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Gao X, Kaluarachchi H, Zhang Y, Hwang S, Hannoush RN. A phage-displayed disulfide constrained peptide discovery platform yields novel human plasma protein binders. PLoS One 2024; 19:e0299804. [PMID: 38547072 PMCID: PMC10977726 DOI: 10.1371/journal.pone.0299804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/15/2024] [Indexed: 04/02/2024] Open
Abstract
Disulfide constrained peptides (DCPs) show great potential as templates for drug discovery. They are characterized by conserved cysteine residues that form intramolecular disulfide bonds. Taking advantage of phage display technology, we designed and generated twenty-six DCP phage libraries with enriched molecular diversity to enable the discovery of ligands against disease-causing proteins of interest. The libraries were designed based on five DCP scaffolds, namely Momordica charantia 1 (Mch1), gurmarin, Asteropsin-A, antimicrobial peptide-1 (AMP-1), and potato carboxypeptidase inhibitor (CPI). We also report optimized workflows for screening and producing synthetic and recombinant DCPs. Examples of novel DCP binders identified against various protein targets are presented, including human IgG Fc, serum albumin, vascular endothelial growth factor-A (VEGF-A) and platelet-derived growth factor (PDGF). We identified DCPs against human IgG Fc and serum albumin with sub-micromolar affinity from primary panning campaigns, providing alternative tools for potential half-life extension of peptides and small protein therapeutics. Overall, the molecular diversity of the DCP scaffolds included in the designed libraries, coupled with their distinct biochemical and biophysical properties, enables efficient and robust identification of de novo binders to drug targets of therapeutic relevance.
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Affiliation(s)
- Xinxin Gao
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, United States of America
- Department of Peptide Therapeutics, Genentech, South San Francisco, California, United States of America
| | - Harini Kaluarachchi
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, United States of America
| | - Yingnan Zhang
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, United States of America
- Department of Biological Chemistry, Genentech, South San Francisco, California, United States of America
| | - Sunhee Hwang
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, United States of America
- Department of Peptide Therapeutics, Genentech, South San Francisco, California, United States of America
| | - Rami N. Hannoush
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, United States of America
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2
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Tran HNT, McMahon KL, Deuis JR, Vetter I, Schroeder CI. Structural and functional insights into the inhibition of human voltage-gated sodium channels by μ-conotoxin KIIIA disulfide isomers. J Biol Chem 2022; 298:101728. [PMID: 35167877 PMCID: PMC8927997 DOI: 10.1016/j.jbc.2022.101728] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 12/13/2022] Open
Abstract
μ-Conotoxins are components of cone snail venom, well-known for their analgesic activity through potent inhibition of voltage-gated sodium channel (NaV) subtypes, including NaV1.7. These small, disulfide-rich peptides are typically stabilized by three disulfide bonds arranged in a ‘native’ CysI-CysIV, CysII-CysV, CysIII-CysVI pattern of disulfide connectivity. However, μ-conotoxin KIIIA, the smallest and most studied μ-conotoxin with inhibitory activity at NaV1.7, forms two distinct disulfide bond isomers during thermodynamic oxidative folding, including Isomer 1 (CysI-CysV, CysII-CysIV, CysIII-CysVI) and Isomer 2 (CysI-CysVI, CysII-CysIV, CysIII-CysV), but not the native μ-conotoxin arrangement. To date, there has been no study on the structure and activity of KIIIA comprising the native μ-conotoxin disulfide bond arrangement. Here, we evaluated the synthesis, potency, sodium channel subtype selectivity, and 3D structure of the three isomers of KIIIA. Using a regioselective disulfide bond-forming strategy, we synthetically produced the three μ-conotoxin KIIIA isomers displaying distinct bioactivity and NaV subtype selectivity across human NaV channel subtypes 1.2, 1.4, and 1.7. We show that Isomer 1 inhibits NaV subtypes with a rank order of potency of NaV1.4 > 1.2 > 1.7 and Isomer 2 in the order of NaV1.4≈1.2 > 1.7, while the native isomer inhibited NaV1.4 > 1.7≈1.2. The three KIIIA isomers were further evaluated by NMR solution structure analysis and molecular docking with hNaV1.2. Our study highlights the importance of investigating alternate disulfide isomers, as disulfide connectivity affects not only the overall structure of the peptides but also the potency and subtype selectivity of μ-conotoxins targeting therapeutically relevant NaV subtypes.
