 resulted in increased activity in competition binding assays and more efficient restoration of LDL receptor levels with clearance of extracellular LDL cholesterol in functional cell assays. These results confirm that TEX-S2_03 is a promising therapeutic lead for treating hypercholesterolemia. Many EGF-like domains are involved in disease-related protein-protein interactions; therefore, our strategy for engineering EGF-like domains has the potential to be broadly implemented in EGF-based drug design.
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Affiliation(s)
- Benjamin J. Tombling
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Carmen Lammi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Nicole Lawrence
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jianqiang Li
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Anna Arnoldi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - David J. Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
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20
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Abstract
Molecular grafting is a strategy for the engineering of molecular scaffolds into new functional agents, such as next-generation therapeutics. Despite its wide use, studies so far have focused almost exclusively on demonstrating its utility rather than understanding the factors that lead to either poor or successful grafting outcomes. Here, we examine protein evolution and identify parallels between the natural process of protein functional diversification and the artificial process of molecular grafting. We discuss features of natural proteins that are correlated to innovability-the capacity to acquire new functions-and describe their implications to molecular grafting scaffolds. Disulfide-rich peptides are used as exemplars because they are particularly promising scaffolds onto which new functions can be grafted. This article provides a perspective on why some scaffolds are more suitable for grafting than others, identifying opportunities on how molecular grafting might be improved.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia.
| | - David J Craik
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
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21
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Tombling BJ, Lammi C, Lawrence N, Gilding EK, Grazioso G, Craik DJ, Wang CK. Bioactive Cyclization Optimizes the Affinity of a Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) Peptide Inhibitor. J Med Chem 2020; 64:2523-2533. [PMID: 33356222 DOI: 10.1021/acs.jmedchem.0c01766] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Peptides are regarded as promising next-generation therapeutics. However, an analysis of over 1000 bioactive peptide candidates suggests that many have underdeveloped affinities and could benefit from cyclization using a bridging linker sequence. Until now, the primary focus has been on the use of inert peptide linkers. Here, we show that affinity can be significantly improved by enriching the linker with functional amino acids. We engineered a peptide inhibitor of PCSK9, a target for clinical management of hypercholesterolemia, to demonstrate this concept. Cyclization linker optimization from library screening produced a cyclic peptide with ∼100-fold improved activity over the parent peptide and efficiently restored low-density lipoprotein (LDL) receptor levels and cleared extracellular LDL. The linker forms favorable interactions with PCSK9 as evidenced by thermodynamics, structure-activity relationship (SAR), NMR, and molecular dynamics (MD) studies. This PCSK9 inhibitor is one of many peptides that could benefit from bioactive cyclization, a strategy that is amenable to broad application in pharmaceutical design.
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Affiliation(s)
- Benjamin J Tombling
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Carmen Lammi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Nicole Lawrence
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld 4072, Australia
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22
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Handley TNG, Wang CK, Harvey PJ, Lawrence N, Craik DJ. Front Cover: Cyclotide Structures Revealed by NMR, with a Little Help from X‐ray Crystallography (ChemBioChem 24/2020). Chembiochem 2020. [DOI: 10.1002/cbic.202000778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Thomas N. G. Handley
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Peta J. Harvey
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - David J. Craik
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
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23
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Handley TNG, Wang CK, Harvey PJ, Lawrence N, Craik DJ. Cyclotide Structures Revealed by NMR, with a Little Help from X‐ray Crystallography. Chembiochem 2020; 21:3463-3475. [DOI: 10.1002/cbic.202000315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/08/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Thomas N. G. Handley
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Peta J. Harvey
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - David J. Craik
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
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24
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Lin HC, Wang CK, Tung YC, Chiu FY, Su YP. Increased vasculogenesis of endothelial cells in hyaluronic acid augmented fibrin-based natural hydrogels - from in vitro to in vivo models. Eur Cell Mater 2020; 40:133-145. [PMID: 32951194 DOI: 10.22203/ecm.v040a08] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Vascularisation efficiency plays an essential role in the success of bulk transplantation, while biocompatibility and safety are major concerns in clinical applications. Fibrin-based hydrogels have been exploited as scaffolds for their advantages in biocompatibility, degradability and mass transportation in various forms. However, the mechanical strength and degree of vascularisation remain unsatisfactory for clinical usage. An interpenetrating hydrogel was developed by adding hyaluronic acid (HA) to a fibrin-based natural hydrogel. The vasculogenesis of endothelial cells (human umbilical vein endothelial cells, HUVECs) was characterised within the gel using both in vitro and in vivo animal studies. The in vitro vascular morphology analysis showed 17.9 % longer mean tube length and 14.3 % higher average thickness in 7 d cultivation within the HA-supplemented hydrogel. The in vivo results showed 51.6 % larger total tube area, 1.8 × longer average tube length and 81.6 % higher cell number in the HA-supplemented hydrogel compared to the hydrogel without HA. The experimental results demonstrated better vascularisation and cell recruitment in the HA- supplemented hydrogel. The material properties of the hydrogels were also analysed using atomic force microscopy (AFM). The results revealed 3.7 × higher elasticity of the HA-supplemented hydrogel, which provided better mechanical strength and support for easy handling during procedures. With the demonstrated advantages, the developed hydrogels showed promise for exploitation in various practical clinical applications.
