1
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Song L, Liu H, Li M, Yang Y, Dong H, Li J, Shao J, Zhi L, Sun H, Li Z, Sui H, Zhang Y, Wu C, Yin Y. Ribosomal Incorporation of Lithocholic Acid into Peptides for the De Novo Discovery Of Peptide-Lithocholic Acid Hybrid Macrocyclic Peptides. ACS Chem Biol 2024. [PMID: 38901034 DOI: 10.1021/acschembio.4c00298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Peptide-bile acid hybrids offer promising drug candidates due to enhanced pharmacological properties, such as improved protease resistance and oral bioavailability. However, it remains unknown whether bile acids can be incorporated into peptide chains by the ribosome to produce a peptide-bile acid hybrid macrocyclic peptide library for target-based de novo screening. In this study, we achieved the ribosomal incorporation of lithocholic acid (LCA)-d-tyrosine into peptide chains. This led to the construction of a peptide-LCA hybrid macrocyclic peptide library, which enabled the identification of peptides TP-2C-4L3 (targeting Trop2) and EP-2C-4L5 (targeting EphA2) with strong binding affinities. Notably, LCA was found to directly participate in binding to EphA2 and confer on the peptides improved stability and resistance to proteases. Cell staining experiments confirmed the high specificity of the peptides for targeting Trop2 and EphA2. This study highlights the benefits of LCA in peptides and paves the way for de novo discovery of stable peptide-LCA hybrid drugs.
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Affiliation(s)
- Lulu Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Hongtan Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Maolin Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yawen Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Huilei Dong
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Jinjing Li
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Jiaqi Shao
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lixu Zhi
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Sun
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhifeng Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Haiyan Sui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Chuanliu Wu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Yizhen Yin
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
- Shandong Research Institute of Industrial Technology, Jinan 250101, China
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2
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Bohley M, Leroux JC. Gastrointestinal Permeation Enhancers Beyond Sodium Caprate and SNAC - What is Coming Next? ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400843. [PMID: 38884149 DOI: 10.1002/advs.202400843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/13/2024] [Indexed: 06/18/2024]
Abstract
Oral peptide delivery is trending again. Among the possible reasons are the recent approvals of two oral peptide formulations, which represent a huge stride in the field. For the first time, gastrointestinal (GI) permeation enhancers (PEs) are leveraged to overcome the main limitation of oral peptide delivery-low permeability through the intestinal epithelium. Despite some success, the application of current PEs, such as salcaprozate sodium (SNAC), sodium caprylate (C8), and sodium caprate (C10), is generally resulting in relatively low oral bioavailabilities (BAs)-even for carefully selected therapeutics. With several hundred peptide-based drugs presently in the pipeline, there is a huge unmet need for more effective PEs. Aiming to provide useful insights for the development of novel PEs, this review summarizes the biological hurdles to oral peptide delivery with special emphasis on the epithelial barrier. It describes the concepts and action modes of PEs and mentions possible new targets. It further states the benchmark that is set by current PEs, while critically assessing and evaluating emerging PEs regarding translatability, safety, and efficacy. Additionally, examples of novel PEs under preclinical and clinical evaluation and future directions are discussed.
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Affiliation(s)
- Marilena Bohley
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Jean-Christophe Leroux
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
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3
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Bak-Sypien I, Pawlak T, Paluch P, Wroblewska A, Dolot R, Pawlowicz A, Szczesio M, Wielgus E, Kaźmierski S, Górecki M, Pawlowska R, Chworos A, Potrzebowski MJ. Influence of heterochirality on the structure, dynamics, biological properties of cyclic(PFPF) tetrapeptides obtained by solvent-free ball mill mechanosynthesis. Sci Rep 2024; 14:12825. [PMID: 38834643 DOI: 10.1038/s41598-024-63552-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
Cyclic tetrapeptides c(Pro-Phe-Pro-Phe) obtained by the mechanosynthetic method using a ball mill were isolated in a pure stereochemical form as a homochiral system (all L-amino acids, sample A) and as a heterochiral system with D configuration at one of the stereogenic centers of Phe (sample B). The structure and stereochemistry of both samples were determined by X-ray diffraction studies of single crystals. In DMSO and acetonitrile, sample A exists as an equimolar mixture of two conformers, while only one is monitored for sample B. The conformational space and energetic preferences for possible conformers were calculated using DFT methods. The distinctly different conformational flexibility of the two samples was experimentally proven by Variable Temperature (VT) and 2D EXSY NMR measurements. Both samples were docked to histone deacetylase HDAC8. Cytotoxic studies proved that none of the tested cyclic peptide is toxic.
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Affiliation(s)
- Irena Bak-Sypien
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Piotr Paluch
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Aneta Wroblewska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Rafał Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Aleksandra Pawlowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 St., 61-704, Poznan, Poland
| | - Małgorzata Szczesio
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116 St., 90-924, Lodz, Poland
| | - Ewelina Wielgus
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Sławomir Kaźmierski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224, Warsaw, Poland
| | - Roza Pawlowska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Arkadiusz Chworos
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Marek J Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland.
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4
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Matsuda K, Wakimoto T. Penicillin-binding protein-type thioesterases: An emerging family of non-ribosomal peptide cyclases with biocatalytic potentials. Curr Opin Chem Biol 2024; 80:102465. [PMID: 38759287 DOI: 10.1016/j.cbpa.2024.102465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/19/2024]
Abstract
Macrocyclization of peptides reduces conformational flexibilities, potentially leading to improved drug-like properties, such as target specificities and metabolic stabilities. As chemical methodologies often allow side reactions like epimerization and oligomerization, keen attention has been directed toward enzymatic peptide cyclization using peptide cyclases from specialized metabolic pathways. Penicillin-binding protein-type thioesterases (PBP-type TEs) are a recently identified family of peptide cyclases involved in the biosynthesis of non-ribosomal peptides in actinobacteria. PBP-type TEs have undergone intensive investigation due to their outstanding potential as biocatalysts. This review summarizes the rapidly growing knowledge on PBP-type TEs, with special emphasis on their functions, scopes, and structures, and efforts towards their biocatalytic applications.
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Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.
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5
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Zuo Q, Li Y, Lai X, Bao G, Chen L, He Z, Song X, E R, Wang P, Shi Y, Luo H, Sun W, Wang R. Cysteine-Specific Multifaceted Bioconjugation of Peptides and Proteins Using 5-Substituted 1,2,3-Triazines. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308491. [PMID: 38466927 DOI: 10.1002/advs.202308491] [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: 11/07/2023] [Revised: 02/08/2024] [Indexed: 03/13/2024]
Abstract
Peptide and protein postmodification have gained significant attention due to their extensive impact on biomolecule engineering and drug discovery, of which cysteine-specific modification strategies are prominent due to their inherent nucleophilicity and low abundance. Herein, the study introduces a novel approach utilizing multifunctional 5-substituted 1,2,3-triazine derivatives to achieve multifaceted bioconjugation targeting cysteine-containing peptides and proteins. On the one hand, this represents an inaugural instance of employing 1,2,3-triazine in biomolecular-specific modification within a physiological solution. On the other hand, as a powerful combination of precision modification and biorthogonality, this strategy allows for the one-pot dual-orthogonal functionalization of biomolecules utilizing the aldehyde group generated simultaneously. 1,2,3-Triazine derivatives with diverse functional groups allow conjugation to peptides or proteins, while bi-triazines enable peptide cyclization and dimerization. The examination of the stability of bi-triazines revealed their potential for reversible peptide modification. This work establishes a comprehensive platform for identifying cysteine-selective modifications, providing new avenues for peptide-based drug development, protein bioconjugation, and chemical biology research.
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Affiliation(s)
- Quan Zuo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street, Beijing, 100050, P. R. China
| | - Yiping Li
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, Lanzhou University, 199 West Donggang Road, Lanzhou, Gansu, 730000, P. R. China
| | - Xuanliang Lai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street, Beijing, 100050, P. R. China
| | - Guangjun Bao
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, Lanzhou University, 199 West Donggang Road, Lanzhou, Gansu, 730000, P. R. China
| | - Lu Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street, Beijing, 100050, P. R. China
| | - Zeyuan He
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, Lanzhou University, 199 West Donggang Road, Lanzhou, Gansu, 730000, P. R. China
| | - Xinyi Song
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, Lanzhou University, 199 West Donggang Road, Lanzhou, Gansu, 730000, P. R. China
| | - Ruiyao E
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, Lanzhou University, 199 West Donggang Road, Lanzhou, Gansu, 730000, P. R. China
| | - Pengxin Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street, Beijing, 100050, P. R. China
| | - Yuntao Shi
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street, Beijing, 100050, P. R. China
| | - Huixin Luo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street, Beijing, 100050, P. R. China
| | - Wangsheng Sun
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, Lanzhou University, 199 West Donggang Road, Lanzhou, Gansu, 730000, P. R. China
| | - Rui Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street, Beijing, 100050, P. R. China
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, Lanzhou University, 199 West Donggang Road, Lanzhou, Gansu, 730000, P. R. China
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6
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Fan XZ, Song JQ, Zhang LJ, Wang R, Liu T, Bai WJ, Kong XQ, Huang YS, Liang H, Liao HB. Picrachinentins A-F, 14-Membered Cyclopeptide Alkaloid-Type Burpitides with Uncommon N-Terminal Modifications from Picrasma chinensis and Their Neuroprotective Activity. Org Lett 2024. [PMID: 38787765 DOI: 10.1021/acs.orglett.4c01390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Picrachinentins A-F (1-6, respectively), six novel cyclopeptide alkaloid-type burpitides (CPABs), were isolated and fully elucidated from the EtOH extract of the stems and leaves of Picrasma chinensis. Structurally, compounds 1-6 have a 14-membered paracyclophane ring system that was closed through an ether bond between the β-hydroxy amino acid and tyrosine and modified with a 4,5-methylenedioxybenzoyloxy (MDBz, 3 and 5) or hexanoyl (Hexa, 1, 2, 4, and 6) group at the N-terminus. Interestingly, this is the first report on the isolation and characterization of CPABs from plants of the Simaroubaceae family. In addition, all compounds showed a neuroprotective effect against H2O2-damaged SH-SY5Y cells. Compound 1 was further investigated for its neuroprotective activities using a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced Parkinson's disease animal model, and it dramatically improved MPTP-impaired motor behavioral performance. Biochemical analysis revealed compound 1 restored the tyrosine hydroxylase expression in the striatum of the MPTP-damaged mouse brain, which demonstrates its protective effect on dopaminergic neurons.
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Affiliation(s)
- Xian-Zhe Fan
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Jia-Qi Song
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Li-Jun Zhang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Rong Wang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Ting Liu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Wen-Jing Bai
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiang-Qian Kong
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Ya-Si Huang
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Hong Liang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Hai-Bing Liao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
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7
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Bruce A, Adebomi V, Czabala P, Palmer J, McFadden WM, Lorson ZC, Slack RL, Bhardwaj G, Sarafianos SG, Raj M. A Tag-Free Platform for Synthesis and Screening of Cyclic Peptide Libraries. Angew Chem Int Ed Engl 2024; 63:e202320045. [PMID: 38529717 DOI: 10.1002/anie.202320045] [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: 12/26/2023] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
In the realm of high-throughput screening (HTS), macrocyclic peptide libraries traditionally necessitate decoding tags, essential for both library synthesis and identifying hit peptide sequences post-screening. Our innovation introduces a tag-free technology platform for synthesizing cyclic peptide libraries in solution and facilitates screening against biological targets to identify peptide binders through unconventional intramolecular CyClick and DeClick chemistries (CCDC) discovered through our research. This combination allows for the synthesis of diverse cyclic peptide libraries, the incorporation of various amino acids, and facile linearization and decoding of cyclic peptide binder sequences. Our sensitivity-enhancing derivatization method, utilized in tandem with nano LC-MS/MS, enables the sequencing of peptides even at exceedingly low picomolar concentrations. Employing our technology platform, we have successfully unearthed novel cyclic peptide binders against a monoclonal antibody and the first cyclic peptide binder of HIV capsid protein responsible for viral infections as validated by microscale thermal shift assays (TSA), biolayer interferometry (BLI) and functional assays.
