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Nazeer N, Kooner N, Ghimire A, Rainey JK, Lubell WD, Meneksedag-Erol D, Ahmed M. Secondary Structure Stabilization of Macrocyclic Antimicrobial Peptides via Cross-Link Swapping. J Med Chem 2024; 67:8693-8707. [PMID: 38771638 DOI: 10.1021/acs.jmedchem.4c00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Lactam cross-links have been employed to stabilize the helical secondary structure and enhance the activity and physiological stability of antimicrobial peptides; however, stabilization of β-sheets via lactamization has not been observed. In the present study, lactams between the side chains of C- and N-terminal residues have been used to stabilize the β-sheet conformation in a short ten-residue analogue of chicken angiogenin-4. Designed using a combination of molecular dynamics simulations and Markov state models, the lactam cross-linked peptides are shown to adopt stabilized β-sheet conformations consistent with simulated structures. Replacement of the peptide side-chain Cys-Cys disulfide by a lactam cross-link enhanced the broad-spectrum antibacterial activity compared to the parent peptide and exhibited greater propensity to induce proinflammatory activity in macrophages. The combination of molecular simulations and conformational and biological analyses of the synthetic peptides provides a useful paradigm for the rational design of therapeutically active peptides with constrained β-sheet structures.
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Affiliation(s)
- Nauman Nazeer
- Department of Chemistry, University of Prince Edward Island, Charlottetown C1A 4P3, Prince Edward Island, Canada
| | - Navjote Kooner
- Department of Chemistry and Biochemistry, Concordia University, Montreal H4B 1R6, Quebec, Canada
| | - Anupama Ghimire
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax B3H 4R2, Nova Scotia, Canada
| | - Jan K Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax B3H 4R2, Nova Scotia, Canada
- Department of Chemistry, Dalhousie University, Halifax B3H 4R2, Nova Scotia, Canada
- School of Biomedical Engineering, Dalhousie University, Halifax B3H 4R2, Nova Scotia, Canada
| | - William D Lubell
- Département de Chimie, Université de Montréal, 1375 Ave. Thérèse-Lavoie-Roux, Montréal H2 V 0B3, Québec, Canada
| | - Deniz Meneksedag-Erol
- Department of Chemistry and Biochemistry, Concordia University, Montreal H4B 1R6, Quebec, Canada
- Department of Chemical and Materials Engineering, Concordia University, Montreal H4B 1R6, Quebec, Canada
| | - Marya Ahmed
- Department of Chemistry, University of Prince Edward Island, Charlottetown C1A 4P3, Prince Edward Island, Canada
- Faculty of Sustainable Design Engineering, University of Prince Edward Island, Charlottetown C1A 4P3, Prince Edward Island, Canada
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2
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Langley DB, Schofield P, Jackson J, Herzog H, Christ D. Crystal structures of human neuropeptide Y (NPY) and peptide YY (PYY). Neuropeptides 2022; 92:102231. [PMID: 35180645 DOI: 10.1016/j.npep.2022.102231] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/18/2022] [Accepted: 02/03/2022] [Indexed: 10/19/2022]
Abstract
Neuropeptide Y (NPY), peptide YY (PYY) and pancreatic polypeptide (PP) form the evolutionarily conserved pancreatic polypeptide family. While the fold is widely utilized in nature, crystal structures remain elusive, particularly for the human forms, with only the structure of a distant avian form of PP reported. Here we utilize a crystallization chaperone (antibody Fab fragment), specifically recognizing the amidated peptide termini, to solve the structures of human NPY and human PYY. Intriguingly, and despite limited sequence identity (~50%), the structure of human PYY closely resembles that of avian PP, highlighting the broad structural conservation of the fold throughout evolution. Specifically, the PYY structure is characterized by a C-terminal amidated α-helix, preceded by a backfolded poly-proline N-terminus, with the termini in close proximity to each other. In contrast, in the structure of human NPY the N-terminal component is disordered, while the helical component of the peptide is observed in a four-helix bundle type arrangement, consistent with a propensity for multimerization suggested by NMR studies.
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Affiliation(s)
- David B Langley
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales 2010, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales 2010, Australia
| | - Jenny Jackson
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales 2010, Australia
| | - Herbert Herzog
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, Australia.
