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Karami Y, Murail S, Giribaldi J, Lefranc B, Defontaine F, Lesouhaitier O, Leprince J, de Vries S, Tufféry P. Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization. J Chem Inf Model 2023; 63:6436-6450. [PMID: 37827517 PMCID: PMC10599322 DOI: 10.1021/acs.jcim.3c00865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Indexed: 10/14/2023]
Abstract
Peptides have recently regained interest as therapeutic candidates, but their development remains confronted with several limitations including low bioavailability. Backbone head-to-tail cyclization, i.e., setting a covalent peptide bond linking the last amino acid with the first one, is one effective strategy of peptide-based drug design to stabilize the conformation of bioactive peptides while preserving peptide properties in terms of low toxicity, binding affinity, target selectivity, and preventing enzymatic degradation. Starting from an active peptide, it usually requires the design of a linker of a few amino acids to make it possible to cyclize the peptide, possibly preserving the conformation of the initial peptide and not affecting its activity. However, very little is known about the sequence-structure relationship requirements of designing linkers for peptide cyclization in a rational manner. Recently, we have shown that large-scale data-mining of available protein structures can lead to the precise identification of protein loop conformations, even from remote structural classes. Here, we transpose this approach to linkers, allowing head-to-tail peptide cyclization. First we show that given a linker sequence and the conformation of the linear peptide, it is possible to accurately predict the cyclized peptide conformation. Second, and more importantly, we show that it seems possible to elaborate on the information inferred from protein structures to propose effective candidate linker sequences constrained by length and amino acid composition, providing the first framework for the rational design of head-to-tail cyclization linkers. Finally, we illustrate this for two peptides using a limited set of amino-acids likely not to interfere with peptide function. For a linear peptide derived from Nrf2, the peptide cyclized starting from the experimental structure showed a 26-fold increase in the binding affinity. For urotensin II, a peptide already cyclized by a disulfide bond that exerts a broad array of biological activities, we were able, starting from models of the structure, to design a head-to-tail cyclized peptide, the first synthesized bicyclic 14-residue long urotensin II analogue, showing a retention of in vitro activity. Although preliminary, our results strongly suggest that such an approach has strong potential for cyclic peptide-based drug design.
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Affiliation(s)
- Yasaman Karami
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
| | - Samuel Murail
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
| | - Julien Giribaldi
- Institut
des Biomolécules Max Mousseron, UMR 5247, Université de Montpellier-CNRS, 34293 Montpellier, France
| | - Benjamin Lefranc
- Université
de Rouen Normandie, INSERM U1239 NorDiC, Neuroendocrine, Endocrine and Germinal Differentiation and Communication,
INSERM US51 HeRacLeS, F-76000 Rouen, France
| | - Florian Defontaine
- Université
de Rouen Normandie, UR CBSA, Research Unit
Bacterial Communication and Anti-infectious Strategies, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Université
de Rouen Normandie, UR CBSA, Research Unit
Bacterial Communication and Anti-infectious Strategies, 27000 Evreux, France
| | - Jérôme Leprince
- Université
de Rouen Normandie, INSERM U1239 NorDiC, Neuroendocrine, Endocrine and Germinal Differentiation and Communication,
INSERM US51 HeRacLeS, F-76000 Rouen, France
| | - Sjoerd de Vries
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
| | - Pierre Tufféry
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
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Jin AH, Muttenthaler M, Dutertre S, Himaya SWA, Kaas Q, Craik DJ, Lewis RJ, Alewood PF. Conotoxins: Chemistry and Biology. Chem Rev 2019; 119:11510-11549. [PMID: 31633928 DOI: 10.1021/acs.chemrev.9b00207] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The venom of the marine predatory cone snails (genus Conus) has evolved for prey capture and defense, providing the basis for survival and rapid diversification of the now estimated 750+ species. A typical Conus venom contains hundreds to thousands of bioactive peptides known as conotoxins. These mostly disulfide-rich and well-structured peptides act on a wide range of targets such as ion channels, G protein-coupled receptors, transporters, and enzymes. Conotoxins are of interest to neuroscientists as well as drug developers due to their exquisite potency and selectivity, not just against prey but also mammalian targets, thereby providing a rich source of molecular probes and therapeutic leads. The rise of integrated venomics has accelerated conotoxin discovery with now well over 10,000 conotoxin sequences published. However, their structural and pharmacological characterization lags considerably behind. In this review, we highlight the diversity of new conotoxins uncovered since 2014, their three-dimensional structures and folds, novel chemical approaches to their syntheses, and their value as pharmacological tools to unravel complex biology. Additionally, we discuss challenges and future directions for the field.
