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Chen FJ, Pinnette N, Gao J. Strategies for the Construction of Multicyclic Phage Display Libraries. Chembiochem 2024; 25:e202400072. [PMID: 38466139 DOI: 10.1002/cbic.202400072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/12/2024]
Abstract
Peptide therapeutics have gained great interest due to their multiple advantages over small molecule and antibody-based drugs. Peptide drugs are easier to synthesize, have the potential for oral bioavailability, and are large enough to target protein-protein interactions that are undruggable by small molecules. However, two major limitations have made it difficult to develop novel peptide therapeutics not derived from natural products, including the metabolic instability of peptides and the difficulty of reaching antibody-like potencies and specificities. Compared to linear and disulfide-monocyclized peptides, multicyclic peptides can provide increased conformational rigidity, enhanced metabolic stability, and higher potency in inhibiting protein-protein interactions. The identification of novel multicyclic peptide binders can be difficult, however, recent advancements in the construction of multicyclic phage libraries have greatly advanced the process of identifying novel multicyclic peptide binders for therapeutically relevant protein targets. This review will describe the current approaches used to create multicyclic peptide libraries, highlighting the novel chemistries developed and the proof-of-concept work done on validating these libraries against different protein targets.
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Affiliation(s)
- Fa-Jie Chen
- College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Nicole Pinnette
- Department of Chemistry, Boston College, Merkert Chemistry Center 2609 Beacon Street, Chestnut Hill, MA-02467, USA
| | - Jianmin Gao
- Department of Chemistry, Boston College, Merkert Chemistry Center 2609 Beacon Street, Chestnut Hill, MA-02467, USA
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2
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Chen FJ, Lin W, Chen FE. Non-symmetric stapling of native peptides. Nat Rev Chem 2024; 8:304-318. [PMID: 38575678 DOI: 10.1038/s41570-024-00591-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2024] [Indexed: 04/06/2024]
Abstract
Stapling has emerged as a powerful technique in peptide chemistry. It enables precise control over peptide conformation leading to enhanced properties such as improved stability and enhanced binding affinity. Although symmetric stapling methods have been extensively explored, the field of non-symmetric stapling of native peptides has received less attention, largely as a result of the formidable challenges it poses - in particular the complexities involved in achieving the high chemo-selectivity and site-selectivity required to simultaneously modify distinct proteinogenic residues. Over the past 5 years, there have been significant breakthroughs in addressing these challenges. In this Review, we describe the latest strategies for non-symmetric stapling of native peptides, elucidating the protocols, reaction mechanisms and underlying design principles. We also discuss current challenges and opportunities this field offers for future applications, such as ligand discovery and peptide-based therapeutics.
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Affiliation(s)
- Fa-Jie Chen
- College of Chemistry, Fuzhou University, Fuzhou, P. R. China.
| | - Wanzhen Lin
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, P. R. China
| | - Fen-Er Chen
- College of Chemistry, Fuzhou University, Fuzhou, P. R. China.
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, P. R. China.
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, Fudan University, Shanghai, P. R. China.
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3
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Yu L, Barros SA, Sun C, Somani S. Cyclic Peptide Linker Design and Optimization by Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:6863-6876. [PMID: 37903231 DOI: 10.1021/acs.jcim.3c01359] [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: 11/01/2023]
Abstract
Cyclic peptides are an emerging therapeutic modality that can target protein-protein interaction sites with high affinity and selectivity. A common medicinal chemistry strategy for the optimization of peptide hits is conformational stabilization through macrocyclization. We present a method based on explicit solvent enhanced sampling molecular dynamics simulations for estimating the impact of varying linker lengths and chemistry on the conformational stability of a peptide. The method is demonstrated on three cyclic peptide series that bind to proteins PCSK9, trypsin, and MDM2 adopting loop, β-sheet, and helical secondary structures. In general, the simulations show greater solution stability of the receptor-bound conformation for the higher-affinity peptides, consistent with the idea that preorganizing a ligand for binding can enhance binding affinity. The impact of the force field and sampling is discussed for one series that does not follow this trend. We have successfully applied this method to internal discovery programs to design peptides with increased potency and chemical stability.
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Affiliation(s)
- Lei Yu
- Janssen Research & Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Stephanie A Barros
- Janssen Research & Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Chengzao Sun
- Janssen Research & Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Sandeep Somani
- Janssen Research & Development, LLC, Spring House, Pennsylvania 19477, United States
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4
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Chen FJ, Pinnette N, Yang F, Gao J. A Cysteine-Directed Proximity-Driven Crosslinking Method for Native Peptide Bicyclization. Angew Chem Int Ed Engl 2023; 62:e202306813. [PMID: 37285100 PMCID: PMC10527288 DOI: 10.1002/anie.202306813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/08/2023]
Abstract
Efficient and site-specific modification of native peptides and proteins is desirable for synthesizing antibody-drug conjugates as well as for constructing chemically modified peptide libraries using genetically encoded platforms such as phage display. In particular, there is much interest in efficient multicyclization of native peptides due to the appeals of multicyclic peptides as therapeutics. However, conventional approaches for multicyclic peptide synthesis require orthogonal protecting groups or non-proteinogenic clickable handles. Herein, we report a cysteine-directed proximity-driven strategy for the constructing bicyclic peptides from simple natural peptide precursors. This linear to bicycle transformation initiates with rapid cysteine labeling, which then triggers proximity-driven amine-selective cyclization. This bicyclization proceeds rapidly under physiologic conditions, yielding bicyclic peptides with a Cys-Lys-Cys, Lys-Cys-Lys or N-terminus-Cys-Cys stapling pattern. We demonstrate the utility and power of this strategy by constructing bicyclic peptides fused to proteins as well as to the M13 phage, paving the way to phage display of novel bicyclic peptide libraries.
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Affiliation(s)
- Fa-Jie Chen
- Department of Chemistry, Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Nicole Pinnette
- Department of Chemistry, Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Fan Yang
- Department of Chemistry, Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Jianmin Gao
- Department of Chemistry, Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
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5
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Kamstrup Sell D, Sinkjaer AW, Bakhshinejad B, Kjaer A. Propagation Capacity of Phage Display Peptide Libraries Is Affected by the Length and Conformation of Displayed Peptide. Molecules 2023; 28:5318. [PMID: 37513190 PMCID: PMC10386350 DOI: 10.3390/molecules28145318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The larger size and diversity of phage display peptide libraries enhance the probability of finding clinically valuable ligands. A simple way of increasing the throughput of selection is to mix multiple peptide libraries with different characteristics of displayed peptides and use it as biopanning input. In phage display, the peptide is genetically coupled with a biological entity (the phage), and the representation of peptides in the selection system is dependent on the propagation capacity of phages. Little is known about how the characteristics of displayed peptides affect the propagation capacity of the pooled library. In this work, next-generation sequencing (NGS) was used to investigate the amplification capacity of three widely used commercial phage display peptide libraries (Ph.D.™-7, Ph.D.™-12, and Ph.D.™-C7C from New England Biolabs). The three libraries were pooled and subjected to competitive propagation, and the proportion of each library in the pool was quantitated at two time points during propagation. The results of the inter-library competitive propagation assay led to the conclusion that the propagation capacity of phage libraries on a population level is decreased with increasing length and cyclic conformation of displayed peptides. Moreover, the enrichment factor (EF) analysis of the phage population revealed a higher propagation capacity of the Ph.D.TM-7 library. Our findings provide evidence for the contribution of the length and structural conformation of displayed peptides to the unequal propagation rates of phage display libraries and suggest that it is important to take peptide characteristics into account once pooling multiple combinatorial libraries for phage display selection through biopanning.
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Affiliation(s)
- Danna Kamstrup Sell
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anders Wilgaard Sinkjaer
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Babak Bakhshinejad
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Andreas Kjaer
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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6
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Palma M. Epitopes and Mimotopes Identification Using Phage Display for Vaccine Development against Infectious Pathogens. Vaccines (Basel) 2023; 11:1176. [PMID: 37514992 PMCID: PMC10384025 DOI: 10.3390/vaccines11071176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Traditional vaccines use inactivated or weakened forms of pathogens which could have side effects and inadequate immune responses. To overcome these challenges, phage display has emerged as a valuable tool for identifying specific epitopes that could be used in vaccines. This review emphasizes the direct connection between epitope identification and vaccine development, filling a crucial gap in the field. This technique allows vaccines to be engineered to effectively stimulate the immune system by presenting carefully selected epitopes. Phage display involves screening libraries of random peptides or gene/genome fragments using serum samples from infected, convalescent, or vaccinated individuals. This method has been used to identify epitopes from various pathogens including SARS-CoV-2, Mycobacterium tuberculosis, hepatitis viruses, H5N1, HIV-1, Human T-lymphotropic virus 1, Plasmodium falciparum, Trypanosoma cruzi, and Dirofilaria repens. Bacteriophages offer advantages such as being immunogenic carriers, low production costs, and customization options, making them a promising alternative to traditional vaccines. The purpose of this study has been to highlight an approach that encompasses the entire process from epitope identification to vaccine production using a single technique, without requiring additional manipulation. Unlike conventional methods, phage display demonstrates exceptional efficiency and speed, which could provide significant advantages in critical scenarios such as pandemics.