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3
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Ahangarpour M, Kavianinia I, Harris PWR, Brimble MA. Photo-induced radical thiol-ene chemistry: a versatile toolbox for peptide-based drug design. Chem Soc Rev 2021; 50:898-944. [PMID: 33404559 DOI: 10.1039/d0cs00354a] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While the global market for peptide/protein-based therapeutics is witnessing significant growth, the development of peptide drugs remains challenging due to their low oral bioavailability, poor membrane permeability, and reduced metabolic stability. However, a toolbox of chemical approaches has been explored for peptide modification to overcome these obstacles. In recent years, there has been a revival of interest in photoinduced radical thiol-ene chemistry as a powerful tool for the construction of therapeutic peptides.
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Affiliation(s)
- Marzieh Ahangarpour
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand.
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4
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Sánchez-Murcia PA, Ruiz-Santaquiteria M, Toro MA, de Lucio H, Jiménez MÁ, Gago F, Jiménez-Ruiz A, Camarasa MJ, Velázquez S. Comparison of hydrocarbon-and lactam-bridged cyclic peptides as dimerization inhibitors of Leishmania infantum trypanothione reductase. RSC Adv 2015. [DOI: 10.1039/c5ra06853c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Helical peptides stabilizedviaall-hydrocarbon or lactam side-chain bridging were investigated as disruptors ofLeishmania infantumtrypanothione reductase.
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Affiliation(s)
| | | | - Miguel A. Toro
- Departamento de Biología de Sistemas
- Universidad de Alcalá
- Madrid
- Spain
| | - Héctor de Lucio
- Departamento de Biología de Sistemas
- Universidad de Alcalá
- Madrid
- Spain
| | | | - Federico Gago
- Departamento de Ciencias Biomédicas
- Unidad Asociada al CSIC
- Universidad de Alcalá
- Madrid
- Spain
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5
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Domin H, Pięta E, Piergies N, Święch D, Kim Y, Proniewicz LM, Proniewicz E. Neuropeptide Y and its C-terminal fragments acting on Y2 receptor: Raman and SERS spectroscopy studies. J Colloid Interface Sci 2014; 437:111-118. [PMID: 25313473 DOI: 10.1016/j.jcis.2014.09.053] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 09/17/2014] [Accepted: 09/19/2014] [Indexed: 12/12/2022]
Abstract
In this paper, we present spectroscopic studies of neuropeptide Y (NPY) and its native NPY(3-36), NPY(13-36), and NPY(22-36) and mutated acetyl-(Leu(28,31))-NPY(24-36)C-terminal fragments acting on Y2 receptor. Since there is some evidence for the correlation between the SERS patterns and the receptor binding ability, we performed a detailed analysis for these compounds at the metal/water interface using Raman spectroscopy (RS) and surface-enhanced Raman spectroscopy (SERS) methods. Many studies have suggested that interactions of this kind are crucial for a variety of biomedical and biochemical phenomena. The identification of amino acids in these peptide sequences by SERS allowed us to determine which molecular fragments were responsible for the interaction with the silver nanoparticle surface. Our findings demonstrated that in all of the investigated compounds, the NPY(32-36)C-terminal fragment (Thr(32)-Arg(33)-Gln(34)-Arg(35)-Tyr(36)NH2) was involved in the adsorption process onto metal substrate. The results of the present study suggest that the same molecular fragment interacts with the Y2 receptor, what proved the usefulness of the SERS method in the study of these biologically active compounds. The search for analogs acting on Y2 receptor may be important from the viewpoint of possible future clinical applications.
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Affiliation(s)
- Helena Domin
- Department of Neurobiology, Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Kraków, Poland
| | - Ewa Pięta
- Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Kraków, Poland
| | - Natalia Piergies
- Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Kraków, Poland
| | - Dominika Święch
- Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Kraków, Poland
| | - Younkyoo Kim
- Department of Chemistry, Hankuk University of Foreign Studies, Yongin, Kyunggi-Do 449-791, Republic of Korea
| | - Leonard M Proniewicz
- Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Kraków, Poland
| | - Edyta Proniewicz
- Faculty of Foundry Engineering, AGH University of Science and Technology, ul. Reymonta 23, 30-059 Kraków, Poland.