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Affiliation(s)
- Angele Bruce
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
| | - Victor Adebomi
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States, 98195
| | - Patrick Czabala
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
| | - Jonathan Palmer
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States, 98195
| | - William M McFadden
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA, 30322, United States
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, United States
| | - Zachary C Lorson
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA, 30322, United States
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, United States
| | - Ryan L Slack
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA, 30322, United States
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, United States
| | - Gaurav Bhardwaj
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States, 98195
| | - Stefan G Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA, 30322, United States
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, United States
| | - Monika Raj
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
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8
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Saunders GJ, Spring SA, Jayawant E, Wilkening I, Roesner S, Clarkson GJ, Dixon AM, Notman R, Shipman M. Synthesis and Functionalization of Azetidine-Containing Small Macrocyclic Peptides. Chemistry 2024; 30:e202400308. [PMID: 38488326 DOI: 10.1002/chem.202400308] [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: 02/25/2024] [Indexed: 04/11/2024]
Abstract
Cyclic peptides are increasingly important structures in drugs but their development can be impeded by difficulties associated with their synthesis. Here, we introduce the 3-aminoazetidine (3-AAz) subunit as a new turn-inducing element for the efficient synthesis of small head-to-tail cyclic peptides. Greatly improved cyclizations of tetra-, penta- and hexapeptides (28 examples) under standard reaction conditions are achieved by introduction of this element within the linear peptide precursor. Post-cyclization deprotection of the amino acid side chains with strong acid is realized without degradation of the strained four-membered azetidine. A special feature of this chemistry is that further late-stage modification of the resultant macrocyclic peptides can be achieved via the 3-AAz unit. This is done by: (i) chemoselective deprotection and substitution at the azetidine nitrogen, or by (ii) a click-based approach employing a 2-propynyl carbamate on the azetidine nitrogen. In this way, a range of dye and biotin tagged macrocycles are readily produced. Structural insights gained by XRD analysis of a cyclic tetrapeptide indicate that the azetidine ring encourages access to the less stable, all-trans conformation. Moreover, introduction of a 3-AAz into a representative cyclohexapeptide improves stability towards proteases compared to the homodetic macrocycle.
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Affiliation(s)
- George J Saunders
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Sam A Spring
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Eleanor Jayawant
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Ina Wilkening
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Stefan Roesner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Guy J Clarkson
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Ann M Dixon
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Rebecca Notman
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Michael Shipman
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
- The Palatine Centre, Stockton Road, Durham, DH1 3LE, U.K
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9
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Hampton JT, Liu WR. Diversification of Phage-Displayed Peptide Libraries with Noncanonical Amino Acid Mutagenesis and Chemical Modification. Chem Rev 2024; 124:6051-6077. [PMID: 38686960 PMCID: PMC11082904 DOI: 10.1021/acs.chemrev.4c00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Sitting on the interface between biologics and small molecules, peptides represent an emerging class of therapeutics. Numerous techniques have been developed in the past 30 years to take advantage of biological methods to generate and screen peptide libraries for the identification of therapeutic compounds, with phage display being one of the most accessible techniques. Although traditional phage display can generate billions of peptides simultaneously, it is limited to expression of canonical amino acids. Recently, several groups have successfully undergone efforts to apply genetic code expansion to introduce noncanonical amino acids (ncAAs) with novel reactivities and chemistries into phage-displayed peptide libraries. In addition to biological methods, several different chemical approaches have also been used to install noncanonical motifs into phage libraries. This review focuses on these recent advances that have taken advantage of both biological and chemical means for diversification of phage libraries with ncAAs.
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Affiliation(s)
- J. Trae Hampton
- Texas
A&M Drug Discovery Center and Department of Chemistry, College
of Arts and Sciences, Texas A&M University, College Station, Texas 77843, United States
| | - Wenshe Ray Liu
- Texas
A&M Drug Discovery Center and Department of Chemistry, College
of Arts and Sciences, Texas A&M University, College Station, Texas 77843, United States
- Institute
of Biosciences and Technology and Department of Translational Medical
Sciences, College of Medicine, Texas A&M
University, Houston, Texas 77030, United States
- Department
of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas 77843, United States
- Department
of Cell Biology and Genetics, College of Medicine, Texas A&M University, College
Station, Texas 77843, United States
- Department
of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas 77843, United States
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10
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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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11
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Keyes ED, Mifflin MC, Austin MJ, Sandres J, Roberts AG. Chemical cyclization of tyrosine-containing peptides via in situ generated triazolinedione peptides. Methods Enzymol 2024; 698:89-109. [PMID: 38886041 DOI: 10.1016/bs.mie.2024.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Tyr-derived cyclic peptide natural products are formed by enzymatic manifolds that oxidatively cross-link embedded phenolic side chains of tyrosine (Tyr) and 4-hydroxyphenylglycine residues during their controlled production. Bioactive Tyr-derived cyclic peptides, such as the arylomycins and vancomycins, continue to motivate the development of enzymatic and chemical strategies for their de novo assembly and modification. However, chemical access to these structurally diverse natural cycles can be challenging and step intensive. Therefore, we developed an oxidative procedure to selectively convert Tyr-containing N4-substituted 1,2,4-triazolidine-3,5-dione peptides (urazole peptides) into stable Tyr-linked cyclic peptides. We show that Tyr-containing urazole peptides are simple to prepare and convert into reactive N4-substituted 1,2,4-triazoline-3,5-dione peptides by oxidation, which then undergo spontaneous cyclization under mildly basic aqueous conditions to form a cross-linkage with the phenol side chain of embedded Tyr residues. Using this approach, we have demonstrated access to over 25 Tyr-linked cyclic peptides (3- to 11-residue cycles) with good tolerance of native residue side chain functionalities. Importantly, this method is simple to perform, and product formation can be quickly confirmed by mass spectrometric and 1H NMR spectroscopic analyses.
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Affiliation(s)
- E Dalles Keyes
- Department of Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Marcus C Mifflin
- Department of Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Maxwell J Austin
- Department of Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Jesus Sandres
- Department of Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Andrew G Roberts
- Department of Chemistry, University of Utah, Salt Lake City, UT, United States.
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12
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Frazee N, Billlings KR, Mertz B. Gaussian accelerated molecular dynamics simulations facilitate prediction of the permeability of cyclic peptides. PLoS One 2024; 19:e0300688. [PMID: 38652734 PMCID: PMC11037548 DOI: 10.1371/journal.pone.0300688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 03/02/2024] [Indexed: 04/25/2024] Open
Abstract
Despite their widespread use as therapeutics, clinical development of small molecule drugs remains challenging. Among the many parameters that undergo optimization during the drug development process, increasing passive cell permeability (i.e., log(P)) can have some of the largest impact on potency. Cyclic peptides (CPs) have emerged as a viable alternative to small molecules, as they retain many of the advantages of small molecules (oral availability, target specificity) while being highly effective at traversing the plasma membrane. However, the relationship between the dominant conformations that typify CPs in an aqueous versus a membrane environment and cell permeability remain poorly characterized. In this study, we have used Gaussian accelerated molecular dynamics (GaMD) simulations to characterize the effect of solvent on the free energy landscape of lariat peptides, a subset of CPs that have recently shown potential for drug development (Kelly et al., JACS 2021). Differences in the free energy of lariat peptides as a function of solvent can be used to predict permeability of these molecules, and our results show that permeability is most greatly influenced by N-methylation and exposure to solvent. Our approach lays the groundwork for using GaMD as a way to virtually screen large libraries of CPs and drive forward development of CP-based therapeutics.
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Affiliation(s)
- Nicolas Frazee
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, United States of America
| | - Kyle R. Billlings
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, United States of America
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, United States of America
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13
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Limbach M, Lindberg ET, Olivos HJ, van Tetering L, Steren CA, Martens J, Ngo VA, Oomens J, Do TD. Taming Conformational Heterogeneity on Ion Racetrack to Unveil Principles that Drive Membrane Permeation of Cyclosporines. JACS AU 2024; 4:1458-1470. [PMID: 38665661 PMCID: PMC11040698 DOI: 10.1021/jacsau.4c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 04/28/2024]
Abstract
Our study reveals the underlying principles governing the passive membrane permeability in three large N-methylated macrocyclic peptides (N-MeMPs): cyclosporine A (CycA), Alisporivir (ALI), and cyclosporine H (CycH). We determine a series of conformers required for robust passive membrane diffusion and those relevant to other functions, such as binding to protein targets or intermediates, in the presence of solvent additives. We investigate the conformational interconversions and establish correlations with the membrane permeability. Nuclear magnetic resonance (NMR) and cyclic ion-mobility spectrometry-mass spectrometry (cIMS-MS) are employed to characterize conformational heterogeneity and identify cis-amides relevant for good membrane permeability. In addition, ion mobility selected cIMS-MS and infrared (IR) multiple-photon dissociation (IRMPD) spectroscopy experiments are conducted to evaluate the energy barriers between conformations. We observe that CycA and ALI, both cyclosporines with favorable membrane permeabilities, display multiple stable and well-defined conformers. In contrast, CycH, an epimer of CycA with limited permeability, exhibits fewer and fewer stable conformers. We demonstrate the essential role of the conformational shift from the aqueous cis MeVal11-MeBmt1 state (A1) to the closed conformation featuring cis MeLeu9-MeLeu10 (C1) in facilitating membrane permeation. Additionally, we highlight that the transition from A1 to the all-trans open conformation (O1) is specifically triggered by the presence of CaCl2. We also capture a set of conformers with cis Sar3-MeLeu4, MeLeu9-MeLeu10, denoted as I. Conformationally selected cIMS-MS and IRMPD data of [CycA+Ca]2+ show immediate repopulation of the original population distribution, suggesting that CaCl2 smooths out the energy barriers. Finally, our work presents an improved sampling molecular dynamics approach based on a refined force field that not only consistently and accurately captures established conformers of cyclosporines but also exhibits strong predictive capabilities for novel conformers.
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Affiliation(s)
- Miranda
N. Limbach
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Edward T. Lindberg
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | | | - Lara van Tetering
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, The Netherlands
| | - Carlos A. Steren
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jonathan Martens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, The Netherlands
| | - Van A. Ngo
- Advanced
Computing for Life Sciences and Engineering Group, Science Engagement
Section, National Center for Computational Sciences, Computing and
Computational Sciences Directorate, Oak
Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, The Netherlands
| | - Thanh D. Do
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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14
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Bao Y, Xing M, Matthew N, Chen X, Wang X, Lu X. Macrocyclizing DNA-Linked Peptides via Three-Component Cyclization and Photoinduced Chemistry. Org Lett 2024; 26:2763-2767. [PMID: 37382883 DOI: 10.1021/acs.orglett.3c01817] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
While DNA-encoded macrocyclic libraries have gained substantial attention and several hit compounds have been identified from DNA-encoded library technology, efficient on-DNA macrocyclic methods are also required to construct DNA-linked libraries with a high degree of cyclization and DNA integrity. In this paper, we reported a set of on-DNA methodologies, including the use of an OPA-mediated three-component cyclization with native handles of amino acids and photoredox chemistries. These chemistries proceed smoothly under mild conditions in good to excellent conversions, successfully generating novel isoindole, isoindoline, indazolone, and bicyclic scaffolds.