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Affiliation(s)
- Marco Palma
- Institute for Globally Distributed Open Research and Education (IGDORE), 03181 Torrevieja, Spain
- Protheragen Inc., Ronkonkoma, NY 11779, USA
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7
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Randall JR, Wang X, Groover KE, O'Donnell AC, Davies BW. Using display technologies to identify macrocyclic peptide antibiotics. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119473. [PMID: 37011732 PMCID: PMC10198949 DOI: 10.1016/j.bbamcr.2023.119473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 02/09/2023] [Accepted: 02/19/2023] [Indexed: 04/03/2023]
Abstract
Antibiotic resistant bacterial infections are now a leading cause of global mortality. While drug resistance continues to spread, the clinical antibiotic pipeline has become bare. This discord has focused attention on developing new strategies for antimicrobial discovery. Natural macrocyclic peptide-based products have provided novel antibiotics and antibiotic scaffolds targeting several essential bacterial cell envelope processes, but discovery of such natural products remains a slow and inefficient process. Synthetic strategies employing peptide display technologies can quickly screen large libraries of macrocyclic sequences for specific target binding and general antibacterial potential providing alternative approaches for new antibiotic discovery. Here we review cell envelope processes that can be targeted with macrocyclic peptide therapeutics, outline important macrocyclic peptide display technologies, and discuss future strategies for both library design and screening.
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Affiliation(s)
- Justin R Randall
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA.
| | - Xun Wang
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA
| | - Kyra E Groover
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA
| | - Angela C O'Donnell
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA
| | - Bryan W Davies
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA.
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8
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Díaz-Perlas C, Ricken B, Farrera-Soler L, Guschin D, Pojer F, Lau K, Gerhold CB, Heinis C. High-affinity peptides developed against calprotectin and their application as synthetic ligands in diagnostic assays. Nat Commun 2023; 14:2774. [PMID: 37198182 DOI: 10.1038/s41467-023-38075-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
Common inflammatory disorders such as ulcerative colitis and Crohn's disease are non-invasively diagnosed or monitored by the biomarker calprotectin. However, current quantitative tests for calprotectin are antibody-based and vary depending on the type of antibody and assay used. Additionally, the binding epitopes of applied antibodies are not characterized by structures and for most antibodies it is unclear if they detect calprotectin dimer, tetramer, or both. Herein, we develop calprotectin ligands based on peptides, that offer advantages such as homogenous chemical composition, heat-stability, site-directed immobilization, and chemical synthesis at high purity and at low cost. By screening a 100-billion peptide phage display library against calprotectin, we identified a high-affinity peptide (Kd = 26 ± 3 nM) that binds to a large surface region (951 Å2) as shown by X-ray structure analysis. The peptide uniquely binds the calprotectin tetramer, which enabled robust and sensitive quantification of a defined species of calprotectin by ELISA and lateral flow assays in patient samples, and thus offers an ideal affinity reagent for next-generation inflammatory disease diagnostic assays.
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Affiliation(s)
- Cristina Díaz-Perlas
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Benjamin Ricken
- BÜHLMANN Laboratories AG, Baselstrasse 55, CH-4124, Schönenbuch, Switzerland
| | - Lluc Farrera-Soler
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Dmitrii Guschin
- BÜHLMANN Laboratories AG, Baselstrasse 55, CH-4124, Schönenbuch, Switzerland
| | - Florence Pojer
- Protein Production and Structure Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Kelvin Lau
- Protein Production and Structure Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
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9
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Anand U, Bandyopadhyay A, Jha NK, Pérez de la Lastra JM, Dey A. Translational aspect in peptide drug discovery and development: An emerging therapeutic candidate. Biofactors 2022; 49:251-269. [PMID: 36326181 DOI: 10.1002/biof.1913] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/11/2022] [Indexed: 11/06/2022]
Abstract
In the last two decades, protein-protein interactions (PPIs) have been used as the main target for drug development. However, with larger or superficial binding sites, it has been extremely difficult to disrupt PPIs with small molecules. On the other hand, intracellular PPIs cannot be targeted by antibodies that cannot penetrate the cell membrane. Peptides that have a combination of conformational rigidity and flexibility can be used to target difficult binding interfaces with appropriate binding affinity and specificity. Since the introduction of insulin nearly a century ago, more than 80 peptide drugs have been approved to treat a variety of diseases. These include deadly diseases such as cancer and human immunodeficiency virus infection. It is also useful against diabetes, chronic pain, and osteoporosis. Today, more research is being done on these drugs as lessons learned from earlier approaches, which are still valid today, complement newer approaches such as peptide display libraries. At the same time, integrated genomics and peptide display libraries are new strategies that open new avenues for peptide drug discovery. The purpose of this review is to examine the problems in elucidating the peptide-protein recognition mechanism. This is important to develop peptide-based interventions that interfere with endogenous protein interactions. New approaches are being developed to improve the binding affinity and specificity of existing approaches and to develop peptide agents as potentially useful drugs. We also highlight the key challenges that must be overcome in peptide drug development to realize their potential and provide an overview of recent trends in peptide drug development. In addition, we take an in-depth look at early efforts in human hormone discovery, smart medicinal chemistry and design, natural peptide drugs, and breakthrough advances in molecular biology and peptide chemistry.
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Affiliation(s)
- Uttpal Anand
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, Punjab, India
- Department of Biotechnology, School of Applied and Life Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - José M Pérez de la Lastra
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología, IPNA-CSIC, Tenerife, Spain
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
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10
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Feng D, Liu L, Shi Y, Du P, Xu S, Zhu Z, Xu J, Yao H. Current development of bicyclic peptides. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.108026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Gonschorek P, Zorzi A, Maric T, Le Jeune M, Schüttel M, Montagnon M, Gómez-Ojea R, Vollmar DP, Whitfield C, Reymond L, Carle V, Verma H, Schilling O, Hovnanian A, Heinis C. Phage Display Selected Cyclic Peptide Inhibitors of Kallikrein-Related Peptidases 5 and 7 and Their In Vivo Delivery to the Skin. J Med Chem 2022; 65:9735-9749. [PMID: 35653695 DOI: 10.1021/acs.jmedchem.2c00306] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kallikrein-related peptidases 5 (KLK5) and 7 (KLK7) are serine proteases with homeostatic functions in the epidermis that play a critical role in Netherton syndrome (NS), a rare yet life-threatening genetic disorder that currently lacks specific treatment. Previous research suggests that controlling KLKs could lead to the development of NS therapies, but existing synthetic inhibitors have limitations. Herein, we used phage display to screen libraries comprising more than 100 billion different cyclic peptides and found selective, high-affinity inhibitors of KLK5 (Ki = 2.2 ± 0.1 nM) and KLK7 (Ki = 16 ± 4 nM). By eliminating protease-prone sites and conjugating the inhibitors to an albumin-binding peptide, we enhanced the inhibitor stability and prolonged the elimination half-life to around 5 h in mice. In tissue sections taken from mice, a fluorescently labeled peptide was detected in the epidermis, suggesting that the inhibitors can reach the KLKs upon systemic delivery and should be suited to control deregulated protease activity in NS.
