1
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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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Duffy F, Maheshwari N, Buchete NV, Shields D. Computational Opportunities and Challenges in Finding Cyclic Peptide Modulators of Protein-Protein Interactions. Methods Mol Biol 2019; 2001:73-95. [PMID: 31134568 DOI: 10.1007/978-1-4939-9504-2_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Peptide cyclization can improve stability, conformational constraint, and compactness. However, apart from beta-turn structures, which are well incorporated into cyclic peptides (CPs), many primary peptide structures and functions are markedly altered by cyclization. Accordingly, to mimic linear peptide interfaces with cyclic peptides, it can be beneficial to screen combinatorial cyclic peptide libraries. Computational methods have been developed to screen CPs, but face a number of challenges. Here, we review methods to develop in silico computational libraries, and the potential for screening naturally occurring libraries of CPs. The simplest and most rapid computational pharmacophore methods that estimate peptide three-dimensional structures to be screened versus targets are relatively easy to implement, and while the constraint on structure imposed by cyclization makes them more effective than the same approaches with linear peptides, there are a large number of limiting assumptions. In contrast, full molecular dynamics simulations of cyclic peptide structures not only are costly to implement, but also require careful attention to interpretation, so that not only is the computation time rate limiting, but the interpretation time is also rate limiting due to the analysis of the typically complex underlying conformational space of CPs. A challenge for the field of computational cyclic peptide screening is to bridge this gap effectively. Natural compound libraries of short cyclic peptides, and short cyclized regions of proteins, encoded in the genomes of many organisms present a potential treasure trove of novel functionality which may be screened via combined computational and experimental screening approaches.
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Affiliation(s)
- Fergal Duffy
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Nikunj Maheshwari
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | | | - Denis Shields
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
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3
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Zhao B, Yang D, Wong JH, Wang J, Yin C, Zhu Y, Fan S, Ng TB, Xia J, Li Z. A Thioether-Stabilizedd-Proline-l-Proline-Induced β-Hairpin Peptide of Defensin Segment Increases Its Anti-Candida albicansAbility. Chembiochem 2016; 17:1416-20. [DOI: 10.1002/cbic.201600179] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Bingchuan Zhao
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
| | - Dan Yang
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
| | - Jack Ho Wong
- School of Biomedical Sciences; Faculty of Medicine; The Chinese University of Hong Kong; Shatin Hong Kong SAR China
| | - Jianpeng Wang
- Department of Chemistry; The Chinese University of Hong Kong; Shatin Hong Kong SAR China
| | - Cuiming Yin
- School of Biomedical Sciences; Faculty of Medicine; The Chinese University of Hong Kong; Shatin Hong Kong SAR China
| | - Yuxia Zhu
- Department of Obstetrics and Gynecology; Peking University Shenzhen Hospital; Shenzhen 518036 China
| | - Shangrong Fan
- Department of Obstetrics and Gynecology; Peking University Shenzhen Hospital; Shenzhen 518036 China
| | - Tzi Bun Ng
- School of Biomedical Sciences; Faculty of Medicine; The Chinese University of Hong Kong; Shatin Hong Kong SAR China
| | - Jiang Xia
- Department of Chemistry; The Chinese University of Hong Kong; Shatin Hong Kong SAR China
| | - Zigang Li
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
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4
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Real Fernández F, Di Pisa M, Rossi G, Auberger N, Lequin O, Larregola M, Benchohra A, Mansuy C, Chassaing G, Lolli F, Hayek J, Lavielle S, Rovero P, Mallet JM, Papini AM. Antibody Recognition in multiple sclerosis and rett syndrome using a collection of linear and cyclicN-glucosylated antigenic probes. Biopolymers 2015; 104:560-76. [DOI: 10.1002/bip.22677] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/17/2015] [Accepted: 05/04/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Feliciana Real Fernández
- French-Italian Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, PeptLab (http://www.peptlab.eu)
- Department of Neurosciences, Psychology, Drug Research and Child Health, Section of Pharmaceutical Sciences and Nutraceutics; University of Florence; Via Ugo Schiff 6, 50019 Sesto Fiorentino Italy
| | - Margherita Di Pisa
- Département de Chimie; École Normale Supérieure-PSL Research University; 24 rue Lhomond, Sorbonne Universités, UPMC Univ Paris 06, LBM, 4 place Jussieu, CNRS, UMR 7203 LBM 75005 Paris France