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Affiliation(s)
- Yandan Bao
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China
| | - Minyan Xing
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Jiangning District, Nanjing 211198, China
| | - Naylor Matthew
- UCB, 87 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Xiaohua Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China
| | - Xiaojie Lu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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15
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Chen Z, Li Y, Wang X, Qiu X, Wang C, Wang Z, Chen X, Wang J. A high-throughput molecular dynamics screening (HTMDS) approach to the design of novel cyclopeptide inhibitors of ATAD2B based on the non-canonical combinatorial library. J Biomol Struct Dyn 2024; 42:2809-2824. [PMID: 37194299 DOI: 10.1080/07391102.2023.2212796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 04/19/2023] [Indexed: 05/18/2023]
Abstract
Cyclic peptides (CPs) are a promising class of drugs because of their high biological activity and specificity. However, the design of CP remains challenging due to their conformational flexibility and difficulties in designing stable binding conformation. Herein, we present a high-throughput MD screening (HTMDS) process for the iterative design of stable CP binders with a combinatorial CP library composed of canonical and non-canonical amino acids. As a proof of concept, we apply our methods to design CP inhibitors for the bromodomain (BrD) of ATAD2B. 698,800 CP candidates with a total of 25,570 ns MD simulations were performed to study the protein-ligand binding interactions. The binding free energies (ΔGbind) estimated by MM/PBSA approach for eight lead CP designs were found to be low. CP-1st.43 was the best CP candidate with an estimated ΔGbind of -28.48 kcal/mol when compared to the standard inhibitor C-38 which has been experimentally validated and shown to exhibit ΔGbind of -17.11 kcal/mol. The major contribution of binding sites for BrD of ATAD2B involved the hydrogen-bonding anchor within the Aly-binding pocket, salt bridging, and hydrogen-bonding mediated stabilization of the ZA loop and BC loop, and the complementary Van der Waals attraction. Our methods demonstrate encouraging results by yielding conformationally stable and high-potential CP binders that should have potential applicability in future CP drug development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zhidong Chen
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yongxiao Li
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Xinpei Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Xiaohui Qiu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Chenglin Wang
- Shenzhen Qiyu Biotechnology Co., Ltd, Shenzhen, China
| | - Zhe Wang
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xu Chen
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Junqing Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
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16
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Kobayashi M, Onozawa N, Matsuda K, Wakimoto T. Chemoenzymatic tandem cyclization for the facile synthesis of bicyclic peptides. Commun Chem 2024; 7:67. [PMID: 38548970 PMCID: PMC10978974 DOI: 10.1038/s42004-024-01147-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/13/2024] [Indexed: 04/01/2024] Open
Abstract
Bicyclic peptides exhibit improved metabolic stabilities and target specificities when compared to their linear or mono-cyclic counterparts; however, efficient and straightforward synthesis remains challenging due to their intricate architectures. Here, we present a highly selective and operationally simple one-pot chemoenzymatic tandem cyclization approach to synthesize bicyclic peptides with small to medium ring sizes. Penicillin-binding protein-type thioesterases (PBP-type TEs) efficiently cyclized azide/alkyne-containing peptides in a head-to-tail manner. Successive copper (I)-catalyzed azide-alkyne cycloaddition generated bicyclic peptides in one-pot, thus omitting the purification of monocyclic intermediates. This chemoenzymatic strategy enabled the facile synthesis of bicyclic peptides bearing hexa-, octa-, and undecapeptidyl head-to-tail cyclic scaffolds.
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Affiliation(s)
- Masakazu Kobayashi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Naho Onozawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
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17
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Zhang C, Zhang C, Shang T, Zhu N, Wu X, Duan H. HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints. Brief Bioinform 2024; 25:bbae215. [PMID: 38706323 PMCID: PMC11070728 DOI: 10.1093/bib/bbae215] [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: 09/29/2023] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024] Open
Abstract
In recent years, cyclic peptides have emerged as a promising therapeutic modality due to their diverse biological activities. Understanding the structures of these cyclic peptides and their complexes is crucial for unlocking invaluable insights about protein target-cyclic peptide interaction, which can facilitate the development of novel-related drugs. However, conducting experimental observations is time-consuming and expensive. Computer-aided drug design methods are not practical enough in real-world applications. To tackles this challenge, we introduce HighFold, an AlphaFold-derived model in this study. By integrating specific details about the head-to-tail circle and disulfide bridge structures, the HighFold model can accurately predict the structures of cyclic peptides and their complexes. Our model demonstrates superior predictive performance compared to other existing approaches, representing a significant advancement in structure-activity research. The HighFold model is openly accessible at https://github.com/hongliangduan/HighFold.
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Affiliation(s)
- Chenhao Zhang
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Chengyun Zhang
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
- AI department, Shanghai Highslab Therapeutics. Inc, Shanghai, 201203, China
| | - Tianfeng Shang
- AI department, Shanghai Highslab Therapeutics. Inc, Shanghai, 201203, China
| | - Ning Zhu
- China Pharmaceutical University, Nanjing, Jiangsu, 211198, China
| | - Xinyi Wu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Hongliang Duan
- Faculty of Applied Sciences, Macao Polytechnic University, R. de Luís Gonzaga Gomes, Macao, 999078, China
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18
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Zhang C, Liu F, Zhang Y, Song C. Macrocycles and macrocyclization in anticancer drug discovery: Important pieces of the puzzle. Eur J Med Chem 2024; 268:116234. [PMID: 38401189 DOI: 10.1016/j.ejmech.2024.116234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024]
Abstract
Increasing disease-related proteins have been identified as novel therapeutic targets. Macrocycles are emerging as potential solutions, bridging the gap between conventional small molecules and biomacromolecules in drug discovery. Inspired by successful macrocyclic drugs of natural origins, macrocycles are attracting more attention for enhanced binding affinity and target selectivity. Due to the conformation constraint and structure preorganization, macrocycles can reach bioactive conformations more easily than parent acyclic compounds. Also, rational macrocyclization combined with sequent structural modification will help improve oral bioavailability and combat drug resistance. This review introduces various strategies to enhance membrane permeability in macrocyclization and subsequent modification, such as N-methylation, intramolecular hydrogen bonding modulation, isomerization, and reversible bicyclization. Several case studies highlight macrocyclic inhibitors targeting kinases, HDAC, and protein-protein interactions. Finally, some macrocyclic agents targeting tumor microenvironments are illustrated.
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Affiliation(s)
- Chao Zhang
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Fenfen Liu
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Chun Song
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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19
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Tseng TS, Lee CC, Chen PJ, Lin CY, Chen WC, Lee YC, Lin JH, Chen KW, Tsai KC. Structure-Guided Discovery of PD-1/PD-L1 Interaction Inhibitors: Peptide Design, Screening, and Optimization via Computation-Aided Phage Display Engineering. J Chem Inf Model 2024; 64:1615-1627. [PMID: 38356220 DOI: 10.1021/acs.jcim.3c01500] [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: 02/16/2024]
Abstract
Cancer immunotherapy harnesses the immune system to combat tumors and has emerged as a major cancer treatment modality. The PD-1/PD-L1 immune checkpoint modulates interactions between tumor cells and T cells and has been extensively targeted in cancer immunotherapy. However, the monoclonal antibodies known to target this immune checkpoint have considerable side effects, and novel PD-1/PD-L1 inhibitors are therefore required. Herein, a peptide inhibitor to disrupt PD-1/PD-L1 interactions was designed through structure-driven phage display engineering coupled to computational modification and optimization. BetaPb, a novel peptide library constructed by using the known structure of PD-1/PD-L, was used to develop inhibitors against the immune checkpoint, and specific peptides with high affinity toward PD-1 were screened through enzyme-linked immunosorbent assays, homogeneous time-resolved fluorescence, and biolayer interferometry. A potential inhibitor, B8, was preliminarily screened through biopanning. The binding affinity of B8 toward PD-1 was confirmed through computation-aided optimization. Assessment of B8 variants (B8.1, B8.2, B8.3, B8.4, and B8.5) demonstrated their attenuation of PD-1/PD-L1 interactions. B8.4 exhibited the strongest attenuation efficiency at a half-maximal effective concentration of 0.1 μM and the strongest binding affinity to PD-1 (equilibrium dissociation constant = 0.1 μM). B8.4 outperformed the known PD-1/PD-L1 interaction inhibitor PL120131 in disrupting PD-1/PD-L1 interactions, revealing that B8.4 has remarkable potential for modification to yield an antitumor agent. This study provides valuable information for the future development of peptide-based drugs, therapeutics, and immunotherapies for cancer.
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Affiliation(s)
- Tien-Sheng Tseng
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40202, Taiwan
| | - Chao-Chang Lee
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei 11221, Taiwan
| | - Po-Juei Chen
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40202, Taiwan
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei 11221, Taiwan
| | - Chiu-Yuen Lin
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei 11221, Taiwan
| | - Wang-Chuan Chen
- The School of Chinese Medicine for Post Baccalaureate, I-Shou University, Kaohsiung 824005, Taiwan
- Department of Chinese Medicine, E-Da Hospital, Kaohsiung 824005, Taiwan
| | - Yu-Ching Lee
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Jiun-Han Lin
- Department of Industrial Technology, Ministry of Economic Affairs, Taipei 100210, Taiwan
- Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
| | - Kaun-Wen Chen
- Molecular Science and Digital Innovation Center, Genetics Generation Advancement Corporation, Taipei 11949, Taiwan
| | - Keng-Chang Tsai
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei 11221, Taiwan
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
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20
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Hayward D, Beekman AM. Strategies for converting turn-motif and cyclic peptides to small molecules for targeting protein-protein interactions. RSC Chem Biol 2024; 5:198-208. [PMID: 38456035 PMCID: PMC10915966 DOI: 10.1039/d3cb00222e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/07/2024] [Indexed: 03/09/2024] Open
Abstract
The development of small molecules that interact with protein-protein interactions is an ongoing challenge. Peptides offer a starting point in the drug discovery process for targeting protein-interactions due to their larger, more flexible structure and the structurally diverse properties that allow for a greater interaction with the protein. The techniques for rapidly identifying potent cyclic peptides and turn-motif peptides are highly effective, but this potential has not yet transferred to approved drug candidates. By applying the properties of the peptide-protein interaction the development of small molecules for drug discovery has the potential to be more efficient. In this review, we discuss the methods that allow for the unique binding properties of peptides to proteins, and the methods deployed to transfer these qualities to potent small molecules.