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Affiliation(s)
- Patrick Gonschorek
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Alessandro Zorzi
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Tamara Maric
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Mathilde Le Jeune
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Mischa Schüttel
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Mathilde Montagnon
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Rebeca Gómez-Ojea
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Denis Patrick Vollmar
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Chantal Whitfield
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Luc Reymond
- Biomolecular Screening Facility, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Vanessa Carle
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Hitesh Verma
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg 79106, Germany
| | - Alain Hovnanian
- INSERM UMR1163, Imagine Institute, University of Paris, Paris, France; Department of Genetics, Necker Hospital for Sick Children (AP-HP), 75015 Paris, France
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
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12
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Oppewal TR, Jansen ID, Hekelaar J, Mayer C. A Strategy to Select Macrocyclic Peptides Featuring Asymmetric Molecular Scaffolds as Cyclization Units by Phage Display. J Am Chem Soc 2022; 144:3644-3652. [PMID: 35171585 PMCID: PMC8895403 DOI: 10.1021/jacs.1c12822] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Macrocyclic peptides (MPs) have positioned themselves as a privileged class of compounds for the discovery of therapeutics and development of chemical probes. Aided by the development of powerful selection strategies, high-affinity binders against biomolecular targets can readily be elicited from massive, genetically encoded libraries by affinity selection. For example, in phage display, MPs are accessed on the surface of whole bacteriophages via disulfide formation, the use of (symmetric) crosslinkers, or the incorporation of non-canonical amino acids. To facilitate a straightforward cyclization of linear precursors with asymmetric molecular scaffolds, which are often found at the core of naturally occurring MPs, we report an efficient two-step strategy to access MPs via the programmed modification of a unique cysteine residue and an N-terminal amine. We demonstrate that this approach yields MPs featuring asymmetric cyclization units from both synthetic peptides and when linear precursors are appended onto a phage-coat protein. Finally, we showcase that our cyclization strategy is compatible with traditional phage-display protocols and enables the selection of MP binders against a model target protein from naïve libraries. By enabling the incorporation of non-peptidic moieties that (1) can serve as cyclization units, (2) provide interactions for binding, and/or (3) tailor pharmacological properties, our head-to-side-chain cyclization strategy provides access to a currently under-explored chemical space for the development of chemical probes and therapeutics.
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Affiliation(s)
- Titia Rixt Oppewal
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9474 AG, The Netherlands
| | - Ivar D Jansen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9474 AG, The Netherlands
| | - Johan Hekelaar
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9474 AG, The Netherlands
| | - Clemens Mayer
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9474 AG, The Netherlands
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13
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Gu Y, Iannuzzelli JA, Fasan R. MOrPH-PhD: A Phage Display System for the Functional Selection of Genetically Encoded Macrocyclic Peptides. Methods Mol Biol 2022; 2371:261-286. [PMID: 34596853 PMCID: PMC8493807 DOI: 10.1007/978-1-0716-1689-5_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Macrocyclic peptides represent promising scaffolds for targeting biomolecules with high affinity and selectivity, making methods for the diversification and functional selection of these macrocycles highly valuable for drug discovery purposes. We recently reported a novel phage display platform (called MOrPH-PhD) for the creation and functional exploration of combinatorial libraries of genetically encoded cyclic peptides. In this system, spontaneous, posttranslational peptide cyclization by means of a cysteine-reactive non-canonical amino acid is integrated with M13 bacteriophage display, enabling the creation of genetically encoded macrocyclic peptide libraries displayed on phage particles. Using this system, it is possible to rapidly generate and screen large libraries of phage-displayed macrocyclic peptides (up to 108 to 1010 members) in order to identify high-affinity binders of a target protein of interest. Herein, we describe step-by-step protocols for the production of MOrPH-PhD libraries, the screening of these libraries against an immobilized protein target, and the isolation and characterization of functional macrocyclic peptides from these genetically encoded libraries.
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Affiliation(s)
- Yu Gu
- Department of Chemistry, University of Rochester, Rochester, NY, USA
| | | | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, NY, USA.
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14
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Carle V, Kong XD, Comberlato A, Edwards C, Díaz-Perlas C, Heinis C. Generation of a 100-billion cyclic peptide phage display library having a high skeletal diversity. Protein Eng Des Sel 2021; 34:6333815. [PMID: 34341825 DOI: 10.1093/protein/gzab018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/09/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
Phage display is a powerful technique routinely used for the generation of peptide- or protein-based ligands. The success of phage display selections critically depends on the size and structural diversity of the libraries, but the generation of large libraries remains challenging. In this work, we have succeeded in developing a phage display library comprising around 100 billion different (bi)cyclic peptides and thus more structures than any previously reported cyclic peptide phage display library. Building such a high diversity was achieved by combining a recently reported library cloning technique, based on whole plasmid PCR, with a small plasmid that facilitated bacterial transformation. The library cloned is based on 273 different peptide backbones and thus has a large skeletal diversity. Panning of the peptide repertoire against the important thrombosis target coagulation factor XI enriched high-affinity peptides with long consensus sequences that can only be found if the library diversity is large.
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Affiliation(s)
- Vanessa Carle
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Xu-Dong Kong
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Alice Comberlato
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Chelsea Edwards
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Cristina Díaz-Perlas
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
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15
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Gübeli RJ, Bertoldo D, Shimada K, Gerhold CB, Hurst V, Takahashi Y, Harada K, Mothukuri GK, Wilbs J, Harata M, Gasser SM, Heinis C. In Vitro-Evolved Peptides Bind Monomeric Actin and Mimic Actin-Binding Protein Thymosin-β4. ACS Chem Biol 2021; 16:820-828. [PMID: 33843189 DOI: 10.1021/acschembio.0c00825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Actin is the most abundant protein in eukaryotic cells and is key to many cellular functions. The filamentous form of actin (F-actin) can be studied with help of natural products that specifically recognize it, as for example fluorophore-labeled probes of the bicyclic peptide phalloidin, but no synthetic probes exist for the monomeric form of actin (G-actin). Herein, we have panned a phage display library consisting of more than 10 billion bicyclic peptides against G-actin and isolated binders with low nanomolar affinity and greater than 1000-fold selectivity over F-actin. Sequence analysis revealed a strong similarity to a region of thymosin-β4, a protein that weakly binds G-actin, and competition binding experiments confirmed a common binding region at the cleft between actin subdomains 1 and 3. Together with F-actin-specific peptides that we also isolated, we evaluated the G-actin peptides as probes in pull-down, imaging, and competition binding experiments. While the F-actin peptides were applied successfully for capturing actin in cell lysates and for imaging, the G-actin peptides did not bind in the cellular context, most likely due to competition with thymosin-β4 or related endogenous proteins for the same binding site.
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Affiliation(s)
- Raphael J. Gübeli
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Davide Bertoldo
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Christian B. Gerhold
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Verena Hurst
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
- Faculty of Natural Sciences, University of Basel, 4056 Basel, Switzerland
| | - Yuichiro Takahashi
- Laboratory of Molecular Biology, Tohoku University, Tsutsumidori-Amamiyamachi 1-1, Aoba-ku, Sendai 981-8555, Japan
| | - Kai Harada
- Laboratory of Molecular Biology, Tohoku University, Tsutsumidori-Amamiyamachi 1-1, Aoba-ku, Sendai 981-8555, Japan
| | - Ganesh K. Mothukuri
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jonas Wilbs
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Masahiko Harata
- Laboratory of Molecular Biology, Tohoku University, Tsutsumidori-Amamiyamachi 1-1, Aoba-ku, Sendai 981-8555, Japan
| | - Susan M. Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
- Faculty of Natural Sciences, University of Basel, 4056 Basel, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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Abstract
Since the introduction of insulin almost a century ago, more than 80 peptide drugs have reached the market for a wide range of diseases, including diabetes, cancer, osteoporosis, multiple sclerosis, HIV infection and chronic pain. In this Perspective, we summarize key trends in peptide drug discovery and development, covering the early efforts focused on human hormones, elegant medicinal chemistry and rational design strategies, peptide drugs derived from nature, and major breakthroughs in molecular biology and peptide chemistry that continue to advance the field. We emphasize lessons from earlier approaches that are still relevant today as well as emerging strategies such as integrated venomics and peptide-display libraries that create new avenues for peptide drug discovery. We also discuss the pharmaceutical landscape in which peptide drugs could be particularly valuable and analyse the challenges that need to be addressed for them to reach their full potential.
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17
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Cao J, Fan T, Li Y, Du Z, Chen L, Wang Y, Wang X, Shen J, Huang X, Xiong B, Cao D. Phage-Display Based Discovery and Characterization of Peptide Ligands against WDR5. Molecules 2021; 26:1225. [PMID: 33668971 PMCID: PMC7956166 DOI: 10.3390/molecules26051225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/17/2021] [Accepted: 02/21/2021] [Indexed: 11/16/2022] Open
Abstract
WD40 is a ubiquitous domain presented in at least 361 human proteins and acts as scaffold to form protein complexes. Among them, WDR5 protein is an important mediator in several protein complexes to exert its functions in histone modification and chromatin remodeling. Therefore, it was considered as a promising epigenetic target involving in anti-cancer drug development. In view of the protein-protein interaction nature of WDR5, we initialized a campaign to discover new peptide-mimic inhibitors of WDR5. In current study, we utilized the phage display technique and screened with a disulfide-based cyclic peptide phage library. Five rounds of biopanning were performed and isolated clones were sequenced. By analyzing the sequences, total five peptides were synthesized for binding assay. The four peptides are shown to have the moderate binding affinity. Finally, the detailed binding interactions were revealed by solving a WDR5-peptide cocrystal structure.