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Affiliation(s)
- Hue N T Tran
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Kirsten L McMahon
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Jennifer R Deuis
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Irina Vetter
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia; School of Pharmacy, The University of Queensland, Woolloongabba, Queensland, Australia.
| | - Christina I Schroeder
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia; Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA.
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3
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Chakraborty A, Albericio F, de la Torre BG. Chemoselective Disulfide Formation by Thiol-Disulfide Interchange in SIT-Protected Cysteinyl Peptides. J Org Chem 2021; 87:708-712. [PMID: 34910477 DOI: 10.1021/acs.joc.1c02705] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemoselective disulfide formation is accomplished through a thiol-disulfide interchange approach using sec-isoamyl mercaptan (SIT) as an alkyl sulfenyl-protecting group of one of the Cys residues involved in the pairing. SIT has a dual and unique characteristic, acting as a masking group during the synthesis and directing disulfide formation in the presence of a free thiol. This novel approach is illustrated by the synthesis of several peptides of biological interest.
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Affiliation(s)
- Amit Chakraborty
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa.,Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona 08034, Spain.,CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, and Department of Organic Chemistry, University of Barcelona, Barcelona 08028, Spain
| | - Beatriz G de la Torre
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory of Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
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4
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Chakraborty A, Sharma A, Albericio F, de la Torre BG. Disulfide-Based Protecting Groups for the Cysteine Side Chain. Org Lett 2020; 22:9644-9647. [PMID: 33232171 DOI: 10.1021/acs.orglett.0c03705] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Two new disulfide-based protecting groups (SIT and MOT) are proposed for Cys thiol in the substitution of StBu, which is often difficult to remove. Both groups are based on a secondary thiol with a branched point in the β-position for an efficient modulation of its lability and/or stability. This unique structure allows them to be fully compatible with Fmoc/tBu SPPS. At the end of the synthesis, these groups are removed in a straightforward manner with dithiothreitol with some H2O.
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Affiliation(s)
- Amit Chakraborty
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Anamika Sharma
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa.,KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa.,Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), 08034 Barcelona, Spain.,CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain
| | - Beatriz G de la Torre
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
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5
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Saltiel MY, Kuhre RE, Christiansen CB, Eliasen R, Conde-Frieboes KW, Rosenkilde MM, Holst JJ. Sweet Taste Receptor Activation in the Gut Is of Limited Importance for Glucose-Stimulated GLP-1 and GIP Secretion. Nutrients 2017; 9:nu9040418. [PMID: 28441725 PMCID: PMC5409757 DOI: 10.3390/nu9040418] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/11/2017] [Accepted: 04/18/2017] [Indexed: 01/14/2023] Open
Abstract
Glucose stimulates the secretion of the incretin hormones: glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic peptide (GIP). It is debated whether the sweet taste receptor (STR) triggers this secretion. We investigated the role of STR activation for glucose-stimulated incretin secretion from an isolated perfused rat small intestine and whether selective STR activation by artificial sweeteners stimulates secretion. Intra-luminal administration of the STR agonists, acesulfame K (3.85% w/v), but not sucralose (1.25% w/v) and stevioside (2.5% w/v), stimulated GLP-1 secretion (acesulfame K: 31 ± 3 pmol/L vs. 21 ± 2 pmol/L, p < 0.05, n = 6). In contrast, intra-arterial administration of sucralose (10 mM) and stevioside (10 mM), but not acesulfame K, stimulated GLP-1 secretion (sucralose: 51 ± 6 pmol/L vs. 34 ± 4 pmol/L, p < 0.05; stevioside: 54 ± 6 pmol/L vs. 32 ± 2 pmol/L, p < 0.05, n = 6), while 0.1 mM and 1 mM sucralose did not affect the secretion. Luminal glucose (20% w/v) doubled GLP-1 and GIP secretion, but basolateral STR inhibition by gurmarin (2.5 µg/mL) or the inhibition of the transient receptor potential cation channel 5 (TRPM5) by triphenylphosphine oxide (TPPO) (100 µM) did not attenuate the responses. In conclusion, STR activation does not drive GIP/GLP-1 secretion itself, nor does it have a role for glucose-stimulated GLP-1 or GIP secretion.