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Affiliation(s)
| | | | | | | | - Y P Su
- Department of Orthopaedics and Traumatology, Taipei Veteran General Hospital, 201, Sec. 2, Shih-Pai Road, Taipei 112, Taiwan.
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25
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Wang CK, Amiss AS, Weidmann J, Craik DJ. Structure-activity analysis of truncated albumin-binding domains suggests new lead constructs for potential therapeutic delivery. J Biol Chem 2020; 295:12143-12152. [PMID: 32647013 PMCID: PMC7443490 DOI: 10.1074/jbc.ra120.014168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
Rapid clearance by renal filtration is a major impediment to the translation of small bioactive biologics into drugs. To extend serum t1/2, a commonly used approach is to attach drug leads to the G-related albumin-binding domain (ABD) to bind albumin and evade clearance. Despite the success of this approach in extending half-lives of a wide range of biologics, it is unclear whether the existing constructs are optimized for binding and size; any improvements along these lines could lead to improved drugs. Characterization of the biophysics of binding of an ABD to albumin in solution could shed light on this question. Here, we examine the binding of an ABD to human serum albumin using isothermal titration calorimetry and assess the structural integrity of the ABD using CD, NMR, and molecular dynamics. A structure-activity analysis of truncations of the ABD suggests that downsized variants could replace the full-length domain. Reducing size could have the benefit of reducing potential immunogenicity problems. We further showed that one of these variants could be used to design a bifunctional molecule with affinity for albumin and a serum protein involved in cholesterol metabolism, PCSK9, demonstrating the potential utility of these fragments in the design of cholesterol-lowering drugs. Future work could extend these in vitro binding studies to other ABD variants to develop therapeutics. Our study presents new understanding of the solution structural and binding properties of ABDs, which has implications for the design of next-generation long-lasting therapeutics.
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Affiliation(s)
- Conan K. Wang
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Anna S. Amiss
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Joachim Weidmann
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - David J. Craik
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
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26
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White AM, Veer SJ, Wu G, Harvey PJ, Yap K, King GJ, Swedberg JE, Wang CK, Law RHP, Durek T, Craik DJ. Inside Cover: Application and Structural Analysis of Triazole‐Bridged Disulfide Mimetics in Cyclic Peptides (Angew. Chem. Int. Ed. 28/2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/anie.202006713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Andrew M. White
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Simon J. Veer
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Guojie Wu
- ARC Centre of Excellence in Advanced Molecular Imaging Department of Biochemistry and Molecular Biology Biomedicine Discovery Institute Monash University Clayton VIC 3800 Australia
| | - Peta J. Harvey
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Kuok Yap
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Gordon J. King
- The Centre for Microscopy and Microanalysis The University of Queensland Brisbane QLD 4072 Australia
| | - Joakim E. Swedberg
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Conan K. Wang
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Ruby H. P. Law
- ARC Centre of Excellence in Advanced Molecular Imaging Department of Biochemistry and Molecular Biology Biomedicine Discovery Institute Monash University Clayton VIC 3800 Australia
| | - Thomas Durek
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - David J. Craik
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
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27
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White AM, Veer SJ, Wu G, Harvey PJ, Yap K, King GJ, Swedberg JE, Wang CK, Law RHP, Durek T, Craik DJ. Innentitelbild: Application and Structural Analysis of Triazole‐Bridged Disulfide Mimetics in Cyclic Peptides (Angew. Chem. 28/2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andrew M. White
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Simon J. Veer
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Guojie Wu
- ARC Centre of Excellence in Advanced Molecular Imaging Department of Biochemistry and Molecular Biology Biomedicine Discovery Institute Monash University Clayton VIC 3800 Australia
| | - Peta J. Harvey
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Kuok Yap
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Gordon J. King
- The Centre for Microscopy and Microanalysis The University of Queensland Brisbane QLD 4072 Australia
| | - Joakim E. Swedberg
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Conan K. Wang
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Ruby H. P. Law
- ARC Centre of Excellence in Advanced Molecular Imaging Department of Biochemistry and Molecular Biology Biomedicine Discovery Institute Monash University Clayton VIC 3800 Australia
| | - Thomas Durek
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - David J. Craik
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
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28