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Strategies for the development of conotoxins as new therapeutic leads. Mar Drugs 2013; 11:2293-313. [PMID: 23812174 PMCID: PMC3736424 DOI: 10.3390/md11072293] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 05/27/2013] [Accepted: 06/06/2013] [Indexed: 11/24/2022] Open
Abstract
Peptide toxins typically bind to their target ion channels or receptors with high potency and selectivity, making them attractive leads for therapeutic development. In some cases the native peptide as it is found in the venom from which it originates can be used directly, but in many instances it is desirable to truncate and/or stabilize the peptide to improve its therapeutic properties. A complementary strategy is to display the key residues that make up the pharmacophore of the peptide toxin on a non-peptidic scaffold, thereby creating a peptidomimetic. This review exemplifies these approaches with peptide toxins from marine organisms, with a particular focus on conotoxins.
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7
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Green BR, Klein BD, Lee HK, Smith MD, Steve White H, Bulaj G. Cyclic analogs of galanin and neuropeptide Y by hydrocarbon stapling. Bioorg Med Chem 2012. [PMID: 23176753 DOI: 10.1016/j.bmc.2012.10.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hydrocarbon stapling is an effective strategy to stabilize the helical conformation of bioactive peptides. Here we describe application of stapling to anticonvulsant neuropeptides, galanin (GAL) and neuropeptide Y (NPY), that are implicated in modulating seizures in the brain. Dicarba bridges were rationally introduced into minimized analogs of GAL and NPY resulting in increased α-helical content, in vitro metabolic stability and n-octanol/water partitioning coefficient (logD). The stapled analogs retained agonist activities towards their respective receptors and suppressed seizures in a mouse model of epilepsy.
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Affiliation(s)
- Brad R Green
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84108, USA.
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8
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Khoo KK, Wilson MJ, Smith BJ, Zhang MM, Gulyas J, Yoshikami D, Rivier JE, Bulaj G, Norton RS. Lactam-stabilized helical analogues of the analgesic μ-conotoxin KIIIA. J Med Chem 2011; 54:7558-66. [PMID: 21962108 DOI: 10.1021/jm200839a] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
μ-Conotoxin KIIIA (μ-KIIIA) blocks mammalian voltage-gated sodium channels (VGSCs) and is a potent analgesic following systemic administration in mice. Previous structure-activity studies of μ-KIIIA identified a helical pharmacophore for VGSC blockade. This suggested a route for designing truncated analogues of μ-KIIIA by incorporating the key residues into an α-helical scaffold. As (i, i+4) lactam bridges constitute a proven approach for stabilizing α-helices, we designed and synthesized six truncated analogues of μ-KIIIA containing single lactam bridges at various locations. The helicity of these lactam analogues was analyzed by NMR spectroscopy, and their activities were tested against mammalian VGSC subtypes Na(V)1.1 through 1.7. Two of the analogues, Ac-cyclo9/13[Asp9,Lys13]KIIIA7-14 and Ac-cyclo9/13[Lys9,Asp13]KIIIA7-14, displayed μM activity against VGSC subtypes Na(V)1.2 and Na(V)1.6; importantly, the subtype selectivity profile for these peptides matched that of μ-KIIIA. Our study highlights structure-activity relationships within these helical mimetics and provides a basis for the design of additional truncated peptides as potential analgesics.
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Affiliation(s)
- Keith K Khoo
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Australia
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Robertson CR, Flynn SP, White HS, Bulaj G. Anticonvulsant neuropeptides as drug leads for neurological diseases. Nat Prod Rep 2011; 28:741-62. [PMID: 21340067 DOI: 10.1039/c0np00048e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Anticonvulsant neuropeptides are best known for their ability to suppress seizures and modulate pain pathways. Galanin, neuropeptide Y, somatostatin, neurotensin, dynorphin, among others, have been validated as potential first-in-class anti-epileptic or/and analgesic compounds in animal models of epilepsy and pain, but their therapeutic potential extends to other neurological indications, including neurodegenerative and psychatric disorders. Disease-modifying properties of neuropeptides make them even more attractive templates for developing new-generation neurotherapeutics. Arguably, efforts to transform this class of neuropeptides into drugs have been limited compared to those for other bioactive peptides. Key challenges in developing neuropeptide-based anticonvulsants are: to engineer optimal receptor-subtype selectivity, to improve metabolic stability and to enhance their bioavailability, including penetration across the blood–brain barrier (BBB). Here, we summarize advances toward developing systemically active and CNS-penetrant neuropeptide analogs. Two main objectives of this review are: (1) to provide an overview of structural and pharmacological properties for selected anticonvulsant neuropeptides and their analogs and (2) to encourage broader efforts to convert these endogenous natural products into drug leads for pain, epilepsy and other neurological diseases.