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Affiliation(s)
- Deanne Hayward
- School of Pharmacy, University of East Anglia, Norwich Research Park Norwich Norfolk NR47TJ UK
| | - Andrew M Beekman
- School of Pharmacy, University of East Anglia, Norwich Research Park Norwich Norfolk NR47TJ UK
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21
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Liu CL, Wang ZJ, Shi J, Yan ZY, Zhang GD, Jiao RH, Tan RX, Ge HM. P450-Modified Multicyclic Cyclophane-Containing Ribosomally Synthesized and Post-Translationally Modified Peptides. Angew Chem Int Ed Engl 2024; 63:e202314046. [PMID: 38072825 DOI: 10.1002/anie.202314046] [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: 09/19/2023] [Indexed: 01/24/2024]
Abstract
Cyclic peptides with cyclophane linkers are an attractive compound type owing to the fine-tuned rigid three-dimensional structures and unusual biophysical features. Cytochrome P450 enzymes are capable of catalyzing not only the C-C and C-O oxidative coupling reactions found in vancomycin and other nonribosomal peptides (NRPs), but they also exhibit novel catalytic activities to generate cyclic ribosomally synthesized and post-translationally modified peptides (RiPPs) through cyclophane linkage. To discover more P450-modified multicyclic RiPPs, we set out to find cryptic and unknown P450-modified RiPP biosynthetic gene clusters (BGCs) through genome mining. Synergized bioinformatic analysis reveals that P450-modified RiPP BGCs are broadly distributed in bacteria and can be classified into 11 classes. Focusing on two classes of P450-modified RiPP BGCs where precursor peptides contain multiple conserved aromatic amino acid residues, we characterized 11 novel P450-modified multicyclic RiPPs with different cyclophane linkers through heterologous expression. Further mutation of the key ring-forming residues and combinatorial biosynthesis study revealed the order of bond formation and the specificity of P450s. This study reveals the functional diversity of P450 enzymes involved in the cyclophane-containing RiPPs and indicates that P450 enzymes are promising tools for rapidly obtaining structurally diverse cyclic peptide derivatives.
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Affiliation(s)
- Cheng Li Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Zi Jie Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Zhang Yuan Yan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Guo Dong Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
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22
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Geers DWT, Gavriel K, Neumann K. Rapid, traceless and facile peptide cyclization enabled by tetrazine-thiol exchange. J Pept Sci 2024; 30:e3548. [PMID: 37779097 DOI: 10.1002/psc.3548] [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: 06/02/2023] [Revised: 08/25/2023] [Accepted: 09/14/2023] [Indexed: 10/03/2023]
Abstract
Cyclic peptides offer many advantages compared to their linear counterparts, including prolonged stability within the biological environment and enhanced binding affinity. Typically, peptides are cyclized by forming an amide bond, either on-resin or in solution, through extensive use of orthogonal protecting groups or chemoselective ligation strategies, respectively. Here, we show that the chemoselective tetrazine-thiol exchange is a powerful tool for rapid in situ cyclization of peptides without the need for additional activation reagents or extensive protecting group reshuffling. The reaction between N-terminal sulfide-bearing unsymmetric tetrazines and internal cysteines occurs spontaneously within a mildly acidic environment (pH 6.5) and is of traceless nature. The rapidly available unsymmetric sulfide tetrazine building blocks can be incorporated on resin using standard solid-phase peptide synthesis protocols and are orthogonal to trifluoroacetic acid cleavage conditions. The cyclized peptides display high stability, even when incubated with a large excess of free thiols. Due to its traceless and mild nature, we expect that the tetrazine-thiol exchange will be of high value for the in situ formation of cyclic peptide libraries, thus being applicable in drug discovery and development.
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Affiliation(s)
- Daniëlle W T Geers
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Katerina Gavriel
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Kevin Neumann
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
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23
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Di Matteo V, Esposito G, Costantino V, Della Sala G, Teta R, Mangoni A. When Synthesis Gets It Wrong: Unexpected Epimerization Using PyBOP in the Synthesis of the Cyclic Peptide Thermoactinoamide A. JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 38411075 DOI: 10.1021/acs.jnatprod.3c01229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Chemical synthesis is commonly seen as the final proof of the structure of complex natural products, but even a seemingly easy and well-established synthetic procedure may lead to an unexpected result. This is what happened with the synthesis of thermoactinoamide A (1a), an antimicrobial and antitumor nonribosomal cyclic hexapeptide produced by the thermophilic bacterium Thermoactinomyces vulgaris. The synthetic thermoactinoamide A outsourced to a company and the one described in a synthetic paper showed spectroscopic data identical to each other but different from those of the natural product. After a detailed spectroscopic, degradative, and synthetic study, the synthetic compound was shown to be an epimer (1b) of the intended target compound, originating during the cyclization reaction by extensive epimerization at the activated C-terminal amino acid. This allowed confirmation of the structure of the natural product.
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Affiliation(s)
- Viviana Di Matteo
- Department of Pharmacy, Universitá degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Germana Esposito
- Department of Pharmacy, Universitá degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Valeria Costantino
- Department of Pharmacy, Universitá degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Gerardo Della Sala
- Department of Eco-Sustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via F.A. Acton, Molosiglio, 80133 Napoli, Italy
| | - Roberta Teta
- Department of Pharmacy, Universitá degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Alfonso Mangoni
- Department of Pharmacy, Universitá degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
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24
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Faris JH, Adaligil E, Popovych N, Ono S, Takahashi M, Nguyen H, Plise E, Taechalertpaisarn J, Lee HW, Koehler MFT, Cunningham CN, Lokey RS. Membrane Permeability in a Large Macrocyclic Peptide Driven by a Saddle-Shaped Conformation. J Am Chem Soc 2024; 146:4582-4591. [PMID: 38330910 PMCID: PMC10885153 DOI: 10.1021/jacs.3c10949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
The effort to modulate challenging protein targets has stimulated interest in ligands that are larger and more complex than typical small-molecule drugs. While combinatorial techniques such as mRNA display routinely produce high-affinity macrocyclic peptides against classically undruggable targets, poor membrane permeability has limited their use toward primarily extracellular targets. Understanding the passive membrane permeability of macrocyclic peptides would, in principle, improve our ability to design libraries whose leads can be more readily optimized against intracellular targets. Here, we investigate the permeabilities of over 200 macrocyclic 10-mers using the thioether cyclization motif commonly found in mRNA display macrocycle libraries. We identified the optimal lipophilicity range for achieving permeability in thioether-cyclized 10-mer cyclic peptide-peptoid hybrid scaffolds and showed that permeability could be maintained upon extensive permutation in the backbone. In one case, changing a single amino acid from d-Pro to d-NMe-Ala, representing the loss of a single methylene group in the side chain, resulted in a highly permeable scaffold in which the low-dielectric conformation shifted from the canonical cross-beta geometry of the parent compounds into a novel saddle-shaped fold in which all four backbone NH groups were sequestered from the solvent. This work provides an example by which pre-existing physicochemical knowledge of a scaffold can benefit the design of macrocyclic peptide mRNA display libraries, pointing toward an approach for biasing libraries toward permeability by design. Moreover, the compounds described herein are a further demonstration that geometrically diverse, highly permeable scaffolds exist well beyond conventional drug-like chemical space.
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Affiliation(s)
- Justin H Faris
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Emel Adaligil
- Department of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Nataliya Popovych
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, United States
| | - Satoshi Ono
- Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Kanagawa 227-0033, Japan
| | - Mifune Takahashi
- Department of Drug Metabolism and Pharmacokinetics, Genentech, South San Francisco, California 94080, United States
| | - Huy Nguyen
- Department of Analytical Research, Genentech, South San Francisco, California 94080, United States
| | - Emile Plise
- Department of Drug Metabolism and Pharmacokinetics, Genentech, South San Francisco, California 94080, United States
| | - Jaru Taechalertpaisarn
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Michael F T Koehler
- Department of Medicinal Chemistry, Genentech, South San Francisco, California 94080, United States
| | - Christian N Cunningham
- Department of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
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25
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Cao L, Xu Z, Shang T, Zhang C, Wu X, Wu Y, Zhai S, Zhan Z, Duan H. Multi_CycGT: A Deep Learning-Based Multimodal Model for Predicting the Membrane Permeability of Cyclic Peptides. J Med Chem 2024; 67:1888-1899. [PMID: 38270541 DOI: 10.1021/acs.jmedchem.3c01611] [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: 01/26/2024]
Abstract
Cyclic peptides are gaining attention for their strong binding affinity, low toxicity, and ability to target "undruggable" proteins; however, their therapeutic potential against intracellular targets is constrained by their limited membrane permeability, and researchers need much time and money to test this property in the laboratory. Herein, we propose an innovative multimodal model called Multi_CycGT, which combines a graph convolutional network (GCN) and a transformer to extract one- and two-dimensional features for predicting cyclic peptide permeability. The extensive benchmarking experiments show that our Multi_CycGT model can attain state-of-the-art performance, with an average accuracy of 0.8206 and an area under the curve of 0.8650, and demonstrates satisfactory generalization ability on several external data sets. To the best of our knowledge, it is the first deep learning-based attempt to predict the membrane permeability of cyclic peptides, which is beneficial in accelerating the design of cyclic peptide active drugs in medicinal chemistry and chemical biology applications.
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Affiliation(s)
- Lujing Cao
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Zhenyu Xu
- AI Department, Shanghai Highslab Therapeutics, Inc., Shanghai 201203, China
| | - Tianfeng Shang
- AI Department, Shanghai Highslab Therapeutics, Inc., Shanghai 201203, China
| | - Chengyun Zhang
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
- AI Department, Shanghai Highslab Therapeutics, Inc., Shanghai 201203, China
| | - Xinyi Wu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Yejian Wu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Silong Zhai
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Zhajun Zhan
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Hongliang Duan
- Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
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26
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Caceres-Cortes J, Falk B, Mueller L, Dhar TGM. Perspectives on Nuclear Magnetic Resonance Spectroscopy in Drug Discovery Research. J Med Chem 2024; 67:1701-1733. [PMID: 38290426 DOI: 10.1021/acs.jmedchem.3c02389] [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: 02/01/2024]
Abstract
The drug discovery landscape has undergone a significant transformation over the past decade, owing to research endeavors in a wide range of areas leading to strategies for pursuing new drug targets and the emergence of novel drug modalities. NMR spectroscopy has been a technology of fundamental importance to these research pursuits and has seen its use expanded both within and outside of traditional medicinal chemistry applications. In this perspective, we will present advancement of NMR-derived methods that have facilitated the characterization of small molecules and novel drug modalities including macrocyclic peptides, cyclic dinucleotides, and ligands for protein degradation. We will discuss innovations in NMR spectroscopy at the chemistry and biology interface that have broadened NMR's utility from hit identification through lead optimization activities. We will also discuss the promise of emerging NMR approaches in bridging our understanding and addressing challenges in the pursuit of the therapeutic agents of the future.
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Affiliation(s)
- Janet Caceres-Cortes
- Synthesis and Enabling Technologies, Small Molecule Drug Discovery, Bristol-Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Bradley Falk
- Synthesis and Enabling Technologies, Small Molecule Drug Discovery, Bristol-Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Luciano Mueller
- Synthesis and Enabling Technologies, Small Molecule Drug Discovery, Bristol-Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - T G Murali Dhar
- Discovery Chemistry, Small Molecule Drug Discovery, Bristol-Myers Squibb Company, Princeton, New Jersey 085401, United States
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27
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Wang M, Liu J, Xia M, Yin L, Zhang L, Liu X, Cheng Y. Peptide-drug conjugates: A new paradigm for targeted cancer therapy. Eur J Med Chem 2024; 265:116119. [PMID: 38194773 DOI: 10.1016/j.ejmech.2023.116119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/14/2023] [Accepted: 12/31/2023] [Indexed: 01/11/2024]
Abstract
Peptide-drug conjugates (PDCs) are the new hope for targeted therapy after antibody-drug conjugates (ADCs). Compared with ADCs, the core advantages of PDCs are enhanced tissue penetration, easier chemical synthesis, and lower production costs. Two PDCs have been approved by the US Food and Drug Administration (FDA) for the treatment of cancer. The therapeutic effects of PDCs are remarkable, but PDCs also encounter problems when used as targeted therapeutics, such as poor stability, a short blood circulation time, a long research and development time frame, and a slow clinical development process. Therefore, it is very urgent and important to understand the latest research progress of cancer cells targeting PDC, the solution to its stability problem, the scheme of computer technology to assist its research and development, and the direction of its future development. In this manuscript, based on the structure and function of PDCs, the latest research progress on PDCs from the aspects of cancer cell-targeting peptide (CTP) selection, pharmacokinetic characteristics, stability regulation and so on were systematically reviewed, hoping to highlight the current problems and future development directions of PDCs.