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Yin H, Huang YH, Deprey K, Condon ND, Kritzer JA, Craik DJ, Wang CK. Cellular Uptake and Cytosolic Delivery of a Cyclic Cystine Knot Scaffold. ACS Chem Biol 2020; 15:1650-1661. [PMID: 32315152 DOI: 10.1021/acschembio.0c00297] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclotides are macrocyclic peptides with exceptionally stable structures and have been reported to penetrate cells, making them promising scaffolds for the delivery of inhibitory peptides to target intracellular proteins. However, their cellular uptake and cytosolic localization have been poorly understood until now, which has limited their therapeutic potential. In this study, the recently developed chloroalkane penetration assay was combined with established assays to characterize the cellular uptake and cytosolic delivery of the prototypic cyclotide, kalata B1. We show that kalata B1 enters the cytosol at low efficiency. A structure-activity study of residues in loop 6 showed that some modifications, such as increasing cationic residue content, did not affect delivery efficiency, whereas others, including introducing a single hydrophobic amino acid, did significantly improve cytosolic delivery. Our results provide a foundation for the further development of a structurally unique class of scaffolds for the delivery of therapeutic cargoes into cells.
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Affiliation(s)
- Huawu Yin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kirsten Deprey
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Nicholas D. Condon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joshua A. Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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29
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White AM, Veer SJ, Wu G, Harvey PJ, Yap K, King GJ, Swedberg JE, Wang CK, Law RHP, Durek T, Craik DJ. Application and Structural Analysis of Triazole‐Bridged Disulfide Mimetics in Cyclic Peptides. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003435] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Andrew M. White
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Simon J. Veer
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Guojie Wu
- ARC Centre of Excellence in Advanced Molecular Imaging Department of Biochemistry and Molecular Biology Biomedicine Discovery Institute Monash University Clayton VIC 3800 Australia
| | - Peta J. Harvey
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Kuok Yap
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Gordon J. King
- The Centre for Microscopy and Microanalysis The University of Queensland Brisbane QLD 4072 Australia
| | - Joakim E. Swedberg
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Conan K. Wang
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Ruby H. P. Law
- ARC Centre of Excellence in Advanced Molecular Imaging Department of Biochemistry and Molecular Biology Biomedicine Discovery Institute Monash University Clayton VIC 3800 Australia
| | - Thomas Durek
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - David J. Craik
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
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30
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White AM, Veer SJ, Wu G, Harvey PJ, Yap K, King GJ, Swedberg JE, Wang CK, Law RHP, Durek T, Craik DJ. Application and Structural Analysis of Triazole‐Bridged Disulfide Mimetics in Cyclic Peptides. Angew Chem Int Ed Engl 2020; 59:11273-11277. [DOI: 10.1002/anie.202003435] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Andrew M. White
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Simon J. Veer
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Guojie Wu
- ARC Centre of Excellence in Advanced Molecular Imaging Department of Biochemistry and Molecular Biology Biomedicine Discovery Institute Monash University Clayton VIC 3800 Australia
| | - Peta J. Harvey
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Kuok Yap
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Gordon J. King
- The Centre for Microscopy and Microanalysis The University of Queensland Brisbane QLD 4072 Australia
| | - Joakim E. Swedberg
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Conan K. Wang
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Ruby H. P. Law
- ARC Centre of Excellence in Advanced Molecular Imaging Department of Biochemistry and Molecular Biology Biomedicine Discovery Institute Monash University Clayton VIC 3800 Australia
| | - Thomas Durek
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - David J. Craik
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
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31
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Affiliation(s)
- Benjamin J. Tombling
- Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australien
| | - Conan K. Wang
- Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australien
| | - David J. Craik
- Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australien
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32
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Tombling BJ, Wang CK, Craik DJ. EGF-like and Other Disulfide-rich Microdomains as Therapeutic Scaffolds. Angew Chem Int Ed Engl 2020; 59:11218-11232. [PMID: 31867866 DOI: 10.1002/anie.201913809] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Indexed: 12/20/2022]
Abstract
Disulfide bonds typically introduce conformational constraints into peptides and proteins, conferring improved biopharmaceutical properties and greater therapeutic potential. In our opinion, disulfide-rich microdomains from proteins are potentially a rich and under-explored source of drug leads. A survey of the UniProt protein database shows that these domains are widely distributed throughout the plant and animal kingdoms, with the EGF-like domain being the most abundant of these domains. EGF-like domains exhibit large diversity in their disulfide bond topologies and calcium binding modes, which we classify in detail here. We found that many EGF-like domains are associated with disease phenotypes, and the interactions they mediate are potential therapeutic targets. Indeed, EGF-based therapeutic leads have been identified, and we further propose that these domains can be optimized to expand their therapeutic potential using chemical design strategies. This Review highlights the potential of disulfide-rich microdomains as future peptide therapeutics.