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Affiliation(s)
- Jiawen Cao
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Tiantian Fan
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yanlian Li
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhiyan Du
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Lin Chen
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Ying Wang
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xin Wang
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jingkang Shen
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xun Huang
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Division of Anti-Tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Bing Xiong
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Danyan Cao
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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18
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Small and Simple, yet Sturdy: Conformationally Constrained Peptides with Remarkable Properties. Int J Mol Sci 2021; 22:ijms22041611. [PMID: 33562633 PMCID: PMC7915549 DOI: 10.3390/ijms22041611] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/20/2022] Open
Abstract
The sheer size and vast chemical space (i.e., diverse repertoire and spatial distribution of functional groups) underlie peptides’ ability to engage in specific interactions with targets of various structures. However, the inherent flexibility of the peptide chain negatively affects binding affinity and metabolic stability, thereby severely limiting the use of peptides as medicines. Imposing conformational constraints to the peptide chain offers to solve these problems but typically requires laborious structure optimization. Alternatively, libraries of constrained peptides with randomized modules can be screened for specific functions. Here, we present the properties of conformationally constrained peptides and review rigidification chemistries/strategies, as well as synthetic and enzymatic methods of producing macrocyclic peptides. Furthermore, we discuss the in vitro molecular evolution methods for the development of constrained peptides with pre-defined functions. Finally, we briefly present applications of selected constrained peptides to illustrate their exceptional properties as drug candidates, molecular recognition probes, and minimalist catalysts.
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19
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Dotter H, Boll M, Eder M, Eder AC. Library and post-translational modifications of peptide-based display systems. Biotechnol Adv 2021; 47:107699. [PMID: 33513435 DOI: 10.1016/j.biotechadv.2021.107699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 01/04/2021] [Accepted: 01/14/2021] [Indexed: 12/27/2022]
Abstract
Innovative biotechnological methods empower the successful identification of new drug candidates. Phage, ribosome and mRNA display represent high throughput screenings, allowing fast and efficient progress in the field of targeted drug discovery. The identification range comprises low molecular weight peptides up to whole antibodies. However, a major challenge poses the stability and affinity in particular of peptides. Chemical modifications e.g. the introduction of unnatural amino acids or cyclization, have been proven to be essential tools to overcome these limitations. This review article particularly focuses on available methods for the targeted chemical modification of peptides and peptide libraries in selected display approaches.
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Affiliation(s)
- Hanna Dotter
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Melanie Boll
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Matthias Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Ann-Christin Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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20
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Luo Y, Schofield JA, Na Z, Hann T, Simon MD, Slavoff SA. Discovery of cellular substrates of human RNA-decapping enzyme DCP2 using a stapled bicyclic peptide inhibitor. Cell Chem Biol 2020; 28:463-474.e7. [PMID: 33357462 DOI: 10.1016/j.chembiol.2020.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/29/2020] [Accepted: 12/04/2020] [Indexed: 01/23/2023]
Abstract
DCP2 is an RNA-decapping enzyme that controls the stability of human RNAs that encode factors functioning in transcription and the immune response. While >1,800 human DCP2 substrates have been identified, compensatory expression changes secondary to genetic ablation of DCP2 have complicated a complete mapping of its regulome. Cell-permeable, selective chemical inhibitors of DCP2 could provide a powerful tool to study DCP2 specificity. Here, we report phage display selection of CP21, a bicyclic peptide ligand to DCP2. CP21 has high affinity and selectivity for DCP2 and inhibits DCP2 decapping activity toward selected RNA substrates in human cells. CP21 increases formation of P-bodies, liquid condensates enriched in intermediates of RNA decay, in a manner that resembles the deletion or mutation of DCP2. We used CP21 to identify 76 previously unreported DCP2 substrates. This work demonstrates that DCP2 inhibition can complement genetic approaches to study RNA decay.
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Affiliation(s)
- Yang Luo
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jeremy A Schofield
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA
| | - Zhenkun Na
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Tanja Hann
- Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT 06520, USA
| | - Matthew D Simon
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA
| | - Sarah A Slavoff
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA.
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21
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Iskandar SE, Haberman VA, Bowers AA. Expanding the Chemical Diversity of Genetically Encoded Libraries. ACS COMBINATORIAL SCIENCE 2020; 22:712-733. [PMID: 33167616 PMCID: PMC8284915 DOI: 10.1021/acscombsci.0c00179] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The power of ribosomes has increasingly been harnessed for the synthesis and selection of molecular libraries. Technologies, such as phage display, yeast display, and mRNA display, effectively couple genotype to phenotype for the molecular evolution of high affinity epitopes for many therapeutic targets. Genetic code expansion is central to the success of these technologies, allowing researchers to surpass the intrinsic capabilities of the ribosome and access new, genetically encoded materials for these selections. Here, we review techniques for the chemical expansion of genetically encoded libraries, their abilities and limits, and opportunities for further development. Importantly, we also discuss methods and metrics used to assess the efficiency of modification and library diversity with these new techniques.
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Affiliation(s)
- Sabrina E Iskandar
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Victoria A Haberman
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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22
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Structure-based design of small bicyclic peptide inhibitors of Cripto-1 activity. Biochem J 2020; 477:1391-1407. [PMID: 32215602 DOI: 10.1042/bcj20190953] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/21/2020] [Accepted: 03/26/2020] [Indexed: 12/12/2022]
Abstract
Bicyclic peptides assembled around small organic scaffolds are gaining an increasing interest as new potent, stable and highly selective therapeutics because of their uncommon ability to specifically recognize protein targets, of their small size that favor tissue penetration and of the versatility and easiness of the synthesis. We have here rationally designed bicyclic peptides assembled around a common tri-bromo-methylbenzene moiety in order to mimic the structure of the CFC domain of the oncogene Cripto-1 and, more specifically, to orient in the most fruitful way the hot spot residues H120 and W123. Through the CFC domain, Cripto-1 binds the ALK4 receptor and other protein partners supporting uncontrolled cell growth and proliferation. Soluble variants of CFC have the potential to inhibit these interactions suppressing the protein activity. A CFC analog named B3 binds ALK4 in vitro with an affinity in the nanomolar range. Structural analyses in solution via NMR and CD show that B3 has rather flexible conformations, like the parent CFC domain. The functional effects of B3 on the Cripto-1-positive NTERA cancer cell line have been evaluated showing that both CFC and B3 are cytotoxic for the cells and block the Cripto-1 intracellular signaling. Altogether, the data suggest that the administration of the soluble CFC and of the structurally related analog has the potential to inhibit tumor growth.
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23
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Kong XD, Carle V, Díaz-Perlas C, Butler K, Heinis C. Generation of a Large Peptide Phage Display Library by Self-Ligation of Whole-Plasmid PCR Product. ACS Chem Biol 2020; 15:2907-2915. [PMID: 33125222 DOI: 10.1021/acschembio.0c00497] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The success of phage display, used for developing target-specific binders based on peptides and proteins, depends on the size and diversity of the library screened, but generating large libraries of phage-encoded polypeptides remains challenging. New peptide phage display libraries developed in recent years rarely contained more than 1 billion clones, which appears to have become the upper size limit for libraries generated with reasonable effort. Here, we established a strategy based on whole-plasmid PCR and self-ligation to clone a library with more than 2 × 1010 members. The enormous library size could be obtained through amplifying the entire vector DNA by PCR, which omitted the step of vector isolation from bacterial cells, and through appending DNA coding for the peptide library via a PCR primer, which enabled efficient DNA circularization by end-ligation to facilitate the difficult step of vector-insertion of DNA fragments. Panning the peptide repertoires against a target yielded high-affinity ligands and validated the quality of the library and thus the new library cloning strategy. This simple and efficient strategy places larger libraries within reach for nonspecialist researchers to hopefully expand the possible targets of phage display applications.