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Affiliation(s)
- Mo Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology; Hebei Anti-Tumor Molecular Target Technology Innovation Center; Hebei Research Center of the Basic Discipline of Cell Biology; College of Life Science, Hebei Normal University, Shijiazhuang, 050024, PR China
| | - Jiawei Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology; Hebei Anti-Tumor Molecular Target Technology Innovation Center; Hebei Research Center of the Basic Discipline of Cell Biology; College of Life Science, Hebei Normal University, Shijiazhuang, 050024, PR China
| | - Mingjing Xia
- Ministry of Education Key Laboratory of Molecular and Cellular Biology; Hebei Anti-Tumor Molecular Target Technology Innovation Center; Hebei Research Center of the Basic Discipline of Cell Biology; College of Life Science, Hebei Normal University, Shijiazhuang, 050024, PR China
| | - Libinghan Yin
- Ministry of Education Key Laboratory of Molecular and Cellular Biology; Hebei Anti-Tumor Molecular Target Technology Innovation Center; Hebei Research Center of the Basic Discipline of Cell Biology; College of Life Science, Hebei Normal University, Shijiazhuang, 050024, PR China
| | - Ling Zhang
- School of Chemical Technology, Shijiazhuang University, Shijiazhuang, 050035, PR China.
| | - Xifu Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology; Hebei Anti-Tumor Molecular Target Technology Innovation Center; Hebei Research Center of the Basic Discipline of Cell Biology; College of Life Science, Hebei Normal University, Shijiazhuang, 050024, PR China.
| | - Yu Cheng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology; Hebei Anti-Tumor Molecular Target Technology Innovation Center; Hebei Research Center of the Basic Discipline of Cell Biology; College of Life Science, Hebei Normal University, Shijiazhuang, 050024, PR China.
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28
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Diaz DB, Rowshanpour R, Saunders GJ, Dudding T, Yudin AK. The Role of Attractive Non-Covalent Interactions in Peptide Macrocyclization. J Org Chem 2024; 89:1483-1491. [PMID: 38217516 DOI: 10.1021/acs.joc.3c02084] [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: 01/15/2024]
Abstract
The efficiency of macrocyclization reactions relies on the appropriate conformational preorganization of a linear precursor, ensuring that reactive ends are in spatial proximity prior to ring closure. Traditional peptide cyclization approaches that reduce the extent of terminal ion pairing often disfavor cyclization-conducive conformations and can lead to undesired cyclodimerization or oligomerization side reactions, particularly when they are performed without high dilution. To address this challenge, synthetic strategies that leverage attractive noncovalent interactions, such as zwitterionic attraction between chain termini during macrocyclization, offer a potential solution by reducing the entropic penalty associated with linear peptides adopting precyclization conformations. In this study, we investigate the role of (N-isocyanoimino)triphenylphosphorane (Pinc) in facilitating the cyclization of linear peptides into conformationally rigid macrocycles. The observed moderate diastereoselectivity is consistent with the preferential Si-facial addition of Pinc, where the isocyanide adds to the E-iminium ion on the same face as the l-proline amide group. The resulting peptide chain reveals that the activated phosphonium ylide of Pinc brings the reactive ends close together, promoting cyclization by enclosing the carboxylate within the interior of the pentapeptide and preventing the formation of byproducts. For shorter peptides with modified peptide backbones, the cyclization mechanism and outcome are redirected, as nucleophilic motifs such as thiazole and imidazole can covalently trap nitrilium intermediates. The isolation of the intermediate in the unproductive macrocyclization pathway, along with nuclear magnetic resonance and density functional theory studies, provides insights into heterocycle-dependent selectivity. The Pinc-driven macrocyclization process has generated diverse collections of cyclic molecules, and our models offer a comprehensive understanding of observed trends, facilitating the development of other heterocycle-forming macrocyclization reactions.
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Affiliation(s)
- Diego B Diaz
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Rozhin Rowshanpour
- Department of Chemistry, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - George J Saunders
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Travis Dudding
- Department of Chemistry, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Andrei K Yudin
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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29
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Tong Z, Xie X, Ge H, Jiao R, Wang T, Wang X, Zhuang W, Hu G, Tan R. Disulfide bridge-targeted metabolome mining unravels an antiparkinsonian peptide. Acta Pharm Sin B 2024; 14:881-892. [PMID: 38322339 PMCID: PMC10840396 DOI: 10.1016/j.apsb.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/06/2023] [Accepted: 09/13/2023] [Indexed: 02/08/2024] Open
Abstract
Peptides are a particular molecule class with inherent attributes of some small-molecule drugs and macromolecular biologics, thereby inspiring continuous searches for peptides with therapeutic and/or agrochemical potentials. However, the success rate is decreasing, presumably because many interesting but less-abundant peptides are so scarce or labile that they are likely 'overlooked' during the characterization effort. Here, we present the biochemical characterization and druggability improvement of an unprecedented minor fungal RiPP (ribosomally synthesized and post-translationally modified peptide), named acalitide, by taking the relevant advantages of metabolomics approach and disulfide-bridged substructure which is more frequently imprinted in the marketed peptide drug molecules. Acalitide is biosynthetically unique in the macrotricyclization via two disulfide bridges and a protease (AcaB)-catalyzed lactamization of AcaA, an unprecedented precursor peptide. Such a biosynthetic logic was successfully re-edited for its sample supply renewal to facilitate the identification of the in vitro and in vivo antiparkinsonian efficacy of acalitide which was further confirmed safe and rendered brain-targetable by the liposome encapsulation strategy. Taken together, the work updates the mining strategy and biosynthetic complexity of RiPPs to unravel an antiparkinsonian drug candidate valuable for combating Parkinson's disease that is globally prevailing in an alarming manner.
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Affiliation(s)
- Zhiwu Tong
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xiahong Xie
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Huiming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ruihua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Tingting Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xincun Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenying Zhuang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Gang Hu
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Renxiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
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30
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Lacerna N, Cong Y, Schmidt EW. An Autocatalytic Peptide Cyclase Improves Fidelity and Yield of Circular Peptides In Vivo and In Vitro. ACS Synth Biol 2024; 13:394-401. [PMID: 38194299 PMCID: PMC10804404 DOI: 10.1021/acssynbio.3c00645] [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: 10/24/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/10/2024]
Abstract
Peptide cyclization improves conformational rigidity, providing favorable pharmacological properties, such as proteolytic resistance, target specificity, and membrane permeability. Thus, many synthetic and biosynthetic peptide circularization strategies have been developed. PatG and related natural macrocyclases process diverse peptide sequences, generating millions of cyclic derivatives. However, the application of these cyclases is limited by low yields and the potential presence of unwanted intermediates. Here, we designed a covalently fused G macrocyclase with substrates that efficiently and spontaneously release cyclic peptides. To increase the fidelity of synthesis, we developed an orthogonal control mechanism enabling precision synthesis in Escherichia coli. As a result, a library comprising 4.8 million cyclic derivatives was constructed, producing an estimated 2.6 million distinct cyclic peptides with an improved yield and fidelity.
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Affiliation(s)
- Noel Lacerna
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ying Cong
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric W. Schmidt
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United States
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31
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de Raffele D, Ilie IM. Unlocking novel therapies: cyclic peptide design for amyloidogenic targets through synergies of experiments, simulations, and machine learning. Chem Commun (Camb) 2024; 60:632-645. [PMID: 38131333 DOI: 10.1039/d3cc04630c] [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: 12/23/2023]
Abstract
Existing therapies for neurodegenerative diseases like Parkinson's and Alzheimer's address only their symptoms and do not prevent disease onset. Common therapeutic agents, such as small molecules and antibodies struggle with insufficient selectivity, stability and bioavailability, leading to poor performance in clinical trials. Peptide-based therapeutics are emerging as promising candidates, with successful applications for cardiovascular diseases and cancers due to their high bioavailability, good efficacy and specificity. In particular, cyclic peptides have a long in vivo stability, while maintaining a robust antibody-like binding affinity. However, the de novo design of cyclic peptides is challenging due to the lack of long-lived druggable pockets of the target polypeptide, absence of exhaustive conformational distributions of the target and/or the binder, unknown binding site, methodological limitations, associated constraints (failed trials, time, money) and the vast combinatorial sequence space. Hence, efficient alignment and cooperation between disciplines, and synergies between experiments and simulations complemented by popular techniques like machine-learning can significantly speed up the therapeutic cyclic-peptide development for neurodegenerative diseases. We review the latest advancements in cyclic peptide design against amyloidogenic targets from a computational perspective in light of recent advancements and potential of machine learning to optimize the design process. We discuss the difficulties encountered when designing novel peptide-based inhibitors and we propose new strategies incorporating experiments, simulations and machine learning to design cyclic peptides to inhibit the toxic propagation of amyloidogenic polypeptides. Importantly, these strategies extend beyond the mere design of cyclic peptides and serve as template for the de novo generation of (bio)materials with programmable properties.
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Affiliation(s)
- Daria de Raffele
- University of Amsterdam, van 't Hoff Institute for Molecular Sciences, Science Park 904, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands.
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Ioana M Ilie
- University of Amsterdam, van 't Hoff Institute for Molecular Sciences, Science Park 904, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands.
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
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32
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Abstract
Cyclic peptides are fascinating molecules abundantly found in nature and exploited as molecular format for drug development as well as other applications, ranging from research tools to food additives. Advances in peptide technologies made over many years through improved methods for synthesis and drug development have resulted in a steady stream of new drugs, with an average of around one cyclic peptide drug approved per year. Powerful technologies for screening random peptide libraries, and de novo generating ligands, have enabled the development of cyclic peptide drugs independent of naturally derived molecules and now offer virtually unlimited development opportunities. In this review, we feature therapeutically relevant cyclic peptides derived from nature and discuss the unique properties of cyclic peptides, the enormous technological advances in peptide ligand development in recent years, and current challenges and opportunities for developing cyclic peptides that address unmet medical needs.