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Affiliation(s)
- Benjamin J Tombling
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
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33
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Henriques ST, Peacock H, Benfield AH, Wang CK, Craik DJ. Is the Mirror Image a True Reflection? Intrinsic Membrane Chirality Modulates Peptide Binding. J Am Chem Soc 2019; 141:20460-20469. [PMID: 31765148 DOI: 10.1021/jacs.9b11194] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Peptides with pharmaceutical activities are attractive drug leads, and knowledge of their mode-of-action is essential for translation into the clinic. Comparison of native and enantiomeric peptides has long been used as a powerful approach to discriminate membrane- or receptor-mediated modes-of-action on the basis of the assumption that interactions with cell membranes are independent of peptide chirality. Here, we revisit this paradigm with the cyclotide kalata B1, a drug scaffold with intrinsic membrane-binding activity whose enantiomer is less potent than native peptide. To investigate this chirality dependence, we compared peptide-lipid binding using mirror image model membranes. We synthesized phospholipids with non-natural chirality and demonstrate that native kalata B1 binds with higher affinity to phospholipids with chirality found in eukaryotic membranes. This study shows for the first time that the chiral environment of lipid bilayers can modulate the function of membrane-active peptides and challenges the view that peptide-lipid interactions are achiral.
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Affiliation(s)
- Sónia Troeira Henriques
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia.,School of Biomedical Sciences, Faculty of Health, Institute of Health & Biomedical Innovation , Queensland University of Technology , Translational Research Institute , Brisbane , Queensland 4102 , Australia
| | - Hayden Peacock
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Aurélie H Benfield
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia.,School of Biomedical Sciences, Faculty of Health, Institute of Health & Biomedical Innovation , Queensland University of Technology , Translational Research Institute , Brisbane , Queensland 4102 , Australia
| | - Conan K Wang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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34
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Affiliation(s)
- Huawu Yin
- Institute for Molecular BioscienceThe University of Queensland Brisbane Queensland 4072 Australia
| | - David J. Craik
- Institute for Molecular BioscienceThe University of Queensland Brisbane Queensland 4072 Australia
| | - Conan K. Wang
- Institute for Molecular BioscienceThe University of Queensland Brisbane Queensland 4072 Australia
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35
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Chambers C, Cutler P, Huang Y, Goodchild JA, Blythe J, Wang CK, Bigot A, Kaas Q, Craik DJ, Sabbadin D, Earley FG. Insecticidal spider toxins are high affinity positive allosteric modulators of the nicotinic acetylcholine receptor. FEBS Lett 2019; 593:1336-1350. [DOI: 10.1002/1873-3468.13435] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 04/30/2019] [Accepted: 05/08/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Chris Chambers
- Syngenta Jealott's Hill Research Centre Bracknell Berkshire UK
| | - Penny Cutler
- Syngenta Jealott's Hill Research Centre Bracknell Berkshire UK
| | - Yen‐Hua Huang
- Institute for Molecular Bioscience the University of Queensland Brisbane Queensland Australia
| | | | - Judith Blythe
- Syngenta Jealott's Hill Research Centre Bracknell Berkshire UK
| | - Conan K. Wang
- Institute for Molecular Bioscience the University of Queensland Brisbane Queensland Australia
| | | | - Quentin Kaas
- Institute for Molecular Bioscience the University of Queensland Brisbane Queensland Australia
| | - David J. Craik
- Institute for Molecular Bioscience the University of Queensland Brisbane Queensland Australia
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36
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Affiliation(s)
- Huawu Yin
- Institute for Molecular Bioscience The University of Queensland Brisbane Queensland 4072 Australia
| | - David J. Craik
- Institute for Molecular Bioscience The University of Queensland Brisbane Queensland 4072 Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience The University of Queensland Brisbane Queensland 4072 Australia
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37
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Abstract