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Affiliation(s)
- Xu-Dong Kong
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Vanessa Carle
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Cristina Díaz-Perlas
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Kaycie Butler
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
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24
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Li Y, Cao X, Tian C, Zheng JS. Chemical protein synthesis-assisted high-throughput screening strategies for d-peptides in drug discovery. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2020.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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25
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Kong XD, Moriya J, Carle V, Pojer F, Abriata LA, Deyle K, Heinis C. De novo development of proteolytically resistant therapeutic peptides for oral administration. Nat Biomed Eng 2020; 4:560-571. [DOI: 10.1038/s41551-020-0556-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 04/07/2020] [Indexed: 12/13/2022]
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26
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Liu KC, Röder K, Mayer C, Adhikari S, Wales DJ, Balasubramanian S. Affinity-Selected Bicyclic Peptide G-Quadruplex Ligands Mimic a Protein-like Binding Mechanism. J Am Chem Soc 2020; 142:8367-8373. [PMID: 32267689 PMCID: PMC7212521 DOI: 10.1021/jacs.0c01879] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Indexed: 12/14/2022]
Abstract
The study of G-quadruplexes (G4s) in a cellular context has demonstrated links between these nucleic acid secondary structures, gene expression, and DNA replication. Ligands that bind to the G4 structure therefore present an excellent opportunity for influencing gene expression through the targeting of a nucleic acid structure rather than sequence. Here, we explore cyclic peptides as an alternative class of G4 ligands. Specifically, we describe the development of de novo G4-binding bicyclic peptides selected by phage display. Selected bicyclic peptides display submicromolar affinity to G4 structures and high selectivity over double helix DNA. Molecular simulations of the bicyclic peptide-G4 complexes corroborate the experimental binding strengths and reveal molecular insights into G4 recognition by bicyclic peptides via the precise positioning of amino acid side chains, a binding mechanism reminiscent of endogenous G4-binding proteins. Overall, our results demonstrate that selection of (bi)cyclic peptides unlocks a valuable chemical space for targeting nucleic acid structures.
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Affiliation(s)
- Kim C. Liu
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2
1EW Cambridge, U.K.
| | - Konstantin Röder
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2
1EW Cambridge, U.K.
| | - Clemens Mayer
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2
1EW Cambridge, U.K.
- Stratingh Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Santosh Adhikari
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2
1EW Cambridge, U.K.
| | - David J. Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2
1EW Cambridge, U.K.
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2
1EW Cambridge, U.K.
- Cancer
Research U.K., Cambridge Institute, Li Ka
Shing Centre, Robinson
Way, Cambridge CB2 0RE, U.K.
- School of Clinical Medicine, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0SP, U.K.
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Mulligan VK. The emerging role of computational design in peptide macrocycle drug discovery. Expert Opin Drug Discov 2020; 15:833-852. [PMID: 32345066 DOI: 10.1080/17460441.2020.1751117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Drug discovery is a laborious process with rising cost per new drug. Peptide macrocycles are promising therapeutics, though conformational flexibility can reduce target affinity and specificity. Recent computational advancements address this problem by enabling rational design of rigidly folded peptide macrocycles. AREAS COVERED This review summarizes currently approved peptide macrocycle therapeutics and discusses advantages of mesoscale drugs over small molecules or protein therapeutics. It describes the history, rationale, and state of the art of computational tools, such as Rosetta, that allow the design of rigidly structured peptide macrocycles. The emerging pipeline for designing peptide macrocycle drugs is described, including current challenges in designing permeable molecules that can emulate the chameleonic behavior of natural macrocycles. Prospects for reducing computational cost and improving accuracy with emerging computational technologies are also discussed. EXPERT OPINION To embrace computational design of peptide macrocycle drugs, we must shift current attitudes regarding the role of computation in drug discovery, and move beyond Lipinski's rules. This technology has the potential to shift failures to earlier in silico stages of the drug discovery process, improving success rates in costly clinical trials. Given the available tools, now is the time for drug developers to incorporate peptide macrocycle design into drug discovery pipelines.
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Affiliation(s)
- Vikram K Mulligan
- Systems Biology, Center for Computational Biology, Flatiron Institute , New York, NY, USA
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28
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Owens A, Iannuzzelli JA, Gu Y, Fasan R. MOrPH-PhD: An Integrated Phage Display Platform for the Discovery of Functional Genetically Encoded Peptide Macrocycles. ACS CENTRAL SCIENCE 2020; 6:368-381. [PMID: 32232137 PMCID: PMC7099587 DOI: 10.1021/acscentsci.9b00927] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Indexed: 05/04/2023]
Abstract
Macrocyclic peptides represent attractive scaffolds for targeting protein-protein interactions, making methods for the diversification and functional selection of these molecules highly valuable for molecular discovery purposes. Here, we report the development of a novel strategy for the generation and high-throughput screening of combinatorial libraries of macrocyclic peptides constrained by a nonreducible thioether bridge. In this system, spontaneous, posttranslational peptide cyclization by means of a cysteine-reactive noncanonical amino acid was integrated with M13 bacteriophage display, enabling the creation of genetically encoded macrocyclic peptide libraries displayed on phage particles. This platform, named MOrPH-PhD, was successfully applied to produce and screen 105- to 108-member libraries of peptide macrocycles against three different protein targets, resulting in the discovery of a high-affinity binder for streptavidin (K D: 20 nM) and potent inhibitors of the therapeutically relevant proteins Kelch-like ECH-associated protein 1 (K D: 40 nM) and Sonic Hedgehog (K D: 550 nM). This work introduces and validates an efficient and general platform for the discovery and evolution of functional, conformationally constrained macrocyclic peptides useful for targeting proteins and protein-mediated interactions.
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29
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Anananuchatkul T, Chang IV, Miki T, Tsutsumi H, Mihara H. Construction of a Stapled α-Helix Peptide Library Displayed on Phage for the Screening of Galectin-3-Binding Peptide Ligands. ACS OMEGA 2020; 5:5666-5674. [PMID: 32226843 PMCID: PMC7097893 DOI: 10.1021/acsomega.9b03461] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
A stapled α-helix peptide library was designed and constructed using a chemically modified phage display system for screening stapled-peptide ligands against target proteins. The α-helix peptide library, with two cysteine residues on the opposite side of the randomized face, was modified with a rigid hydrocarbon staple linker on a phage. The stapled α-helix peptide phage library was screened against galectin-3 (Gal-3), a cancer-related galactose-binding protein. The obtained stapled peptides showed a high binding affinity (K d = 0.45 μM) despite being nonsugar ligands. The stapled modification played important roles in stabilizing the α-helical structure that contributed to the high binding affinity to Gal-3. In addition, the best stapled peptide ligands showed specific binding to Gal-3 among various carbohydrate-binding proteins. Thus, the designed α-helix peptide phage library with a constrained structure by the staple linker will advance the discovery of peptide ligands with improved specificity and affinity.
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Tharp JM, Hampton JT, Reed CA, Ehnbom A, Chen PHC, Morse JS, Kurra Y, Pérez LM, Xu S, Liu WR. An amber obligate active site-directed ligand evolution technique for phage display. Nat Commun 2020; 11:1392. [PMID: 32170178 PMCID: PMC7070036 DOI: 10.1038/s41467-020-15057-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/14/2020] [Indexed: 01/19/2023] Open
Abstract
Although noncanonical amino acids (ncAAs) were first incorporated into phage libraries through amber suppression nearly two decades ago, their application for use in drug discovery has been limited due to inherent library bias towards sense-containing phages. Here, we report a technique based on superinfection immunity of phages to enrich amber-containing clones, thus avoiding the observed bias that has hindered incorporation of ncAAs into phage libraries. We then take advantage of this technique for development of active site-directed ligand evolution of peptides, where the ncAA serves as an anchor to direct the binding of its peptides to the target’s active site. To demonstrate this, phage-displayed peptide libraries are developed that contain a genetically encoded butyryl lysine and are subsequently used to select for ligands that bind SIRT2. These ligands are then modified to develop low nanomolar inhibitors of SIRT2. Most epigenetic regulator inhibitors target tunnels of active sites, rather than the peptide binding groove, leading to concerns with low selectivity. Here the authors use an amber obligate phage library to rapidly identify isoform-selective inhibitors of SIRT2.
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Affiliation(s)
- Jeffery M Tharp
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - J Trae Hampton
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Catrina A Reed
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Andreas Ehnbom
- Laboratory for Molecular Simulation, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Peng-Hsun Chase Chen
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Jared S Morse
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yadagirri Kurra
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Lisa M Pérez
- Laboratory for Molecular Simulation, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Shiqing Xu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA. .,Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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31
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Methods for generating and screening libraries of genetically encoded cyclic peptides in drug discovery. Nat Rev Chem 2020; 4:90-101. [PMID: 37128052 DOI: 10.1038/s41570-019-0159-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2019] [Indexed: 12/14/2022]
Abstract
Drug discovery has traditionally focused on using libraries of small molecules to identify therapeutic drugs, but new modalities, especially libraries of genetically encoded cyclic peptides, are increasingly used for this purpose. Several technologies now exist for the production of libraries of cyclic peptides, including phage display, mRNA display and split-intein circular ligation of peptides and proteins. These different approaches are each compatible with particular methods of screening libraries, such as functional or affinity-based screening, and screening in vitro or in cells. These techniques allow the rapid preparation of libraries of hundreds of millions of molecules without the need for chemical synthesis, and have therefore lowered the entry barrier to generating and screening for inhibitors of a given target. This ease of use combined with the inherent advantages of the cyclic-peptide scaffold has yielded inhibitors of targets that have proved difficult to drug with small molecules. Multiple reports demonstrate that cyclic peptides act as privileged scaffolds in drug discovery, particularly against 'undruggable' targets such as protein-protein interactions. Although substantial challenges remain in the clinical translation of hits from screens of cyclic-peptide libraries, progress continues to be made in this area, with an increasing number of cyclic peptides entering clinical trials. Here, we detail the various platforms for producing and screening libraries of genetically encoded cyclic peptides and discuss and evaluate the advantages and disadvantages of each approach when deployed for drug discovery.