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Affiliation(s)
- Xinjian Ji
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Alexander L Nielsen
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, 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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33
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Tang TM, Mason JM. Intracellular Application of an Asparaginyl Endopeptidase for Producing Recombinant Head-to-Tail Cyclic Proteins. JACS AU 2023; 3:3290-3296. [PMID: 38155637 PMCID: PMC10751764 DOI: 10.1021/jacsau.3c00591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 12/30/2023]
Abstract
Peptide backbone cyclization is commonly observed in nature and is increasingly applied to proteins and peptides to improve thermal and chemical stability and resistance to proteolytic enzymes and enhance biological activity. However, chemical synthesis of head-to-tail cyclic peptides and proteins is challenging, is often low yielding, and employs toxic and unsustainable reagents. Plant derived asparaginyl endopeptidases such as OaAEP1 have been employed to catalyze the head-to-tail cyclization of peptides in vitro, offering a safer and more sustainable alternative to chemical methods. However, while asparaginyl endopeptidases have been used in vitro and in native and transgenic plant species, they have never been used to generate recombinant cyclic proteins in live recombinant organisms outside of plants. Using dihydrofolate reductase as a proof of concept, we show that a truncated OaAEP1 variant C247A is functional in the Escherichia coli physiological environment and can therefore be coexpressed with a substrate protein to enable concomitant in situ cyclization. The bacterial system is ideal for cyclic protein production owing to the fast growth rate, durability, ease of use, and low cost. This streamlines cyclic protein production via a biocatalytic process with fast kinetics and minimal ligation scarring, while negating the need to purify the enzyme, substrate, and reaction mixtures individually. The resulting cyclic protein was characterized in vitro, demonstrating enhanced thermal stability compared to the corresponding linear protein without impacting enzyme activity. We anticipate this convenient method for generating cyclic peptides will have broad utility in a range of biochemical and chemical applications.
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Affiliation(s)
- T. M.
Simon Tang
- Department
of Life Sciences, University of Bath, Claverton Down, Bath, North Somerset BA2
7AY, U.K.
| | - Jody M. Mason
- Department
of Life Sciences, University of Bath, Claverton Down, Bath, North Somerset BA2
7AY, U.K.
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Chen H, Zhang Q. Native Peptide Cyclization, Sequential Chemoselective Amidation in Water. J Am Chem Soc 2023; 145:27218-27224. [PMID: 38079358 PMCID: PMC11131159 DOI: 10.1021/jacs.3c10341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Chemical synthesis offers robust tactics for structural alterations of peptides and proteins. It remains a labor-intensive and complex process due to the challenges in selectively modifying diverse amino acid side chains and termini. Direct α-peptide ligation without premodification is a significant hurdle, especially when aiming to include all proteinogenic amino acids at the ligation site. We introduce Native Peptide Cyclization (NPC), a chemoselective method enabling intramolecular peptidyl ligation without the need for premodification. NPC cyclizes unprotected linear peptides through controlled, sequential C- and N-terminal activation via pH modulation. Water-based NPC simplifies peptide ligation, easing the labor-intensive nature of peptide synthesis, aiding efficient cyclic peptide preparation and enabling cost-effective macrocycle-based therapeutics.
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Affiliation(s)
- Huan Chen
- Department of Chemistry, State University of New York, University at Albany, Albany, New York 12222, United States
| | - Qiang Zhang
- Department of Chemistry, State University of New York, University at Albany, Albany, New York 12222, United States
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35
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Molinaro C, Kelly S, Tang A, Iding H, Stocker P, Linghu X, Gosselin F. Asymmetric Synthesis of N-Alkyl Amino Acids through a Biocatalytic Dynamic Kinetic Resolution of PEGylated N-Alkyl Amino Esters. Org Lett 2023; 25:8927-8931. [PMID: 38051775 DOI: 10.1021/acs.orglett.3c03784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
The first examples of a practical procedure for a lipase-catalyzed dynamic kinetic resolution of PEGylated N-alkyl amino esters is reported. This method allows for the preparation of a broad range of aromatic and aliphatic enantiomerically enriched N-alkyl unnatural amino acids in up to 98% yield and 99% ee. We have found that PEGylated esters have a significant solubility advantage and improved reactivity over traditional hydrophobic lipase substrates, thereby allowing for efficient and scalable dynamic kinetic resolution (DKR) under aqueous conditions.
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Affiliation(s)
- Carmela Molinaro
- Department of Small Molecule Process Chemistry, Genentech USA, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Sean Kelly
- Department of Small Molecule Process Chemistry, Genentech USA, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Allison Tang
- Department of Small Molecule Process Chemistry, Genentech USA, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Hans Iding
- Department of Process Chemistry & Catalysis, Synthetic Molecules Technical Development, F. Hoffmann-La Roche AG Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Patrik Stocker
- Department of Process Chemistry & Catalysis, Synthetic Molecules Technical Development, F. Hoffmann-La Roche AG Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Xin Linghu
- Department of Small Molecule Process Chemistry, Genentech USA, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Francis Gosselin
- Department of Small Molecule Process Chemistry, Genentech USA, Inc. 1 DNA Way, South San Francisco, California 94080, United States
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36
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Gomez-Soler M, Olson EJ, de la Torre ER, Zhao C, Lamberto I, Flood DT, Danho W, Lechtenberg BC, Riedl SJ, Dawson PE, Pasquale EB. Lipidation and PEGylation Strategies to Prolong the in Vivo Half-Life of a Nanomolar EphA4 Receptor Antagonist. Eur J Med Chem 2023; 262:115876. [PMID: 38523699 PMCID: PMC10959496 DOI: 10.1016/j.ejmech.2023.115876] [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] [Indexed: 03/26/2024]
Abstract
The EphA4 receptor tyrosine kinase plays a role in neurodegenerative diseases, inhibition of nerve regeneration, cancer progression and other diseases. Therefore, EphA4 inhibition has potential therapeutic value. Selective EphA4 kinase inhibitors are not available, but we identified peptide antagonists that inhibit ephrin ligand binding to EphA4 with high specificity. One of these peptides is the cyclic APY-d3 (βAPYCVYRβASWSC-NH2), which inhibits ephrin-A5 ligand binding to EphA4 with low nanomolar binding affinity and is highly protease resistant. Here we describe modifications of APY-d3 that yield two different key derivatives with greatly increased half-lives in the mouse circulation, the lipidated APY-d3-laur8 and the PEGylated APY-d3-PEG4. These two derivatives inhibit ligand induced EphA4 activation in cells with sub-micromolar potency. Since they retain high potency and specificity for EphA4, lipidated and PEGylated APY-d3 derivatives represent new tools for discriminating EphA4 activities in vivo and for preclinical testing of EphA4 inhibition in animal disease models.
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Affiliation(s)
- Maricel Gomez-Soler
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Erika J. Olson
- Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Elena Rubio de la Torre
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Chunxia Zhao
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Ilaria Lamberto
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Dillon T. Flood
- Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Waleed Danho
- Del Mar, California 92014, United States
- Deceased
| | - Bernhard C. Lechtenberg
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Stefan J. Riedl
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Philip E. Dawson
- Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Elena B. Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
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37
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Peker T, Zagiel B, Rocard L, Bich C, Sachon E, Moumné R. Analytical Tools for Dynamic Combinatorial Libraries of Cyclic Peptides. Chembiochem 2023; 24:e202300688. [PMID: 37815502 DOI: 10.1002/cbic.202300688] [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: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/11/2023]
Abstract
Target-directed dynamic combinatorial chemistry is a very attractive strategy for the discovery of bioactive peptides. However, its application has not yet been demonstrated, presumably due to analytical challenges that arise from the diversity of a peptide library with combinatorial side-chains. We previously reported an efficient method to generate, under biocompatible conditions, large dynamic libraries of cyclic peptides grafted with amino acid's side-chains, by thiol-to-thioester exchanges. In this work, we present analytical tools to easily characterize such libraries by HPLC and mass spectrometry, and in particular to simplify the isomers' distinction requiring sequencing by MS/MS fragmentations. After structural optimization, the cyclic scaffold exhibits a UV-tag, absorbing at 415 nm, and an ornithine residue which favors the regioselective ring-opening and simultaneous MS/MS fragmentation, in the gas-phase.
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Affiliation(s)
- Taleen Peker
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Benjamin Zagiel
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Lou Rocard
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Claudia Bich
- UMR 5247-CNRS-UM-ENSCM, Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, Montpellier, France
| | - Emmanuelle Sachon
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
- MS3U Platform, Fédération de Chimie Moléculaire de Paris Centre - FR2769, Sorbonne Université, 4 Place Jussieu, 75005, Paris, France
| | - Roba Moumné
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
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38
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Cheng J, Zhou J, Kong L, Wang H, Zhang Y, Wang X, Liu G, Chu Q. Stabilized cyclic peptides as modulators of protein-protein interactions: promising strategies and biological evaluation. RSC Med Chem 2023; 14:2496-2508. [PMID: 38107173 PMCID: PMC10718590 DOI: 10.1039/d3md00487b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/04/2023] [Indexed: 12/19/2023] Open
Abstract
Protein-protein interactions (PPIs) control many essential biological pathways which are often misregulated in disease. As such, selective PPI modulators are desirable to unravel complex functions of PPIs and thus expand the repertoire of therapeutic targets. However, the large size and relative flatness of PPI interfaces make them challenging molecular targets for conventional drug modalities, rendering most PPIs "undruggable". Therefore, there is a growing need to discover innovative molecules that are able to modulate crucial PPIs. Peptides are ideal candidates to deliver such therapeutics attributed to their ability to closely mimic structural features of protein interfaces. However, their inherently poor proteolysis resistance and cell permeability inevitably hamper their biomedical applications. The introduction of a constraint (i.e., peptide cyclization) to stabilize peptides' secondary structure is a promising strategy to address this problem as witnessed by the rapid development of cyclic peptide drugs in the past two decades. Here, we comprehensively review the recent progress on stabilized cyclic peptides in targeting challenging PPIs. Technological advancements and emerging chemical approaches for stabilizing active peptide conformations are categorized in terms of α-helix stapling, β-hairpin mimetics and macrocyclization. To discover potent and selective ligands, cyclic peptide library technologies were updated based on genetic, biochemical or synthetic methodologies. Moreover, several advances to improve the permeability and oral bioavailability of biologically active cyclic peptides enable the de novo development of cyclic peptide ligands with pharmacological properties. In summary, the development of cyclic peptide-based PPI modulators carries tremendous promise for the next generation of therapeutic agents to target historically "intractable" PPI systems.
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Affiliation(s)
- Jiongjia Cheng
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Junlong Zhou
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University 639 Longmian Avenue Nanjing 211198 China
| | - Lingyan Kong
- College of Food Science and Engineering, Nanjing University of Finance and Economics Nanjing 210023 China
| | - Haiying Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Yuchi Zhang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Xiaofeng Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Guangxiang Liu
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Qian Chu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University 639 Longmian Avenue Nanjing 211198 China
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University Nanjing 210009 China
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39
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Miyamoto E, Sato T, Matsubara T. Cyclization of Peptides Enhances the Inhibitory Activity against Ganglioside-Induced Aβ Fibril Formation. ACS Chem Neurosci 2023; 14:4199-4207. [PMID: 37971427 DOI: 10.1021/acschemneuro.3c00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
Alzheimer's disease is a progressive neurodegenerative disease and is the most common cause of dementia. It has been reported that the assembly of amyloid β-protein (Aβ) on the cell membrane is induced by the interaction of the Aβ monomer with gangliosides such as GM1. The ganglioside-bound Aβ (GAβ) complex acts as a seed to promote the toxic assembly of the Aβ fibrils. In a previous study, we found that a GM1 cluster-binding peptide (GCBP) specifically recognizes Aβ-sensitive ganglioside nanoclusters and inhibits the assembly of Aβ on a GM1-containing lipid membrane. In this study, cysteine-substituted double mutants of GCBP were designed and cyclized by intramolecular disulfide bond formation. Affinity assays indicated that one of the cyclic peptides had a higher affinity to a GM1-containing membrane compared to that of GCBP. Furthermore, surface topography analysis indicated that this peptide recognizes GM1 nanoclusters on the lipid membrane. An evaluation of the inhibitory kinetics indicated that the cyclic peptide could inhibit the formation of Aβ fibrils with an IC50 value of 1.2 fM, which is 10,000-fold higher than that of GCBP. The cyclic peptide was also shown to have a clearance effect on Aβ fibrils deposited on the lipid membrane and suppressed the formation of toxic Aβ assemblies. Our results indicate that the cyclic peptide that binds to the Aβ-sensitive ganglioside nanocluster is a potential novel inhibitor of ganglioside-induced Aβ assembly.