Disulfide-rich peptides are a class of molecules for which NMR spectroscopy has been the primary tool for structural characterization. Here, we explore whether the process can be achieved by using structural information encoded in chemical shifts. We examine (i) a representative set of five cyclic disulfide-rich peptides that have high-resolution NMR and X-ray structures and (ii) a larger set of 100 disulfide-rich peptides from the PDB. Accuracy of the calculated structures was dependent on the methods used for searching through conformational space and for identifying native conformations. Although Hα chemical shifts could be predicted reasonably well using SHIFTX, agreement between predicted and experimental chemical shifts was sufficient for identifying native conformations for only some peptides in the representative set. Combining chemical shift data with the secondary structure information and potential energy calculations improved the ability to identify native conformations. Additional use of sparse distance restraints or homology information to restrict the search space also improved the resolution of the calculated structures. This study demonstrates that abbreviated methods have potential for elucidation of peptide structures to high resolution and further optimization of these methods, e.g., improvement in chemical shift prediction accuracy, will likely help transition these methods into the mainstream of disulfide-rich peptide structural biology.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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38
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Wu X, Huang YH, Kaas Q, Harvey PJ, Wang CK, Tae HS, Adams DJ, Craik DJ. Backbone cyclization of analgesic conotoxin gexiva facilitates direct folding of the ribbon isomer. Toxicon 2019. [DOI: 10.1016/j.toxicon.2018.10.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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39
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Ojeda PG, Henriques ST, Pan Y, Nicolazzo JA, Craik DJ, Wang CK. Lysine to arginine mutagenesis of chlorotoxin enhances its cellular uptake. Biopolymers 2018; 108. [PMID: 28459137 DOI: 10.1002/bip.23025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/31/2017] [Accepted: 04/10/2017] [Indexed: 12/14/2022]
Abstract
Chlorotoxin (CTX), a disulfide-rich peptide from the scorpion Leiurus quinquestriatus, has several promising biopharmaceutical properties, including preferential affinity for certain cancer cells, high serum stability, and cell penetration. These properties underpin its potential for use as a drug design scaffold, especially for the treatment of cancer; indeed, several analogs of CTX have reached clinical trials. Here, we focus on its ability to internalize into cells-a trait associated with a privileged subclass of peptides called cell-penetrating peptides-and whether it can be improved through conservative substitutions. Mutants of CTX were made using solid-phase peptide synthesis and internalization into human cervical carcinoma (HeLa) cells was monitored by fluorescence and confocal microscopy. CTX_M1 (ie, [K15R/K23R]CTX) and CTX_M2 (ie, [K15R/K23R/Y29W]CTX) mutants showed at least a twofold improvement in uptake compared to CTX. We further showed that these mutants internalize into HeLa cells largely via an energy-dependent mechanism. Importantly, the mutants have high stability, remaining intact in serum for over 24 h; thus, retaining the characteristic stability of their parent peptide. Overall, we have shown that simple conservative substitutions can enhance the cellular uptake of CTX, suggesting that such type of mutations might be useful for improving uptake of other peptide toxins.
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Affiliation(s)
- Paola G Ojeda
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca, Talca, Chile
| | - Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Yijun Pan
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Joseph A Nicolazzo
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
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40
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Ramalho SD, Wang CK, King GJ, Byriel KA, Huang YH, Bolzani VS, Craik DJ. Synthesis, Racemic X-ray Crystallographic, and Permeability Studies of Bioactive Orbitides from Jatropha Species. J Nat Prod 2018; 81:2436-2445. [PMID: 30345754 DOI: 10.1021/acs.jnatprod.8b00447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Orbitides are small cyclic peptides with a diverse range of therapeutic bioactivities. They are produced by many plant species, including those of the Jatropha genus. Here, the objective was to provide new structural information on orbitides to complement the growing knowledge base on orbitide sequences and activities by focusing on three Jatropha orbitides: ribifolin (1), pohlianin C (7), and jatrophidin (12). To determine three-dimensional structures, racemic crystallography, an emerging structural technique that enables rapid crystallization of biomolecules by combining equal amounts of the two enantiomers, was used. The high-resolution structure of ribifolin (0.99 Å) was elucidated from its racemate and showed it was identical to the structure crystallized from its l-enantiomer only (1.35 Å). Racemic crystallography was also used to elucidate high-resolution structures of pohlianin C (1.20 Å) and jatrophidin (1.03 Å), for which there was difficulty forming crystals without using racemic mixtures. The structures were used to interpret membrane permeability data in PAMPA and a Caco-2 cell assay, showing they had poor permeability. Overall, the results show racemic crystallography can be used to obtain high-resolution structures of orbitides and is useful when enantiopure samples are difficult to crystallize or solution structures from NMR are of low resolution.