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Affiliation(s)
- Ai-Hua Jin
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Markus Muttenthaler
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia.,Institute of Biological Chemistry, Faculty of Chemistry , University of Vienna , 1090 Vienna , Austria
| | - Sebastien Dutertre
- Département des Acides Amines, Peptides et Protéines, Unité Mixte de Recherche 5247, Université Montpellier 2-Centre Nationale de la Recherche Scientifique , Institut des Biomolécules Max Mousseron , Place Eugène Bataillon , 34095 Montpellier Cedex 5 , France
| | - S W A Himaya
- 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
| | - Richard J Lewis
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Paul F Alewood
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
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Denisov SS, Ippel JH, Heinzmann ACA, Koenen RR, Ortega-Gomez A, Soehnlein O, Hackeng TM, Dijkgraaf I. Tick saliva protein Evasin-3 modulates chemotaxis by disrupting CXCL8 interactions with glycosaminoglycans and CXCR2. J Biol Chem 2019; 294:12370-12379. [PMID: 31235521 PMCID: PMC6699855 DOI: 10.1074/jbc.ra119.008902] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/11/2019] [Indexed: 01/22/2023] Open
Abstract
Chemokines are a group of chemotaxis proteins that regulate cell trafficking and play important roles in immune responses and inflammation. Ticks are blood-sucking parasites that secrete numerous immune-modulatory agents in their saliva to evade host immune responses. Evasin-3 is a small salivary protein that belongs to a class of chemokine-binding proteins isolated from the brown dog tick, Rhipicephalus sanguineus. Evasin-3 has been shown to have a high affinity for chemokines CXCL1 and CXCL8 and to diminish inflammation in mice. In the present study, solution NMR spectroscopy was used to investigate the structure of Evasin-3 and its CXCL8–Evasin-3 complex. Evasin-3 is found to disrupt the glycosaminoglycan-binding site of CXCL8 and inhibit the interaction of CXCL8 with CXCR2. Structural data were used to design two novel CXCL8-binding peptides. The linear tEv3 17–56 and cyclic tcEv3 16–56 dPG Evasin-3 variants were chemically synthesized by solid-phase peptide synthesis. The affinity of these newly synthesized variants to CXCL8 was measured by surface plasmon resonance biosensor analysis. The Kd values of tEv3 17–56 and tcEv3 16–56 dPG were 27 and 13 nm, respectively. Both compounds effectively inhibited CXCL8-induced migration of polymorphonuclear neutrophils. The present results suggest utility of synthetic Evasin-3 variants as scaffolds for designing and fine-tuning new chemokine-binding agents that suppress immune responses and inflammation.
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Affiliation(s)
- Stepan S Denisov
- Department of Biochemistry, University of Maastricht, Cardiovascular Research Institute Maastricht, 6229 ER, Maastricht, The Netherlands
| | - Johannes H Ippel
- Department of Biochemistry, University of Maastricht, Cardiovascular Research Institute Maastricht, 6229 ER, Maastricht, The Netherlands
| | - Alexandra C A Heinzmann
- Department of Biochemistry, University of Maastricht, Cardiovascular Research Institute Maastricht, 6229 ER, Maastricht, The Netherlands
| | - Rory R Koenen
- Department of Biochemistry, University of Maastricht, Cardiovascular Research Institute Maastricht, 6229 ER, Maastricht, The Netherlands
| | - Almudena Ortega-Gomez
- Institute for Cardiovascular Prevention, Ludwig Maximilian University, 80336, Munich, Germany
| | - Oliver Soehnlein
- Institute for Cardiovascular Prevention, Ludwig Maximilian University, 80336, Munich, Germany; German Center for Cardiovascular Research, 13316, Berlin, Germany; Partner Site Munich Heart Alliance, 80802 Munich, Germany; Department of Physiology and Pharmacology and Department of Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Tilman M Hackeng
- Department of Biochemistry, University of Maastricht, Cardiovascular Research Institute Maastricht, 6229 ER, Maastricht, The Netherlands
| | - Ingrid Dijkgraaf
- Department of Biochemistry, University of Maastricht, Cardiovascular Research Institute Maastricht, 6229 ER, Maastricht, The Netherlands.