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Affiliation(s)
- Monika Y Saltiel
- NNF Center for Basic Metabolic Research and Department of Biomedical Sciences, Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej, DK-2200, Copenhagen N, Denmark.
| | - Rune E Kuhre
- NNF Center for Basic Metabolic Research and Department of Biomedical Sciences, Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej, DK-2200, Copenhagen N, Denmark.
| | - Charlotte B Christiansen
- NNF Center for Basic Metabolic Research and Department of Biomedical Sciences, Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej, DK-2200, Copenhagen N, Denmark.
| | - Rasmus Eliasen
- Protein & Peptide Chemistry, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark.
| | | | - Mette M Rosenkilde
- NNF Center for Basic Metabolic Research and Department of Biomedical Sciences, Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej, DK-2200, Copenhagen N, Denmark.
| | - Jens J Holst
- NNF Center for Basic Metabolic Research and Department of Biomedical Sciences, Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej, DK-2200, Copenhagen N, Denmark.
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Synthetic Cystine-Knot Miniproteins - Valuable Scaffolds for Polypeptide Engineering. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 917:121-44. [PMID: 27236555 DOI: 10.1007/978-3-319-32805-8_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Peptides with the cystine-knot architecture, often termed knottins, are promising scaffolds for biomolecular engineering. These unique molecules combine diverse bioactivities with excellent structural, thermal, and proteolytical stability. Being different in the composition and structure of their amino acid backbone, knottins share the same core element, namely cystine knot, which is built by six cysteine residues forming three disulfides upon oxidative folding. This motif ensures a notably rigid framework that highly tolerates both rational and combinatorial changes in the primary structure. Being accessible through recombinant production and total chemical synthesis, cystine-knot miniproteins can be endowed with novel bioactivities by variation of surface-exposed loops and incorporation of non-natural elements within their non-conserved regions towards the generation of tailor-made peptidic compounds. In this chapter the topology of cystine-knot peptides, their synthesis and applications for diagnostics and therapy is discussed.
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Dekan Z, Mobli M, Pennington MW, Fung E, Nemeth E, Alewood PF. Total Synthesis of Human Hepcidin through Regioselective Disulfide-Bond Formation by using the Safety-Catch Cysteine Protecting Group 4,4′-Dimethylsulfinylbenzhydryl. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310103] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Dekan Z, Mobli M, Pennington MW, Fung E, Nemeth E, Alewood PF. Total Synthesis of Human Hepcidin through Regioselective Disulfide-Bond Formation by using the Safety-Catch Cysteine Protecting Group 4,4′-Dimethylsulfinylbenzhydryl. Angew Chem Int Ed Engl 2014; 53:2931-4. [DOI: 10.1002/anie.201310103] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 12/30/2013] [Indexed: 11/08/2022]
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9
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Góngora-Benítez M, Tulla-Puche J, Albericio F. Multifaceted Roles of Disulfide Bonds. Peptides as Therapeutics. Chem Rev 2013; 114:901-26. [DOI: 10.1021/cr400031z] [Citation(s) in RCA: 388] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Miriam Góngora-Benítez
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Judit Tulla-Puche
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
- Department
of Organic Chemistry, University of Barcelona, Barcelona, 08028 Spain
- School of Chemistry & Physics, University of KwaZulu-Natal, 4001 Durban, South Africa
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10
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Chemical synthesis, backbone cyclization and oxidative folding of cystine-knot peptides: promising scaffolds for applications in drug design. Molecules 2012; 17:12533-52. [PMID: 23095896 PMCID: PMC6268209 DOI: 10.3390/molecules171112533] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 09/19/2012] [Accepted: 10/22/2012] [Indexed: 02/03/2023] Open
Abstract
Cystine-knot peptides display exceptional structural, thermal, and biological stability. Their eponymous motif consists of six cysteine residues that form three disulfide bonds, resulting in a notably rigid structural core. Since they highly tolerate either rational or combinatorial changes in their primary structure, cystine knots are considered to be promising frameworks for the development of peptide-based pharmaceuticals. Despite their relatively small size (two to three dozens amino acid residues), the chemical synthesis route is challenging since it involves critical steps such as head-to-tail cyclization and oxidative folding towards the respective bioactive isomer. Herein we describe the topology of cystine-knot peptides, their synthetic availability and briefly discuss potential applications of engineered variants in diagnostics and therapy.
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