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32
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Restriction-Free Construction of a Phage-Presented Very Short Macrocyclic Peptide Library. Methods Mol Biol 2019. [PMID: 31625092 DOI: 10.1007/978-1-4939-9853-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Phage display is a commonly used technology for the screening of large clonal libraries of proteins and peptides. The construction of peptide libraries containing very short sequences, however, poses certain problems for conventional restriction-based cloning procedures, which are rooted in the necessity to purify restricted library oligos. Herein, we present an alternative cloning method especially suitable for such very short sequences of about only 21 base pairs resulting in a 60 bp insert. The employed restriction-free hot fusion cloning strategy allows for facile library construction bypassing the need for purification of the small oligo. The library includes one well-defined disulfide bridge rendering the displayed macrocyclic peptide sequences as attractive scaffolds for novel active principles.
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33
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Castillo F, Tavassoli A. Genetic Selections with SICLOPPS Libraries: Toward the Identification of Novel Protein-Protein Interaction Inhibitors and Chemical Tools. Methods Mol Biol 2019; 2001:317-328. [PMID: 31134578 DOI: 10.1007/978-1-4939-9504-2_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cyclic peptide libraries have successfully been employed for the identification of inhibitors of highly challenging targets. While several methodologies exist for the generation of cyclic peptide libraries, genetically encoded libraries hold several advantages over purely in vitro methods of library generation, including the ability to conduct cell-based functional screens and straightforward hit deconvolution. Here we detail the use of split-intein circular ligation of peptides and proteins (SICLOPPS) for the identification and optimization of several first-in-class and best-in-class inhibitors. We describe the current advances in the identification of SICLOPPS-derived inhibitors, as well as the optimization of library generation through the use of new inteins. Finally, we discuss the production of more diverse libraries as a way of enhancing the hit rate against difficult protein-protein interactions.
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Affiliation(s)
| | - Ali Tavassoli
- School of Chemistry, University of Southampton, Southampton, UK.
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34
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Ernst C, Sindlinger J, Schwarzer D, Koch P, Boeckler FM. The Symmetric Tetravalent Sulfhydryl-Specific Linker NATBA Facilitates a Combinatorial "Tool Kit" Strategy for Phage Display-Based Selection of Functionalized Bicyclic Peptides. ACS OMEGA 2018; 3:12361-12368. [PMID: 30411004 PMCID: PMC6217522 DOI: 10.1021/acsomega.8b01814] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/17/2018] [Indexed: 05/12/2023]
Abstract
The rigid conformation of constrained bicyclic peptides provides a number of advantages over larger protein-based ligands, including better chemical stability, enhanced tissue penetration, and a wider field of possible applications. Selective chemical modification strategies are able to extend the scope of applications not only in a therapeutic manner but also for the development of novel tools for protein capturing, bioimaging, and targeted drug delivery. Herein, we report the synthesis of an adamantane-based, symmetrical, tetravalent, sulfhydryl-specific peptide linker. We have developed an in vitro two-step modification strategy that allows the generation of differently functionalized bicyclic peptides. This "tool kit" strategy was applied to cyclize and functionalize a phage-encoded peptide library bearing the sequence CX6CX6C. After phage display against a model target, isolated peptides show strong consensus sequences, indicating target-specific binding. The newly developed symmetric tetravalent linker opens new avenues for the combinatorial selection and functionalization of bicyclic peptide ligands with affinity to virtually any target.
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Affiliation(s)
- Christoph Ernst
- Institute
of Pharmaceutical Sciences, Eberhard Karls
Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Julia Sindlinger
- Interfaculty
Institute of Biochemistry, Eberhard Karls
Universität Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Dirk Schwarzer
- Interfaculty
Institute of Biochemistry, Eberhard Karls
Universität Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Pierre Koch
- Institute
of Pharmaceutical Sciences, Eberhard Karls
Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Frank M. Boeckler
- Institute
of Pharmaceutical Sciences, Eberhard Karls
Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
- E-mail:
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35
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Abstract
With the increasing utilization of high-throughput screening for lead identification in drug discovery, the need for easily constructed and diverse libraries which cover significant chemical space is greater than ever. Cyclic peptides address this need; they combine the advantageous properties of peptides (ease of production, high diversity, high potential specificity) with increased resistance to proteolysis and often increased biological activity (due to conformational locking). There are a number of techniques for the generation and screening of cyclic peptide libraries. As drug discovery moves toward tackling challenging targets, such as protein-protein interactions, cyclic peptide libraries are expected to continue producing hits where small molecule libraries may be stymied. However, it is important to design robust systems for the generation and screening of these large libraries, and to be able to make sense of structure-activity relationships in these highly variable scaffolds. There are a plethora of possible modifications that can be made to cyclic peptides, which is both a weakness and a strength of these scaffolds; high variability will allow more precise tuning of leads to targets, but exploring the whole range of modifications may become an overwhelming challenge.
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36
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Ernst C, Heidrich J, Sessler C, Sindlinger J, Schwarzer D, Koch P, Boeckler FM. Switching Between Bicyclic and Linear Peptides - The Sulfhydryl-Specific Linker TPSMB Enables Reversible Cyclization of Peptides. Front Chem 2018; 6:484. [PMID: 30386769 PMCID: PMC6198510 DOI: 10.3389/fchem.2018.00484] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/24/2018] [Indexed: 11/13/2022] Open
Abstract
Phage display-selected bicyclic peptides have already shown their great potential for the development as bioactive modulators of therapeutic targets. They can provide enhanced proteolytic stability and improved membrane permeability. Molecular design of new linker molecules has led to a variety of new synthetic approaches for the generation of chemically constrained cyclic peptides. This diversity can be useful for the development of novel peptide-based therapeutic, diagnostic, and scientific tools. Herein, we introduce 1,3,5-tris((pyridin-2-yldisulfanyl)methyl)benzene (TPSMB) as a planar, trivalent, sulfhydryl-specific linker that facilitates reversible cyclization and linearization via disulfide bond formation and cleavage of bicyclic peptides of the format CXnCXnC, where X is any proteinogenic amino acid except cysteine. The rapid and highly sulfhydryl-specific reaction of TPSMB under physiological conditions is demonstrated by selecting bicyclic peptide binders against c-Jun N-terminal kinase 3 (JNK3) as a model target. While model peptides remain stably cyclized for several hours in presence of typical blood levels of glutathione in vitro, high cytosolic concentrations of glutathione linearize these peptides completely within 1 h. We propose that reversible linkers can be useful tools for several technical applications where target affinity depends on the bicyclic structure of the peptide.
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Affiliation(s)
- Christoph Ernst
- Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Johannes Heidrich
- Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Catharina Sessler
- Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Julia Sindlinger
- Department of Pharmacy and Biochemistry, Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Dirk Schwarzer
- Department of Pharmacy and Biochemistry, Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Pierre Koch
- Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Frank M. Boeckler
- Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
- Center for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Tübingen, Germany
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38
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van Rosmalen M, Ni Y, Vervoort DFM, Arts R, Ludwig SKJ, Merkx M. Dual-Color Bioluminescent Sensor Proteins for Therapeutic Drug Monitoring of Antitumor Antibodies. Anal Chem 2018; 90:3592-3599. [PMID: 29443503 PMCID: PMC5843950 DOI: 10.1021/acs.analchem.8b00041] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Monitoring the levels of therapeutic antibodies in individual patients would allow patient-specific dose optimization, with the potential for major therapeutic and financial benefits. Our group recently developed a new platform of bioluminescent sensor proteins (LUMABS; LUMinescent AntiBody Sensor) that allow antibody detection directly in blood plasma. In this study, we targeted four clinically important therapeutic antibodies, the Her2-receptor targeting trastuzumab, the anti-CD20 antibodies rituximab and obinutuzumab, and the EGFR-blocking cetuximab. A strong correlation was found between the affinity of the antibody binding peptide and sensor performance. LUMABS sensors with physiologically relevant affinities and decent sensor responses were obtained for trastuzumab and cetuximab using mimotope and meditope peptides, respectively, with affinities in the 10-7 M range. The lower affinity of the CD20-derived cyclic peptide employed in the anti-CD20 LUMABS sensor ( Kd = 10-5 M), translated in a LUMABS sensor with a strongly attenuated sensor response. The trastuzumab and cetuximab sensors were further characterized with respect to binding kinetics and their performance in undiluted blood plasma. For both antibodies, LUMABS-based detection directly in plasma compared well to the analytical performance of commercial ELISA kits. Besides identifying important design parameters for the development of new LUMABS sensors, this work demonstrates the potential of the LUMABS platform for point-of-care detection of therapeutic antibodies.