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Boutin JA, Tartar AL, van Dorsselaer A, Vaudry H. General lack of structural characterization of chemically synthesized long peptides. Protein Sci 2019; 28:857-867. [PMID: 30851143 PMCID: PMC6459998 DOI: 10.1002/pro.3601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 01/01/2023]
Abstract
Many peptide chemistry scientists have been reporting extremely interesting work on the basis of chemical peptides for which the only characterization was their purity, mass, and biological activity. It seems slightly overenthusiastic, as many of these structures should be thoroughly characterized first to demonstrate the uniqueness of the structure, as opposed to the uniqueness of the sequence. Among the peptides of identical sequences in the final chemical preparation, what amount of well-folded peptide supports the measured activity? The activity of a peptide preparation cannot prove the purity of the desired peptide. Therefore, greater care should be taken in characterizing peptides, particularly those coming from chemical synthesis. At a time when the pharmaceutical industry is changing its paradigm by moving substantially from small molecules to biologics to better serve patients' needs, it is important to understand the limitations of the descriptions of these products and to start to apply the same "good laboratory practices" to our peptide research. Here, we attempt to delineate how synthetic peptides are described and characterized and what will be needed to describe them in regards to how they are well-folded and homogeneous in their tertiary structure. Older studies were done when the tools were not yet discovered, but more recent publications are still lacking proper descriptions of these peptides. Modern tools of analysis are capable of segregating folded and unfolded peptides, even if the preparation is biologically active.
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Affiliation(s)
- Jean A. Boutin
- Institut de Recherches Internationales Servier50 rue Carnot, 92284, Suresnes‐CedexFrance
| | - André L. Tartar
- Faculté de Pharmacie 3rue du Professeur Laguesse, BP83 ‐ 59006, Lille‐CedexFrance
| | - Alain van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio‐Organique, Département des Sciences AnalytiquesInstitut Pluridisciplinaire Hubert CurienUMR 7178 (CNRS‐UdS), ECPM, 25 rue Becquerel, F67087, Strasbourg‐Cedex 2France
| | - Hubert Vaudry
- Plate‐Forme de Recherche en Imagerie Cellulaire de Normandie (PRIMACEN)Institut de Recherche et d'Innovation Biomédicales (IRIB), Université de Rouen76821, Mont‐Saint‐Aignan CedexFrance
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5
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Discovery of two P-superfamily conotoxins, lt9a and lt9b, with different modifications on voltage-sensitive sodium channels. Toxicon 2017; 134:6-13. [DOI: 10.1016/j.toxicon.2017.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 12/23/2022]
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Molecular Engineering of Conus Peptides as Therapeutic Leads. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1030:229-254. [DOI: 10.1007/978-3-319-66095-0_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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7
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Carstens BB, Swedberg J, Berecki G, Adams DJ, Craik DJ, Clark RJ. Effects of linker sequence modifications on the structure, stability, and biological activity of a cyclic α-conotoxin. Biopolymers 2016; 106:864-875. [DOI: 10.1002/bip.22848] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/28/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Bodil B. Carstens
- Institute for Molecular Bioscience, the University of Queensland; Brisbane Queensland 4072 Australia
- School of Biomedical Sciences; the University of Queensland; Brisbane Queensland 4072 Australia
| | - Joakim Swedberg
- Institute for Molecular Bioscience, the University of Queensland; Brisbane Queensland 4072 Australia
| | - Géza Berecki
- Health Innovations Research Institute, RMIT University; Melbourne Victoria 3083 Australia
| | - David J. Adams
- Health Innovations Research Institute, RMIT University; Melbourne Victoria 3083 Australia
| | - David J. Craik
- Institute for Molecular Bioscience, the University of Queensland; Brisbane Queensland 4072 Australia
| | - Richard J. Clark
- School of Biomedical Sciences; the University of Queensland; Brisbane Queensland 4072 Australia
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9
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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] [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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10
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Wu X, Huang Y, Kaas Q, Craik DJ. Cyclisation of Disulfide‐Rich Conotoxins in Drug Design Applications. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600402] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xiaosa Wu
- Institute for Molecular BioscienceThe University of Queensland306 Carmody Road (Building 80)4072BrisbaneAustralia
| | - Yen‐Hua Huang
- Institute for Molecular BioscienceThe University of Queensland306 Carmody Road (Building 80)4072BrisbaneAustralia
| | - Quentin Kaas
- Institute for Molecular BioscienceThe University of Queensland306 Carmody Road (Building 80)4072BrisbaneAustralia
| | - David J. Craik
- Institute for Molecular BioscienceThe University of Queensland306 Carmody Road (Building 80)4072BrisbaneAustralia
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