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Affiliation(s)
- Erika Miyamoto
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Toshinori Sato
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Teruhiko Matsubara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
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40
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Ribeiro R, Costa L, Pinto E, Sousa E, Fernandes C. Therapeutic Potential of Marine-Derived Cyclic Peptides as Antiparasitic Agents. Mar Drugs 2023; 21:609. [PMID: 38132930 PMCID: PMC10745025 DOI: 10.3390/md21120609] [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: 11/02/2023] [Revised: 11/18/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Parasitic diseases still compromise human health. Some of the currently available therapeutic drugs have limitations considering their adverse effects, questionable efficacy, and long treatment, which have encouraged drug resistance. There is an urgent need to find new, safe, effective, and affordable antiparasitic drugs. Marine-derived cyclic peptides have been increasingly screened as candidates for developing new drugs. Therefore, in this review, a systematic analysis of the scientific literature was performed and 25 marine-derived cyclic peptides with antiparasitic activity (1-25) were found. Antimalarial activity is the most reported (51%), followed by antileishmanial (27%) and antitrypanosomal (20%) activities. Some compounds showed promising antiparasitic activity at the nM scale, being active against various parasites. The mechanisms of action and targets for some of the compounds have been investigated, revealing different strategies against parasites.
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Affiliation(s)
- Ricardo Ribeiro
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (R.R.); (L.C.); (E.S.)
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal;
| | - Lia Costa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (R.R.); (L.C.); (E.S.)
| | - Eugénia Pinto
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal;
- Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Emília Sousa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (R.R.); (L.C.); (E.S.)
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal;
| | - Carla Fernandes
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (R.R.); (L.C.); (E.S.)
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal;
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41
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Fan L, Yu Y, Jayne C, Frost JR, Scott JD. Synthesis of DNA-Encoded Macrocyclic Peptides via Nitrile-Aminothiol Click Reaction. Org Lett 2023; 25:8038-8042. [PMID: 37889907 DOI: 10.1021/acs.orglett.3c03284] [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: 10/29/2023]
Abstract
DNA-encoded library (DEL) technology holds exciting potential for discovering novel therapeutic macrocyclic peptides (MPs). Herein, we describe the development of a DEL-compatible peptide macrocyclization method that proceeds via intramolecular click-condensation between 3-(2-cyano-4-pyridyl)-l-alanine (Cpa) and an N-terminal cysteine. Cyclization takes place spontaneously in a buffered aqueous solution and affords the cyclized products in excellent yields. The reaction exhibits a broad substrate scope and can be employed to generate MPs of variable ring size and amino acid composition.
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Affiliation(s)
- Lijun Fan
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yang Yu
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Charles Jayne
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - John R Frost
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jack D Scott
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
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42
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Yoshida S, Sako Y, Nikaido E, Ueda T, Kozono I, Ichihashi Y, Nakahashi A, Onishi M, Yamatsu Y, Kato T, Nishikawa J, Tachibana Y. Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of β-Herpesvirus Proteases. ACS Med Chem Lett 2023; 14:1558-1566. [PMID: 37974946 PMCID: PMC10641906 DOI: 10.1021/acsmedchemlett.3c00359] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023] Open
Abstract
Viral proteases, the key enzymes that regulate viral replication and assembly, are promising targets for antiviral drug discovery. Herpesvirus proteases are enzymes with no crystallographically confirmed noncovalent active-site binders, owing to their shallow and polar substrate-binding pockets. Here, we applied our previously reported "Peptide-to-Small Molecule" strategy to generate novel inhibitors of β-herpesvirus proteases. Rapid selection with a display technology was used to identify macrocyclic peptide 1 bound to the active site of human cytomegalovirus protease (HCMVPro) with high affinity, and pharmacophore queries were defined based on the results of subsequent intermolecular interaction analyses. Membrane-permeable small molecule 19, designed de novo according to this hypothesis, exhibited enzyme inhibitory activity (IC50 = 10-6 to 10-7 M) against β-herpesvirus proteases, and the design concept was proved by X-ray cocrystal analysis.
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Affiliation(s)
- Shuhei Yoshida
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yusuke Sako
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Eiji Nikaido
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Taichi Ueda
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Iori Kozono
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yusuke Ichihashi
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Atsufumi Nakahashi
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Motoyasu Onishi
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yukiko Yamatsu
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Teruhisa Kato
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Junichi Nishikawa
- PeptiDream
Inc., 3-25-23 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Yuki Tachibana
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
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43
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Neumann J, Schmidtsdorff S, Schmidt AH, Parr MK. Controlling the elution order of insulin and its analogs in sub-/supercritical fluid chromatography using methanesulfonic acid and 18-crown-6 as mobile phase additives. J Sep Sci 2023; 46:e2300520. [PMID: 37775313 DOI: 10.1002/jssc.202300520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 10/01/2023]
Abstract
The purity analysis of therapeutic peptides can often be challenging, demanding the application of more than a single analytical technique. Supercritical fluid chromatography nowadays is a promising alternative to reversed-phase liquid chromatography, providing orthogonal and complementary information. This study investigated its applicability for the separation of human insulin, its analogs and degradation products. A previously published method development protocol for peptides up to 2000 Da was successfully applied to the higher molecular weight insulins (6 kDa). A single gradient method was optimized for all insulins using a Torus DEA column (100 × 3.0 mm, 1.7 μm), carbon dioxide and a modifier consisting of methanol/acetonitrile/water/methanesulfonic acid (65:35:2:0.1, v/v/v/v). Consecutively, the crown ether 18-crown-6, which is well known to complex charged lysine sidechains and other amino functionalities, was added to the modifier to evaluate its impact on selectivity. A decreased retention and a shift in the elution order for the insulins were observed. An inverse effect on retention was found when combined with a neutral stationary phase chemistry (Viridis BEH).
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Affiliation(s)
- Jonas Neumann
- Department of Biology, Chemistry, and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
- Chromicent GmbH, Berlin, Germany
| | - Sebastian Schmidtsdorff
- Department of Biology, Chemistry, and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
- Chromicent GmbH, Berlin, Germany
| | | | - Maria K Parr
- Department of Biology, Chemistry, and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
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44
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Karami Y, Murail S, Giribaldi J, Lefranc B, Defontaine F, Lesouhaitier O, Leprince J, de Vries S, Tufféry P. Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization. J Chem Inf Model 2023; 63:6436-6450. [PMID: 37827517 PMCID: PMC10599322 DOI: 10.1021/acs.jcim.3c00865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Indexed: 10/14/2023]
Abstract
Peptides have recently regained interest as therapeutic candidates, but their development remains confronted with several limitations including low bioavailability. Backbone head-to-tail cyclization, i.e., setting a covalent peptide bond linking the last amino acid with the first one, is one effective strategy of peptide-based drug design to stabilize the conformation of bioactive peptides while preserving peptide properties in terms of low toxicity, binding affinity, target selectivity, and preventing enzymatic degradation. Starting from an active peptide, it usually requires the design of a linker of a few amino acids to make it possible to cyclize the peptide, possibly preserving the conformation of the initial peptide and not affecting its activity. However, very little is known about the sequence-structure relationship requirements of designing linkers for peptide cyclization in a rational manner. Recently, we have shown that large-scale data-mining of available protein structures can lead to the precise identification of protein loop conformations, even from remote structural classes. Here, we transpose this approach to linkers, allowing head-to-tail peptide cyclization. First we show that given a linker sequence and the conformation of the linear peptide, it is possible to accurately predict the cyclized peptide conformation. Second, and more importantly, we show that it seems possible to elaborate on the information inferred from protein structures to propose effective candidate linker sequences constrained by length and amino acid composition, providing the first framework for the rational design of head-to-tail cyclization linkers. Finally, we illustrate this for two peptides using a limited set of amino-acids likely not to interfere with peptide function. For a linear peptide derived from Nrf2, the peptide cyclized starting from the experimental structure showed a 26-fold increase in the binding affinity. For urotensin II, a peptide already cyclized by a disulfide bond that exerts a broad array of biological activities, we were able, starting from models of the structure, to design a head-to-tail cyclized peptide, the first synthesized bicyclic 14-residue long urotensin II analogue, showing a retention of in vitro activity. Although preliminary, our results strongly suggest that such an approach has strong potential for cyclic peptide-based drug design.
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Affiliation(s)
- Yasaman Karami
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
| | - Samuel Murail
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
| | - Julien Giribaldi
- Institut
des Biomolécules Max Mousseron, UMR 5247, Université de Montpellier-CNRS, 34293 Montpellier, France
| | - Benjamin Lefranc
- Université
de Rouen Normandie, INSERM U1239 NorDiC, Neuroendocrine, Endocrine and Germinal Differentiation and Communication,
INSERM US51 HeRacLeS, F-76000 Rouen, France
| | - Florian Defontaine
- Université
de Rouen Normandie, UR CBSA, Research Unit
Bacterial Communication and Anti-infectious Strategies, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Université
de Rouen Normandie, UR CBSA, Research Unit
Bacterial Communication and Anti-infectious Strategies, 27000 Evreux, France
| | - Jérôme Leprince
- Université
de Rouen Normandie, INSERM U1239 NorDiC, Neuroendocrine, Endocrine and Germinal Differentiation and Communication,
INSERM US51 HeRacLeS, F-76000 Rouen, France
| | - Sjoerd de Vries
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
| | - Pierre Tufféry
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
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45
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Yang Y, Wu H, Gao Y, Tong W, Li K. MFPPDB: a comprehensive multi-functional plant peptide database. FRONTIERS IN PLANT SCIENCE 2023; 14:1224394. [PMID: 37908832 PMCID: PMC10613858 DOI: 10.3389/fpls.2023.1224394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/29/2023] [Indexed: 11/02/2023]
Abstract
Plants produce a wide range of bioactive peptides as part of their innate defense mechanisms. With the explosive growth of plant-derived peptides, verifying the therapeutic function using traditional experimental methods are resources and time consuming. Therefore, it is necessary to predict the therapeutic function of plant-derived peptides more effectively and accurately with reduced waste of resources and thus expedite the development of plant peptides. We herein developed a repository of plant peptides predicted to have multiple therapeutic functions, named as MFPPDB (multi-functional plant peptide database). MFPPDB including 1,482,409 single or multiple functional plant origin therapeutic peptides derived from 121 fundamental plant species. The functional categories of these therapeutic peptides include 41 different features such as anti-bacterial, anti-fungal, anti-HIV, anti-viral, and anti-cancer. The detailed physicochemical information of these peptides was presented in functional search and physicochemical property search module, which can help users easily access the peptide information by the plant peptide species, ID, and functions, or by their peptide ID, isoelectric point, peptide sequence, and molecular weight through web-friendly interface. We further matched the predicted peptides to nine state-of-the-art curated functional peptide databases and found that at least 293,408 of the peptides possess functional potentials. Overall, MFPPDB integrated a massive number of plant peptides have single or multiple therapeutic functions, which will facilitate the comprehensive research in plant peptidomics. MFPPDB can be freely accessed through http://124.223.195.214:9188/mfppdb/index.