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Affiliation(s)
- Charles R Robertson
- College of Pharmacy, Department of Medicinal Chemistry, 421 Wakara Way, STE. 360 Salt Lake City, UT 84108, USA
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10
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Norton RS. Mu-conotoxins as leads in the development of new analgesics. Molecules 2010; 15:2825-44. [PMID: 20428082 PMCID: PMC6257286 DOI: 10.3390/molecules15042825] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Revised: 04/06/2010] [Accepted: 04/12/2010] [Indexed: 02/02/2023] Open
Abstract
Voltage-gated sodium channels (VGSCs) contain a specific binding site for a family of cone shell toxins known as mu-conotoxins. As some VGSCs are involved in pain perception and mu-conotoxins are able to block these channels, mu-conotoxins show considerable potential as analgesics. Recent studies have advanced our understanding of the three-dimensional structures and structure-function relationships of the mu-conotoxins, including their interaction with VGSCs. Truncated peptide analogues of the native toxins have been created in which secondary structure elements are stabilized by non-native linkers such as lactam bridges. Ultimately, it would be desirable to capture the favourable analgesic properties of the native toxins, in particular their potency and channel sub-type selectivity, in non-peptide mimetics. Such mimetics would constitute lead compounds in the development of new therapeutics for the treatment of pain.
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Affiliation(s)
- Raymond S Norton
- Walter and Eliza Hall Institute of Medical Research, Victoria, Australia.
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11
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Solid Phase Synthesis and Circular Dichroism Analysis of (i → i + 4) Cyclic Lactam Analogues of Kisspeptin. Int J Pept Res Ther 2008. [DOI: 10.1007/s10989-008-9140-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Bader R, Zerbe O. Are Hormones from the Neuropeptide Y Family Recognized by Their Receptors from the Membrane-Bound State? Chembiochem 2005; 6:1520-34. [PMID: 16038001 DOI: 10.1002/cbic.200400439] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Hormones and many other neurotransmitters, growth factors, odorant molecules, and light all present stimuli for a class of membrane-anchored receptors called G protein-coupled receptors (GPCRs). The GPCRs are the largest family of cell-surface receptors involved in signal transduction. About 1% of all known genes of Drosophila and more than 5% of the genes of Caenorhabditis elegans encode GPCRs. In addition, more than 50% of current therapeutic agents on the market target these receptors. When the enormous biological and pharmaceutical importance of these receptors is considered, it is surprising how little is known about the mechanism with which these receptors recognize their natural ligands. In this review we present a structural approach, utilizing techniques of high-resolution NMR spectroscopy, to address the question of whether peptides from the neuropeptide Y family of neurohormones are recognized directly from solution or from the membrane-bound state. In our studies we discovered that the structures of the membrane-bound species are better correlated to the pharmacological properties of these peptides than the solution structures are. These findings are supported by the observation that many biophysical properties of these peptides seem to be optimized for membrane binding. We finally present a scenario of possible events during receptor recognition.
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Affiliation(s)
- Reto Bader
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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The Solution Structure of a Cyclic Analog of Neuropeptide Y with High Y1 Receptor Affinity by NMR, CD and MD Simulations. Int J Pept Res Ther 2005. [DOI: 10.1007/s10989-004-4708-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Tyndall JDA, Pfeiffer B, Abbenante G, Fairlie DP. Over One Hundred Peptide-Activated G Protein-Coupled Receptors Recognize Ligands with Turn Structure. Chem Rev 2005; 105:793-826. [PMID: 15755077 DOI: 10.1021/cr040689g] [Citation(s) in RCA: 176] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Joel D A Tyndall
- Center for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
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