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Affiliation(s)
- Suelem D Ramalho
- Institute of Chemistry , São Paulo State University-UNESP , Araraquara , São Paulo 14800-060 , Brazil
| | - Conan K Wang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Gordon J King
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Karl A Byriel
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Vanderlan S Bolzani
- Institute of Chemistry , São Paulo State University-UNESP , Araraquara , São Paulo 14800-060 , Brazil
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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41
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Wang CK, Ghani HA, Bundock A, Weidmann J, Harvey PJ, Edwards IA, Schroeder CI, Swedberg JE, Craik DJ. Calcium-Mediated Allostery of the EGF Fold. ACS Chem Biol 2018; 13:1659-1667. [PMID: 29715432 DOI: 10.1021/acschembio.8b00291] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The epidermal growth factor (EGF)-like domain is one of the most abundant disulfide-containing domains in nature and is involved in many cellular processes critical to life. Although many EGF-like domains participate in calcium-dependent functions by responding to the local calcium concentration, little is known about how this responsiveness is programmed at the molecular level. Here, we reveal the structural and environmental determinants underpinning the folding of a synthetic analogue of the EGF-A domain (from the low-density lipoprotein receptor). We show that calcium sensitivity is enabled by an allosteric folding pathway, in which calcium binding is connected to the peptide core through local inter-residue interactions. In the absence of calcium, the fold favors disorder because the inherently weak core is insufficient to stabilize the active form, resulting in substantial loss in activity of 2 orders of magnitude. The EGF-A fold, which can freely transition between active and disordered states, is volatile, and we found it to be intolerant of mutations, unlike other disulfide-rich peptides that have been used as stabilizing frameworks. This volatility is beneficial for modularity/plasticity and appears to have evolved for such a purpose, allowing cellular pathways to sense and respond to environmental cues.
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Affiliation(s)
- Conan K. Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Hafiza Abdul Ghani
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Anna Bundock
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joachim Weidmann
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Peta J. Harvey
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ingrid A. Edwards
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Christina I. Schroeder
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joakim E. Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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Affiliation(s)
- Conan K. Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joakim E. Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Peta J. Harvey
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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Ye LH, Wang CK, Zhang HC, Liu ZQ, Zheng HW. [Clinicopathologic features of drug-induced vanishing bile duct syndrome]. Zhonghua Gan Zang Bing Za Zhi 2018; 25:317-320. [PMID: 28494557 DOI: 10.3760/cma.j.issn.1007-3418.2017.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Vanishing bile duct syndrome (VBDS) manifests as progressive destruction and disappearance of the intrahepatic bile duct caused by various factors and cholestasis. VBDS associated with drug-induced liver injury (D-VBDS) is an important etiology of VBDS, and immune disorder or immune imbalance may be the main pathogenesis. According to its clinical symptoms, serological markers, and course of the disease, D-VBDS is classified into major form and minor form, and its clinical features are based on various pathomorphological findings. Its prognosis is associated various factors including regeneration of bile duct cells, number of bile duct injuries, level and range of bile duct injury, bile duct proliferation, and compensatory shunt of bile duct branches. This disease has various clinical outcomes; most patients have good prognosis after drug withdrawal, and some patients may experience cholestatic cirrhosis, liver failure, and even death. Due to the clinical manifestation and biochemical changes are similar to the primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC), it need to identify by clinical physician.