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Affiliation(s)
- Martijn van Rosmalen
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands
| | - Yan Ni
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands
| | - Daan F M Vervoort
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands
| | - Remco Arts
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands
| | - Susann K J Ludwig
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands
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39
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Zha M, Lin P, Yao H, Zhao Y, Wu C. A phage display-based strategy for the de novo creation of disulfide-constrained and isomer-free bicyclic peptide affinity reagents. Chem Commun (Camb) 2018; 54:4029-4032. [DOI: 10.1039/c7cc09142g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report a phage-screening strategy for the development of bicyclic peptide ligands constrained with two sterically different and isomerically forbidden noncanonical disulfide bridges without elaborate chemical modifications and recourses to genetic code reprogramming.
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Affiliation(s)
- Mirao Zha
- Department of Chemistry
- College of Chemistry and Chemical Engineering
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Xiamen University
| | - Ping Lin
- Department of Chemistry
- College of Chemistry and Chemical Engineering
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Xiamen University
| | - Hongwei Yao
- Department of Chemistry
- College of Chemistry and Chemical Engineering
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Xiamen University
| | - Yibing Zhao
- Department of Chemistry
- College of Chemistry and Chemical Engineering
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Xiamen University
| | - Chuanliu Wu
- Department of Chemistry
- College of Chemistry and Chemical Engineering
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Xiamen University
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40
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Villequey C, Kong XD, Heinis C. Bypassing bacterial infection in phage display by sequencing DNA released from phage particles. Protein Eng Des Sel 2017; 30:761-768. [PMID: 29194551 DOI: 10.1093/protein/gzx057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/20/2017] [Indexed: 11/12/2022] Open
Abstract
Phage display relies on a bacterial infection step in which the phage particles are replicated to perform multiple affinity selection rounds and to enable the identification of isolated clones by DNA sequencing. While this process is efficient for wild-type phage, the bacterial infection rate of phage with mutant or chemically modified coat proteins can be low. For example, a phage mutant with a disulfide-free p3 coat protein, used for the selection of bicyclic peptides, has a more than 100-fold reduced infection rate compared to the wild-type. A potential strategy for bypassing the bacterial infection step is to directly sequence DNA extracted from phage particles after a single round of phage panning using high-throughput sequencing. In this work, we have quantified the fraction of phage clones that can be identified by directly sequencing DNA from phage particles. The results show that the DNA of essentially all of the phage particles can be 'decoded', and that the sequence coverage for mutants equals that of amplified DNA extracted from cells infected with wild-type phage. This procedure is particularly attractive for selections with phage that have a compromised infection capacity, and it may allow phage display to be performed with particles that are not infective at all.
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Affiliation(s)
- Camille Villequey
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Xu-Dong Kong
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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41
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Schneider IC, Hartmann J, Braun G, Stitz J, Klamp T, Bihi M, Sahin U, Buchholz CJ. Displaying Tetra-Membrane Spanning Claudins on Enveloped Virus-Like Particles for Cancer Immunotherapy. Biotechnol J 2017; 13:e1700345. [DOI: 10.1002/biot.201700345] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 11/06/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Irene C. Schneider
- Molecular Biotechnology and Gene Therapy; Paul-Ehrlich-Institut; Langen Germany
| | - Jessica Hartmann
- Molecular Biotechnology and Gene Therapy; Paul-Ehrlich-Institut; Langen Germany
| | - Gundula Braun
- Molecular Biotechnology and Gene Therapy; Paul-Ehrlich-Institut; Langen Germany
| | - Jörn Stitz
- Faculty of Applied Natural Sciences, TH Köln; University of Applied Sciences Cologne; Leverkusen Germany
| | | | - Mahjoub Bihi
- BioNTech Protein Therapeutics GmbH; Mainz Germany
| | - Ugur Sahin
- BioNTech Protein Therapeutics GmbH; Mainz Germany
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42
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de la Cotte A, Wu C, Trévisan M, Repula A, Grelet E. Rod-Like Virus-Based Multiarm Colloidal Molecules. ACS NANO 2017; 11:10616-10622. [PMID: 28933822 DOI: 10.1021/acsnano.7b06405] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report on the construction of multiarm colloidal molecules by tip-linking filamentous bacteriophages, functionalized either by biological engineering or chemical conjugation. The affinity for streptavidin of a genetically modified vector phage displaying Strep-tags fused to one end of the viral particle is measured by determining the dissociation constant, Kd. In order to improve both the colloidal stability and the efficiency of the self-assembly process, a biotinylation protocol having a chemical yield higher than 90% is presented to regioselectively functionalize the cystein residues located at one end of the bacteriophages. For both viral systems, a theoretical comparison is performed by developing a quantitative model of the self-assembly and interaction of the modified viruses with streptavidin compounds, which accurately accounts for our experimental results. Multiarm colloidal structures of different valencies are then produced by conjugation of these tip-functionalized viruses with streptavidin activated nanoparticles. We succeed to form stable virus-based colloidal molecules, whose number of arms, called valency, is solely controlled by tuning the molar excess. Thanks to a fluorescent labeling of the viral arms, the dynamics of such systems is also presented in real time by fluorescence microscopy.
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Affiliation(s)
- Alexis de la Cotte
- Centre de Recherche Paul-Pascal, CNRS, and Université de Bordeaux , 115 Avenue Schweitzer, 33600 Pessac, France
| | - Cheng Wu
- Centre de Recherche Paul-Pascal, CNRS, and Université de Bordeaux , 115 Avenue Schweitzer, 33600 Pessac, France
| | - Marie Trévisan
- Centre de Recherche Paul-Pascal, CNRS, and Université de Bordeaux , 115 Avenue Schweitzer, 33600 Pessac, France
| | - Andrii Repula
- Centre de Recherche Paul-Pascal, CNRS, and Université de Bordeaux , 115 Avenue Schweitzer, 33600 Pessac, France
| | - Eric Grelet
- Centre de Recherche Paul-Pascal, CNRS, and Université de Bordeaux , 115 Avenue Schweitzer, 33600 Pessac, France
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43
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't Hart P, Wood TM, Tehrani KHME, van Harten RM, Śleszyńska M, Rentero Rebollo I, Hendrickx APA, Willems RJL, Breukink E, Martin NI. De novo identification of lipid II binding lipopeptides with antibacterial activity against vancomycin-resistant bacteria. Chem Sci 2017; 8:7991-7997. [PMID: 29568446 PMCID: PMC5853558 DOI: 10.1039/c7sc03413j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 09/29/2017] [Indexed: 12/20/2022] Open
Abstract
Lipid II binding lipopeptides discovered via bicyclic peptide phage display exhibit promising antibacterial activity.
Creative strategies for identifying new antibiotics are essential to addressing the looming threat of a post-antibiotic era. We here report the use of a targeted peptide phage display screen as a means of generating novel antimicrobial lipopeptides. Specifically, a library of phage displayed bicyclic peptides was screened against a biomolecular target based on the bacterial cell wall precursor lipid II. In doing so we identified unique lipid II binding peptides that upon lipidation were found to be active against a range of Gram-positive bacteria including clinically relevant strains of vancomycin resistant bacteria. Optimization of the peptide sequence led to variants with enhanced antibacterial activity and reduced hemolytic activity. Biochemical experiments further confirm a lipid II mediated mode of action for these new-to-nature antibacterial lipopeptides.