| | - Giada Rossi
- French-Italian Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, PeptLab (http://www.peptlab.eu)
- Department of Neurosciences, Psychology, Drug Research and Child Health, Section of Pharmaceutical Sciences and Nutraceutics; University of Florence; Via Ugo Schiff 6, 50019 Sesto Fiorentino Italy
| | - Nicolas Auberger
- Département de Chimie; École Normale Supérieure-PSL Research University; 24 rue Lhomond, Sorbonne Universités, UPMC Univ Paris 06, LBM, 4 place Jussieu, CNRS, UMR 7203 LBM 75005 Paris France
| | - Olivier Lequin
- Département de Chimie; École Normale Supérieure-PSL Research University; 24 rue Lhomond, Sorbonne Universités, UPMC Univ Paris 06, LBM, 4 place Jussieu, CNRS, UMR 7203 LBM 75005 Paris France
| | - Maud Larregola
- French-Italian Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, PeptLab (http://www.peptlab.eu)
- PeptLab@UCP Platform and Laboratory of Chemical Biology EA4505; University of Cergy-Pontoise; 5 Mail Gay Lussac 95031 Cergy-Pontoise Cedex France
| | - Amina Benchohra
- French-Italian Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, PeptLab (http://www.peptlab.eu)
- Department of Chemistry ‘Ugo Schiff’; University of Florence; Via della Lastruccia 13 50019 Sesto Fiorentino Italy
| | - Christelle Mansuy
- Département de Chimie; École Normale Supérieure-PSL Research University; 24 rue Lhomond, Sorbonne Universités, UPMC Univ Paris 06, LBM, 4 place Jussieu, CNRS, UMR 7203 LBM 75005 Paris France
| | - Gerard Chassaing
- Département de Chimie; École Normale Supérieure-PSL Research University; 24 rue Lhomond, Sorbonne Universités, UPMC Univ Paris 06, LBM, 4 place Jussieu, CNRS, UMR 7203 LBM 75005 Paris France
| | - Francesco Lolli
- French-Italian Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, PeptLab (http://www.peptlab.eu)
- Dipartimento di Scienze Biomediche Sperimentali e Cliniche; University of Florence; Viale Morgagni 50 50134 Firenze Italy
| | - Joussef Hayek
- Child Neuropsychiatry Unit; Azienda Ospedaliera Universitaria Senese (AOUS); 53100 Siena Italy
| | - Solange Lavielle
- Département de Chimie; École Normale Supérieure-PSL Research University; 24 rue Lhomond, Sorbonne Universités, UPMC Univ Paris 06, LBM, 4 place Jussieu, CNRS, UMR 7203 LBM 75005 Paris France
| | - Paolo Rovero
- French-Italian Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, PeptLab (http://www.peptlab.eu)
- Department of Neurosciences, Psychology, Drug Research and Child Health, Section of Pharmaceutical Sciences and Nutraceutics; University of Florence; Via Ugo Schiff 6, 50019 Sesto Fiorentino Italy
| | - Jean-Maurice Mallet
- Département de Chimie; École Normale Supérieure-PSL Research University; 24 rue Lhomond, Sorbonne Universités, UPMC Univ Paris 06, LBM, 4 place Jussieu, CNRS, UMR 7203 LBM 75005 Paris France
| | - Anna Maria Papini
- French-Italian Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, PeptLab (http://www.peptlab.eu)
- PeptLab@UCP Platform and Laboratory of Chemical Biology EA4505; University of Cergy-Pontoise; 5 Mail Gay Lussac 95031 Cergy-Pontoise Cedex France
- Department of Chemistry ‘Ugo Schiff’; University of Florence; Via della Lastruccia 13 50019 Sesto Fiorentino Italy
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5
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Duffy FJ, Devocelle M, Shields DC. Computational approaches to developing short cyclic peptide modulators of protein-protein interactions. Methods Mol Biol 2015; 1268:241-71. [PMID: 25555728 DOI: 10.1007/978-1-4939-2285-7_11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cyclic peptides are a promising class of bioactive molecules potentially capable of modulating "difficult" targets, such as protein-protein interactions. Cyclic peptides have long been used as therapeutics derived from natural product derivatives, but remain an underexplored class of compounds from the perspective of rational drug design, possibly due to the known weaknesses of peptide drugs in general. While cyclic peptides are non"druglike" by the accepted empirical rules, their unique structure may lend itself to both membrane permeability and proteolytic resistance-the main barriers to oral delivery. The constrained shape of cyclic peptides also lends itself better to virtual screening approaches, and new tools and successes in this area have been recently noted. An increasing number of strategies are available, both to generate and screen cyclic peptide libraries, and best practises and current successes are described within. This chapter will describe various computational strategies for virtual screening cyclic peptides, along with known implementations and applications. We will explore the generation and screening of diverse combinatorial virtual libraries, incorporating a range of cyclization strategies and structural modifications. More advanced approaches covered include evolutionary algorithms designed to aid in screening large structural libraries, machine learning approaches, and harnessing bioinformatics resources to bias cyclic peptide virtual libraries towards known bioactive structures.