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Affiliation(s)
- L H Ye
- Department of Pathology, Shijiazhuang Fifth Hospital, Shijiazhuang 050021, China
| | - C K Wang
- Heibei University of Chinese Traditional Medicine, Shijiazhuang 050200, China
| | - H C Zhang
- Department of Pathology, Shijiazhuang Fifth Hospital, Shijiazhuang 050021, China
| | - Z Q Liu
- Department of Pathology, Shijiazhuang Fifth Hospital, Shijiazhuang 050021, China
| | - H W Zheng
- Hepatology center, Shijiazhuang Fifth Hospital, Shijiazhuang 050021, China
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Wu X, Huang YH, Kaas Q, Harvey PJ, Wang CK, Tae HS, Adams DJ, Craik DJ. Backbone cyclization of analgesic conotoxin GeXIVA facilitates direct folding of the ribbon isomer. J Biol Chem 2017; 292:17101-17112. [PMID: 28851841 DOI: 10.1074/jbc.m117.808386] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Indexed: 12/20/2022] Open
Abstract
Conotoxin GeXIVA inhibits the α9α10 nicotinic acetylcholine receptor (nAChR) and is analgesic in animal models of pain. α-Conotoxins have four cysteines that can have three possible disulfide connectivities: globular (CysI-CysIII and CysII-CysIV), ribbon (CysI-CysIV and CysII-CysIII), or bead (CysI-CysII and CysIII-CysIV). Native α-conotoxins preferably adopt the globular connectivity, and previous studies of α-conotoxins have focused on the globular isomers as the ribbon and bead isomers typically have lower potency at nAChRs than the globular form. A recent report showed that the bead and ribbon isomers of GeXIVA are more potent than the globular isomer, with low nanomolar half-maximal inhibitory concentrations (IC50). Despite this high potency, the therapeutic potential of GeXIVA is limited, because like most peptides, it is susceptible to proteolytic degradation and is challenging to synthesize in high yield. Here we used backbone cyclization as a strategy to improve the folding yield as well as increase the serum stability of ribbon GeXIVA while preserving activity at the α9α10 nAChR. Specifically, cyclization of ribbon GeXIVA with a two-residue linker maintained the biological activity at the human α9α10 nAChR and improved stability in human serum. Short linkers led to selective formation of the ribbon disulfide isomer without requiring orthogonal protection. Overall, this study highlights the value of backbone cyclization in directing folding, improving yields, and stabilizing conotoxins with therapeutic potential.
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Affiliation(s)
- Xiaosa Wu
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Yen-Hua Huang
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Quentin Kaas
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Peta J Harvey
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Conan K Wang
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Han-Shen Tae
- the Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - David J Adams
- the Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - David J Craik
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
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Swedberg JE, Li CY, de Veer SJ, Wang CK, Craik DJ. Design of Potent and Selective Cathepsin G Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold. J Med Chem 2017; 60:658-667. [PMID: 28045523 DOI: 10.1021/acs.jmedchem.6b01509] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Neutrophils are directly responsible for destroying invading pathogens via reactive oxygen species, antimicrobial peptides, and neutrophil serine proteases (NSPs). Imbalance between NSP activity and endogenous protease inhibitors is associated with chronic inflammatory disorders, and engineered inhibitors of NSPs are a potential therapeutic pathway. In this study we characterized the extended substrate specificity (P4-P1) of the NSP cathepsin G using a peptide substrate library. Substituting preferred cathepsin G substrate sequences into sunflower trypsin inhibitor-1 (SFTI-1) produced a potent cathepsin G inhibitor (Ki = 0.89 nM). Cathepsin G's P2' preference was determined by screening against a P2' diverse SFTI-based library, and the most preferred residue at P2' was combined in SFTI-1 with a preferred substrate sequence (P4-P2) and a nonproteinogenic P1 residue (4-guanidyl-l-phenylalanine) to produce a potent (Ki = 1.6 nM) and the most selective (≥360-fold) engineered cathepsin G inhibitor reported to date. This compound is a promising lead for further development of cathepsin G inhibitors targeting chronic inflammatory disorders.
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Affiliation(s)
- Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Choi Yi Li
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
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Craik DJ, Wang CK. Forward for ICCP2015 issue of Biopolymers Peptide Science. Biopolymers 2016; 106:772-773. [PMID: 27878993 DOI: 10.1002/bip.22989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Qld, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Qld, Australia
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Wang CK, Craik DJ. Cyclic peptide oral bioavailability: Lessons from the past. Biopolymers 2016; 106:901-909. [DOI: 10.1002/bip.22878] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/19/2016] [Accepted: 05/04/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland; Brisbane Queensland 4072 Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland; Brisbane Queensland 4072 Australia
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48
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Kwon S, Bosmans F, Kaas Q, Cheneval O, Conibear AC, Rosengren KJ, Wang CK, Schroeder CI, Craik DJ. Efficient enzymatic cyclization of an inhibitory cystine knot-containing peptide. Biotechnol Bioeng 2016; 113:2202-12. [PMID: 27093300 DOI: 10.1002/bit.25993] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/04/2016] [Accepted: 04/11/2016] [Indexed: 01/01/2023]
Abstract