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Affiliation(s)
- Yaozu Yang
- School of Information and Computer, Anhui Agricultural University, Hefei, China
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Anhui University, Hefei, Anhui, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Hongwei Wu
- School of Information and Computer, Anhui Agricultural University, Hefei, China
| | - Yu Gao
- School of Information and Computer, Anhui Agricultural University, Hefei, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Ke Li
- School of Information and Computer, Anhui Agricultural University, Hefei, China
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Anhui University, Hefei, Anhui, China
- Anhui Provincial Engineering Laboratory for Beidou Precision Agriculture Information, Anhui Agricultural University, Hefei, Anhui, China
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46
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Shao H, Adebomi V, Bruce A, Raj M, Houk KN. Intramolecular Hydrogen Bonding Enables a Zwitterionic Mechanism for Macrocyclic Peptide Formation: Computational Mechanistic Studies of CyClick Chemistry. Angew Chem Int Ed Engl 2023; 62:e202307210. [PMID: 37475575 PMCID: PMC10592271 DOI: 10.1002/anie.202307210] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/22/2023]
Abstract
Macrocyclic peptides have become increasingly important in the pharmaceutical industry. We present a detailed computational investigation of the reaction mechanism of the recently developed "CyClick" chemistry to selectively form imidazolidinone cyclic peptides from linear peptide aldehydes, without using catalysts or directing groups (Angew. Chem. Int. Ed. 2019, 58, 19073-19080). We conducted computational mechanistic to investigate the effects of intramolecular hydrogen bonds (IMHBs) in promoting a kinetically facile zwitterionic mechanism in "CyClick" of pentapeptide aldehyde AFGPA. Our DFT calculations highlighted the importance of IMHB in pre-organization of the resting state, stabilization of the zwitterion intermediate, and the control of the product stereoselectivity. Furthermore, we have also identified that the low ring strain energy promotes the "CyClick" of hexapeptide aldehyde AAGPFA to form a thermodynamically more stable 15+5 imidazolidinone cyclic peptide product. In contrast, large ring strain energy suppresses "CyClick" reactivity of tetra peptide aldehyde AFPA from forming the 9+5 imidazolidinone cyclic peptide product.
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Affiliation(s)
- Huiling Shao
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Victor Adebomi
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Angele Bruce
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Monika Raj
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
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47
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Dognini P, Chaudhry T, Scagnetti G, Assante M, Hanson GSM, Ross K, Giuntini F, Coxon CR. 5,10,15,20-Tetrakis(pentafluorophenyl)porphyrin as a Functional Platform for Peptide Stapling and Multicyclisation. Chemistry 2023; 29:e202301410. [PMID: 37402229 PMCID: PMC10946732 DOI: 10.1002/chem.202301410] [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: 05/03/2023] [Revised: 06/22/2023] [Accepted: 07/04/2023] [Indexed: 07/06/2023]
Abstract
Polyfluorinated aromatic reagents readily react with thiolates via nucleophilic aromatic substitution (SN Ar) and provide excellent scaffolds for peptide cyclisation. Here we report a robust and versatile platform for peptide stapling and multicyclisation templated by 5,10,15,20-tetrakis(pentafluorophenyl)porphyrin, opening the door to the next generation of functional scaffolds for 3D peptide architectures. We demonstrate that stapling and multicyclisation occurs with a range of non-protected peptides under peptide-compatible conditions, exhibiting chemoselectivity and wide-applicability. Peptides containing two cysteine residues are readily stapled, and the remaining perfluoroaryl groups permit the introduction of a second peptide in a modular fashion to access bicyclic peptides. Similarly, peptides with more than two cysteine residues can afford multicyclic products containing up to three peptide 'loops'. Finally, we demonstrate that a porphyrin-templated stapled peptide containing the Skin Penetrating and Cell Entering (SPACE) peptide affords a skin cell penetrating conjugate with intrinsic fluorescence.
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Affiliation(s)
- Paolo Dognini
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityByrom Street CampusL3 3AFLiverpoolUK
| | - Talhat Chaudhry
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityByrom Street CampusL3 3AFLiverpoolUK
| | - Giulia Scagnetti
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityByrom Street CampusL3 3AFLiverpoolUK
| | - Michele Assante
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityByrom Street CampusL3 3AFLiverpoolUK
| | - George S. M. Hanson
- EaStCHEMSchool of ChemistryThe University of EdinburghJoseph Black Building, David Brewster RoadEH9 3FJEdinburghUK
| | - Kehinde Ross
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityByrom Street CampusL3 3AFLiverpoolUK
| | - Francesca Giuntini
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityByrom Street CampusL3 3AFLiverpoolUK
| | - Christopher R. Coxon
- EaStCHEMSchool of ChemistryThe University of EdinburghJoseph Black Building, David Brewster RoadEH9 3FJEdinburghUK
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48
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Qing X, Wang Q, Xu H, Liu P, Lai L. Designing Cyclic-Constrained Peptides to Inhibit Human Phosphoglycerate Dehydrogenase. Molecules 2023; 28:6430. [PMID: 37687259 PMCID: PMC10563079 DOI: 10.3390/molecules28176430] [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: 08/05/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Although loop epitopes at protein-protein binding interfaces often play key roles in mediating oligomer formation and interaction specificity, their binding sites are underexplored as drug targets owing to their high flexibility, relatively few hot spots, and solvent accessibility. Prior attempts to develop molecules that mimic loop epitopes to disrupt protein oligomers have had limited success. In this study, we used structure-based approaches to design and optimize cyclic-constrained peptides based on loop epitopes at the human phosphoglycerate dehydrogenase (PHGDH) dimer interface, which is an obligate homo-dimer with activity strongly dependent on the oligomeric state. The experimental validations showed that these cyclic peptides inhibit PHGDH activity by directly binding to the dimer interface and disrupting the obligate homo-oligomer formation. Our results demonstrate that loop epitope derived cyclic peptides with rationally designed affinity-enhancing substitutions can modulate obligate protein homo-oligomers, which can be used to design peptide inhibitors for other seemingly intractable oligomeric proteins.
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Affiliation(s)
- Xiaoyu Qing
- BNLMS, Peking-Tsinghua Center for Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (X.Q.); (H.X.); (P.L.)
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China;
| | - Hanyu Xu
- BNLMS, Peking-Tsinghua Center for Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (X.Q.); (H.X.); (P.L.)
| | - Pei Liu
- BNLMS, Peking-Tsinghua Center for Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (X.Q.); (H.X.); (P.L.)
| | - Luhua Lai
- BNLMS, Peking-Tsinghua Center for Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (X.Q.); (H.X.); (P.L.)
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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49
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Chatterjee S, Bandyopadhyay A. Synthesis and characterization of two potential impurities (des-ethyl-Ganirelix) generated in the Ganirelix manufacturing process. J Pept Sci 2023; 29:e3489. [PMID: 36967632 DOI: 10.1002/psc.3489] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
Controlling certain diseases using peptide drugs has remarkably increased in the past two decades. In this regard, a generic formulation is an upfront solution to fulfill market demands. Ganirelix, a leading peptide active pharmaceutical ingredient (API) primarily used as a gonadotropin-releasing hormone antagonist (GnRH), has established a potential market value worldwide. But its generic formulation mandates detailed impurity profiles from a synthetic source and contemplates the sameness of a reference-listed drug (RLD). Post-chemical synthesis and processing of Ganirelix, some commercial sources have revealed two new potential impurities among many known, which show the deletion of an ethyl group from the hArg(Et)2 residue at the sixth and eighth positions, named des-ethyl-Ganirelix. These impurities are unprecedented in traditional peptide chemistry, and such monoethylated-hArg building blocks are not easily accessible commercially to synthesize these two impurities. Here, we have outlined the synthesis, purification, and enantiomeric purity characterization of the amino acids and their incorporation in the Ganirelix peptide sequence to synthesize these potential peptide impurities. This methodology will enable the convenient synthesis of side-chain substituted Arg and hArg derivatives in peptide drug discovery platforms.
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Affiliation(s)
- Saurav Chatterjee
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Punjab, India
| | - Anupam Bandyopadhyay
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Punjab, India
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50
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Kasper SH, Otten S, Squadroni B, Orr‐Terry C, Kuang Y, Mussallem L, Ge L, Yan L, Kannan S, Verma CS, Brown CJ, Johannes CW, Lane DP, Chandramohan A, Partridge AW, Roberts LR, Josien H, Therien AG, Hett EC, Howell BJ, Peier A, Ai X, Cassaday J. A high-throughput microfluidic mechanoporation platform to enable intracellular delivery of cyclic peptides in cell-based assays. Bioeng Transl Med 2023; 8:e10542. [PMID: 37693049 PMCID: PMC10487316 DOI: 10.1002/btm2.10542] [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: 03/25/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 09/12/2023] Open
Abstract
Cyclic peptides are poised to target historically difficult to drug intracellular protein-protein interactions, however, their general cell impermeability poses a challenge for characterizing function. Recent advances in microfluidics have enabled permeabilization of the cytoplasmic membrane by physical cell deformation (i.e., mechanoporation), resulting in intracellular delivery of impermeable macromolecules in vector- and electrophoretic-free approaches. However, the number of payloads (e.g., peptides) and/or concentrations delivered via microfluidic mechanoporation is limited by having to pre-mix cells and payloads, a manually intensive process. In this work, we show that cells are momentarily permeable (t 1/2 = 1.1-2.8 min) after microfluidic vortex shedding (μVS) and that lower molecular weight macromolecules can be cytosolically delivered upon immediate exposure after cells are processed/permeabilized. To increase the ability to screen peptides, we built a system, dispensing-microfluidic vortex shedding (DμVS), that integrates a μVS chip with inline microplate-based dispensing. To do so, we synced an electronic pressure regulator, flow sensor, on/off dispense valve, and an x-y motion platform in a software-driven feedback loop. Using this system, we were able to deliver low microliter-scale volumes of transiently mechanoporated cells to hundreds of wells on microtiter plates in just several minutes (e.g., 96-well plate filled in <2.5 min). We validated the delivery of an impermeable peptide directed at MDM2, a negative regulator of the tumor suppressor p53, using a click chemistry- and NanoBRET-based cell permeability assay in 96-well format, with robust delivery across the full plate. Furthermore, we demonstrated that DμVS could be used to identify functional, low micromolar, cellular activity of otherwise cell-inactive MDM2-binding peptides using a p53 reporter cell assay in 96- and 384-well format. Overall, DμVS can be combined with downstream cell assays to investigate intracellular target engagement in a high-throughput manner, both for improving structure-activity relationship efforts and for early proof-of-biology of non-optimized peptide (or potentially other macromolecular) tools.
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Affiliation(s)
| | | | | | | | - Yi Kuang
- Merck & Co., Inc.CambridgeMassachusettsUSA
| | | | - Lan Ge
- Merck & Co., Inc.KenilworthNew JerseyUSA
| | - Lin Yan
- Merck & Co., Inc.KenilworthNew JerseyUSA
| | | | - Chandra S. Verma
- Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | | | | | - David P. Lane
- Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | | | | | | | | | | | | | | | | | - Xi Ai
- Merck & Co., Inc.KenilworthNew JerseyUSA
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