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Affiliation(s)
- Peter 't Hart
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Thomas M Wood
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Kamaleddin Haj Mohammad Ebrahim Tehrani
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Roel M van Harten
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Małgorzata Śleszyńska
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Inmaculada Rentero Rebollo
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne , Lausanne , Switzerland
| | - Antoni P A Hendrickx
- Department of Medical Microbiology , University Medical Center , Utrecht , The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology , University Medical Center , Utrecht , The Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics Group , Department of Chemistry , Utrecht University , The Netherlands
| | - Nathaniel I Martin
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
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44
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Valeur E, Guéret SM, Adihou H, Gopalakrishnan R, Lemurell M, Waldmann H, Grossmann TN, Plowright AT. New Modalities for Challenging Targets in Drug Discovery. Angew Chem Int Ed Engl 2017; 56:10294-10323. [PMID: 28186380 DOI: 10.1002/anie.201611914] [Citation(s) in RCA: 233] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 01/31/2017] [Indexed: 12/11/2022]
Abstract
Our ever-increasing understanding of biological systems is providing a range of exciting novel biological targets, whose modulation may enable novel therapeutic options for many diseases. These targets include protein-protein and protein-nucleic acid interactions, which are, however, often refractory to classical small-molecule approaches. Other types of molecules, or modalities, are therefore required to address these targets, which has led several academic research groups and pharmaceutical companies to increasingly use the concept of so-called "new modalities". This Review defines for the first time the scope of this term, which includes novel peptidic scaffolds, oligonucleotides, hybrids, molecular conjugates, as well as new uses of classical small molecules. We provide the most representative examples of these modalities to target large binding surface areas such as those found in protein-protein interactions and for biological processes at the center of cell regulation.
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Affiliation(s)
- Eric Valeur
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Stéphanie M Guéret
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Hélène Adihou
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Malin Lemurell
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Herbert Waldmann
- Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany.,Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Germany
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany.,Department of Chemistry & Pharmaceutical Sciences, VU University Amsterdam, The Netherlands
| | - Alleyn T Plowright
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
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45
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Valeur E, Guéret SM, Adihou H, Gopalakrishnan R, Lemurell M, Waldmann H, Grossmann TN, Plowright AT. Neue Modalitäten für schwierige Zielstrukturen in der Wirkstoffentwicklung. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611914] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Eric Valeur
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
| | - Stéphanie M. Guéret
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Hélène Adihou
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Malin Lemurell
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
| | - Herbert Waldmann
- Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
- Fakultät für Chemie and Chemische Biologie; Technische Universität Dortmund; Deutschland
| | - Tom N. Grossmann
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; Niederlande
| | - Alleyn T. Plowright
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
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46
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Short peptides interfering with signaling pathways as new therapeutic tools for cancer treatment. Future Med Chem 2017; 9:199-221. [PMID: 28111982 DOI: 10.4155/fmc-2016-0189] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Short peptides have many advantages, such as low molecular weight, selectivity for a specific target, organelles or cells with minimal toxicity. We describe properties of short peptides, which interfere with communication networks in tumor cells and within microenvironment of malignant gliomas, the most common brain tumors. We focus on ligand/receptor axes and intracellular signaling pathways critical for gliomagenesis that could be targeted with interfering peptides. We review structures and efficacy of organelle-specific and cell-penetrating peptides and describe diverse chemical modifications increasing proteolytic stability and protecting synthetic peptides against degradation. We report results of application of short peptides in glioma therapy clinical trials, their rises and falls. The most advanced examples of therapeutics such as short interfering peptides combined with cell-penetrating peptides that show good effectiveness in disease models are presented. It is foreseen that identification of peptides with better clinical properties may improve their success rates in clinical trials.
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47
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Rentero Rebollo I, McCallin S, Bertoldo D, Entenza JM, Moreillon P, Heinis C. Development of Potent and Selective S. aureus Sortase A Inhibitors Based on Peptide Macrocycles. ACS Med Chem Lett 2016; 7:606-11. [PMID: 27326335 DOI: 10.1021/acsmedchemlett.6b00045] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/14/2016] [Indexed: 11/30/2022] Open
Abstract
Sortases are transpeptidase enzymes that anchor surface proteins, including virulence factors, to the cell wall of Gram-positive bacteria, and they are potential targets for the development of anti-infective agents. While several large compound libraries were searched by high-throughput screening, no high-affinity inhibitors of sortases could be developed to date. Here, we applied phage display to screen billions of peptide macrocycles against sortase A (SrtA) of Staphylococcus aureus (S. aureus). We were able to identify potent and selective inhibitors of SrtA that blocked SrtA-mediated anchoring of synthetic substrates to the surface of live S. aureus cells. A region present in all inhibitory peptides (Leu-Pro-Pro) resembled the natural substrates of SrtA (Leu-Pro-Xaa-Thr-Gly), suggesting that the macrocycles bind to the enzyme's active site and that they form similar molecular contacts as natural substrates. The evolved peptide macrocycles may be used as lead structures for the development of potent peptidomimetic SrtA inhibitors.
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Affiliation(s)
- Inmaculada Rentero Rebollo
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Shawna McCallin
- Department
of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Davide Bertoldo
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - José Manuel Entenza
- Department
of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Philippe Moreillon
- Department
of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Christian Heinis
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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48
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Bertoldo D, Khan MMG, Dessen P, Held W, Huelsken J, Heinis C. Phage Selection of Peptide Macrocycles against β-Catenin To Interfere with Wnt Signaling. ChemMedChem 2016; 11:834-9. [PMID: 26812578 DOI: 10.1002/cmdc.201500557] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Indexed: 12/17/2022]
Abstract
Upregulation of β-catenin, the primary mediator of the Wnt signaling pathway, plays an important role in the tumorigenesis of several types of human cancer. Targeting β-catenin to interfere with its ability to serve as a translational co-activator is considered an attractive therapeutic approach. However, the development of inhibitors has been challenging because of the lack of obvious binding pockets for ligands, and because inhibitors should not interfere with other β-catenin functions. Only two ligands with known molecular interactions with β-catenin have been developed so far, and are based on stabilized α-helical peptides. In this study, we screened a large combinatorial library of bicyclic peptides by phage display. Binders to different surface regions of β-catenin were identified. The binding site of one group of ligands was mapped to the interaction region of the translational Wnt inhibitor ICAT (inhibitor of β-catenin and Tcf), which is a prime target site on β-catenin for therapeutic intervention, and to which no ligands could be developed before.
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Affiliation(s)
- Davide Bertoldo
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Maola M G Khan
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Pierre Dessen
- Ludwig Center for Cancer Research, Department of Oncology, University of Lausanne, 1066, Epalinges, Switzerland
| | - Werner Held
- Swiss Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Joerg Huelsken
- Ludwig Center for Cancer Research, Department of Oncology, University of Lausanne, 1066, Epalinges, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
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49
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Urech-Varenne C, Radtke F, Heinis C. Phage Selection of Bicyclic Peptide Ligands of the Notch1 Receptor. ChemMedChem 2015; 10:1754-61. [DOI: 10.1002/cmdc.201500261] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/07/2015] [Indexed: 12/15/2022]
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50
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Baeriswyl V, Calzavarini S, Chen S, Zorzi A, Bologna L, Angelillo-Scherrer A, Heinis C. A Synthetic Factor XIIa Inhibitor Blocks Selectively Intrinsic Coagulation Initiation. ACS Chem Biol 2015; 10:1861-70. [PMID: 25989088 DOI: 10.1021/acschembio.5b00103] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Coagulation factor XII (FXII) inhibitors are of interest for the study of the protease in the intrinsic coagulation pathway, for the suppression of contact activation in blood coagulation assays, and they have potential application in antithrombotic therapy. However, synthetic FXII inhibitors developed to date have weak binding affinity and/or poor selectivity. Herein, we developed a peptide macrocycle that inhibits activated FXII (FXIIa) with an inhibitory constant Ki of 22 nM and a selectivity of >2000-fold over other proteases. Sequence and structure analysis revealed that one of the two macrocyclic rings of the in vitro evolved peptide mimics the combining loop of corn trypsin inhibitor, a natural protein-based inhibitor of FXIIa. The synthetic inhibitor blocked intrinsic coagulation initiation without affecting extrinsic coagulation. Furthermore, the peptide macrocycle efficiently suppressed plasma coagulation triggered by contact of blood with sample tubes and allowed specific investigation of tissue factor initiated coagulation.
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Affiliation(s)
- Vanessa Baeriswyl
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sara Calzavarini
- University
Clinic of Hematology and Central Hematology Laboratory, Bern University Hospital and the University of Bern, Inselspital, CH-3010 Bern, Switzerland
- Department
of Clinical Research, University of Bern, CH-3010 Bern, Switzerland
| | - Shiyu Chen
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Alessandro Zorzi
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Luca Bologna
- University
Clinic of Hematology and Central Hematology Laboratory, Bern University Hospital and the University of Bern, Inselspital, CH-3010 Bern, Switzerland
- Department
of Clinical Research, University of Bern, CH-3010 Bern, Switzerland
| | - Anne Angelillo-Scherrer
- University
Clinic of Hematology and Central Hematology Laboratory, Bern University Hospital and the University of Bern, Inselspital, CH-3010 Bern, Switzerland
- Department
of Clinical Research, University of Bern, CH-3010 Bern, Switzerland
| | - Christian Heinis
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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