Disulfide-rich peptides isolated from cone snails are of great interest as drug leads due to their high specificity and potency toward therapeutically relevant ion channels and receptors. They commonly contain the inhibitor cystine knot (ICK) motif comprising three disulfide bonds forming a knotted core. Here we report the successful enzymatic backbone cyclization of an ICK-containing peptide κ-PVIIA, a 27-amino acid conopeptide from Conus purpurascens, using a mutated version of the bacterial transpeptidase, sortase A. Although a slight loss of activity was observed compared to native κ-PVIIA, cyclic κ-PVIIA is a functional peptide that inhibits the Shaker voltage-gated potassium (Kv) channel. Molecular modeling suggests that the decrease in potency may be related to the loss of crucial, but previously unidentified electrostatic interactions between the N-terminus of the peptide and the Shaker channel. This hypothesis was confirmed by testing an N-terminally acetylated κ-PVIIA, which shows a similar decrease in activity. We also investigated the conformational dynamics and hydrogen bond network of cyc-PVIIA, both of which are important factors to be considered for successful cyclization of peptides. We found that cyc-PVIIA has the same conformational dynamics, but different hydrogen bond network compared to those of κ-PVIIA. The ability to efficiently cyclize ICK peptides using sortase A will enable future protein engineering for this class of peptides and may help in the development of novel therapeutic molecules. Biotechnol. Bioeng. 2016;113: 2202-2212. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Soohyun Kwon
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Qld, 4072, Australia
| | - Frank Bosmans
- Department of Physiology and Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Quentin Kaas
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Qld, 4072, Australia
| | - Olivier Cheneval
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Qld, 4072, Australia
| | - Anne C Conibear
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Qld, 4072, Australia
| | - K Johan Rosengren
- The University of Queensland, School of Biomedical Sciences, Brisbane, Qld, Australia
| | - Conan K Wang
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Qld, 4072, Australia
| | - Christina I Schroeder
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Qld, 4072, Australia.
| | - David J Craik
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Qld, 4072, Australia.
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Wang CK, King GJ, Conibear AC, Ramos MC, Chaousis S, Henriques ST, Craik DJ. Mirror Images of Antimicrobial Peptides Provide Reflections on Their Functions and Amyloidogenic Properties. J Am Chem Soc 2016; 138:5706-13. [PMID: 27064294 DOI: 10.1021/jacs.6b02575] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Enantiomeric forms of BTD-2, PG-1, and PM-1 were synthesized to delineate the structure and function of these β-sheet antimicrobial peptides. Activity and lipid-binding assays confirm that these peptides act via a receptor-independent mechanism involving membrane interaction. The racemic crystal structure of BTD-2 solved at 1.45 Å revealed a novel oligomeric form of β-sheet antimicrobial peptides within the unit cell: an antiparallel trimer, which we suggest might be related to its membrane-active form. The BTD-2 oligomer extends into a larger supramolecular state that spans the crystal lattice, featuring a steric-zipper motif that is common in structures of amyloid-forming peptides. The supramolecular structure of BTD-2 thus represents a new mode of fibril-like assembly not previously observed for antimicrobial peptides, providing structural evidence linking antimicrobial and amyloid peptides.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Gordon J King
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Anne C Conibear
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Mariana C Ramos
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Stephanie Chaousis
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
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Wang CK, Stalmans S, De Spiegeleer B, Craik DJ. Biodistribution of the cyclotide MCoTI-II, a cyclic disulfide-rich peptide drug scaffold. J Pept Sci 2016; 22:305-10. [PMID: 26929247 DOI: 10.1002/psc.2862] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 12/28/2022]
Abstract
Disulfide-rich macrocyclic peptides are promising templates for drug design because of their unique topology and remarkable stability. However, little is known about their pharmacokinetics. In this study, we characterize the biodistribution in mice of Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II), a cyclic three-disulfide-containing peptide that has been used in a number of studies as a drug scaffold. The distribution of MCoTI-II was compared with that of chlorotoxin, which is a four-disulfide-containing peptide that has been used to develop brain tumor imaging agents; dermorphin, which is a disulfide-less peptide; and bovine serum albumin, a large protein. Both MCoTI-II and chlorotoxin distributed predominantly to the serum and kidneys, confirming that they are stable in serum and suggesting that they are eliminated from the blood through renal clearance. Although cell-penetrating peptides have been reported to be able to transport across the blood-brain barrier, MCoTI-II, which is a cell-penetrating peptide, showed no uptake into the brain. The uptake of chlorotoxin was higher than that of MCoTI-II but lower than that of dermorphin, which is considered to have low uptake into the brain. This study provides insight into the behavior of disulfide-rich peptides in vivo. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Sofie Stalmans
- Drug Quality and Registration (DruQuaR) Group, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Bart De Spiegeleer
- Drug Quality and Registration (DruQuaR) Group, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
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