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Affiliation(s)
- Fergal J Duffy
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
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6
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Auberger N, Pisa MD, Larregola M, Chassaing G, Peroni E, Lavielle S, Papini AM, Lequin O, Mallet JM. Glaser oxidative coupling on peptides: Stabilization of β-turn structure via a 1,3-butadiyne constraint. Bioorg Med Chem 2014; 22:6924-32. [DOI: 10.1016/j.bmc.2014.10.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/13/2014] [Accepted: 10/15/2014] [Indexed: 11/30/2022]
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7
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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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8
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Frankiewicz L, Betti C, Guillemyn K, Tourwé D, Jacquot Y, Ballet S. Stabilisation of a short α
-helical VIP fragment by side chain to side chain cyclisation: a comparison of common cyclisation motifs by circular dichroism. J Pept Sci 2013; 19:423-32. [DOI: 10.1002/psc.2515] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 03/15/2013] [Accepted: 04/08/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Lukasz Frankiewicz
- Department of Organic Chemistry; Vrije Universiteit Brussel; Pleinlaan 2 B-1050 Brussels Belgium
| | - Cecilia Betti
- Department of Organic Chemistry; Vrije Universiteit Brussel; Pleinlaan 2 B-1050 Brussels Belgium
| | - Karel Guillemyn
- Department of Organic Chemistry; Vrije Universiteit Brussel; Pleinlaan 2 B-1050 Brussels Belgium
| | - Dirk Tourwé
- Department of Organic Chemistry; Vrije Universiteit Brussel; Pleinlaan 2 B-1050 Brussels Belgium
| | - Yves Jacquot
- Laboratory of the BioMolécules (LBM), Department of Chemistry, CNRS - UMR 7203; Ecole Normale Supérieure/Université Pierre et Marie Curie Paris 6; 24, rue Lhomond 75231 Paris Cedex 05 France
| | - Steven Ballet
- Department of Organic Chemistry; Vrije Universiteit Brussel; Pleinlaan 2 B-1050 Brussels Belgium
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9
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Chouhan G, James K. Efficient Construction of Proline-Containing β-Turn Mimetic Cyclic Tetrapeptides via CuAAC Macrocyclization. Org Lett 2013; 15:1206-9. [DOI: 10.1021/ol303572t] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Gagan Chouhan
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Keith James
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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10
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Aizpurua JM, Palomo C, Balentová E, Jimenez A, Andreieff E, Sagartzazu-Aizpurua M, Miranda JI, Linden A. Chirality-Driven Folding of Short β-Lactam Pseudopeptides. J Org Chem 2012; 78:224-37. [DOI: 10.1021/jo302368y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jesus M. Aizpurua
- Departamento
de Química
Orgánica-I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal-3,
20018 San Sebastian, Spain
| | - Claudio Palomo
- Departamento de Química Orgánica-I, Joxe Mari Korta R&D Center, Universidad del País Vasco UPV/EHU, Avda Tolosa-72, 20018 San Sebastian, Spain
| | - Eva Balentová
- Departamento
de Química
Orgánica-I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal-3,
20018 San Sebastian, Spain
| | - Azucena Jimenez
- Departamento
de Química
Orgánica-I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal-3,
20018 San Sebastian, Spain
| | - Elena Andreieff
- Departamento
de Química
Orgánica-I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal-3,
20018 San Sebastian, Spain
| | - Maialen Sagartzazu-Aizpurua
- Departamento
de Química
Orgánica-I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal-3,
20018 San Sebastian, Spain
| | - José Ignacio Miranda
- Departamento
de Química
Orgánica-I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal-3,
20018 San Sebastian, Spain
| | - Anthony Linden
- Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190,
CH-8057 Zürich, Switzerland
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11
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Rambarran T, Gonzaga F, Brook MA. Generic, Metal-Free Cross-Linking and Modification of Silicone Elastomers Using Click Ligation. Macromolecules 2012. [DOI: 10.1021/ma202785x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Talena Rambarran
- Department of Chemistry and Chemical
Biology, McMaster University, 1280 Main
Street West, Hamilton,
Ontario, Canada L8S 4M1
| | - Ferdinand Gonzaga
- Department of Chemistry and Chemical
Biology, McMaster University, 1280 Main
Street West, Hamilton,
Ontario, Canada L8S 4M1
| | - Michael A. Brook
- Department of Chemistry and Chemical
Biology, McMaster University, 1280 Main
Street West, Hamilton,
Ontario, Canada L8S 4M1
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