1
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Mi T, Gao Z, Mituta Z, Burgess K. Dual-Capped Helical Interface Mimics. J Am Chem Soc 2024; 146:10331-10341. [PMID: 38573124 PMCID: PMC11027154 DOI: 10.1021/jacs.3c11717] [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: 10/20/2023] [Revised: 02/25/2024] [Accepted: 03/01/2024] [Indexed: 04/05/2024]
Abstract
Disruption of protein-protein interactions is medicinally important. Interface helices may be mimicked in helical probes featuring enhanced rigidities, binding to protein targets, stabilities in serum, and cell uptake. This form of mimicry is dominated by stapling between side chains of helical residues: there has been less progress on helical N-caps, and there were no generalizable C-caps. Conversely, in natural proteins, helicities are stabilized and terminated by C- and N-caps but not staples. Bicyclic caps previously introduced by us enable interface helical mimicry featuring rigid synthetic caps at both termini in this work. An unambiguously helical dual-capped system proved to be conformationally stable, binding cyclins A and E, and showed impressive cellular uptake. In addition, the dual-capped mimic was completely resistant to proteolysis in serum over an extended period when compared with "gold standard" hydrocarbon-stapled controls. Dual-capped peptidomimetics are a new, generalizable paradigm for helical interface probe design.
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Affiliation(s)
- Tianxiong Mi
- Department
of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Zhe Gao
- Department
of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Zeynep Mituta
- ZentriForce
Pharma Research GmbH, Carl-Friedrich-Gauss-Ring 5, 69124 Heidelberg, Germany
| | - Kevin Burgess
- Department
of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
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2
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Ma B, Liu D, Zheng M, Wang Z, Zhang D, Jian Y, Ma J, Fan Y, Chen Y, Gao Y, Liu J, Li X, Li L. Development of a Double-Stapled Peptide Stabilizing Both α-Helix and β-Sheet Structures for Degrading Transcription Factor AR-V7. JACS AU 2024; 4:816-827. [PMID: 38425893 PMCID: PMC10900202 DOI: 10.1021/jacsau.3c00795] [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: 12/14/2023] [Revised: 01/08/2024] [Accepted: 01/08/2024] [Indexed: 03/02/2024]
Abstract
Peptide drugs offer distinct advantages in therapeutics; however, their limited stability and membrane penetration abilities hinder their widespread application. One strategy to overcome these challenges is the hydrocarbon peptide stapling technique, which addresses issues such as poor conformational stability, weak proteolytic resistance, and limited membrane permeability. Nonetheless, while peptide stapling has successfully stabilized α-helical peptides, it has shown limited applicability for most β-sheet peptide motifs. In this study, we present the design of a novel double-stapled peptide capable of simultaneously stabilizing both α-helix and β-sheet structures. Our designed double-stapled peptide, named DSARTC, specifically targets the androgen receptor (AR) DNA binding domain and MDM2 as E3 ligase. Serving as a peptide-based PROTAC (proteolysis-targeting chimera), DSARTC exhibits the ability to degrade both the full-length AR and AR-V7. Molecular dynamics simulations and circular dichroism analysis validate the successful constraint of both secondary structures, demonstrating that DSARTC is a "first-in-class" heterogeneous-conformational double-stapled peptide drug candidate. Compared to its linear counterpart, DSARTC displays enhanced stability and an improved cell penetration ability. In an enzalutamide-resistant prostate cancer animal model, DSARTC effectively inhibits tumor growth and reduces the levels of both AR and AR-V7 proteins. These results highlight the potential of DSARTC as a more potent and specific peptide PROTAC for AR-V7. Furthermore, our findings provide a promising strategy for expanding the design of staple peptide-based PROTAC drugs, targeting a wide range of "undruggable" transcription factors.
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Affiliation(s)
- Bohan Ma
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Donghua Liu
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Mengjun Zheng
- School
of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Zhe Wang
- Institute
of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Dize Zhang
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yanlin Jian
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Jian Ma
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yizeng Fan
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yule Chen
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yang Gao
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Jing Liu
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Xiang Li
- School
of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Lei Li
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
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3
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Ma J, Yan L, Yang J, He Y, Wu L. Effect of Modification Strategies on the Biological Activity of Peptides/Proteins. Chembiochem 2024; 25:e202300481. [PMID: 38009768 DOI: 10.1002/cbic.202300481] [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: 06/28/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 11/29/2023]
Abstract
Covalent attachment of biologically active peptides/proteins with functional moieties is an effective strategy to control their biodistribution, pharmacokinetics, enzymatic digestion, and toxicity. This review focuses on the characteristics of different modification strategies and their effects on the biological activity of peptides/proteins and illustrates their relevant applications and potential.
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Affiliation(s)
- Jian Ma
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Yan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingkui Yang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yujian He
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Li Wu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
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4
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Nelson S, Harris TJ, Muli CS, Maresch ME, Baker B, Smith C, Neumann C, Trader DJ, Parkinson EI. Discovery and Development of Cyclic Peptide Proteasome Stimulators. Chembiochem 2024; 25:e202300671. [PMID: 38055197 PMCID: PMC10993313 DOI: 10.1002/cbic.202300671] [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: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/07/2023]
Abstract
The proteasome degrades proteins, which is essential for cellular homeostasis. Ubiquitin independent proteolysis degrades highly disordered and misfolded proteins. A decline of proteasomal activity has been associated with multiple neurodegenerative diseases due to the accumulation of misfolded proteins. In this work, cyclic peptide proteasome stimulators (CyPPSs) that enhance the clearance of misfolded proteins were discovered. In the initial screen of predicted natural products (pNPs), several cyclic peptides were found to stimulate the 20S core particle (20S CP). Development of a robust structural activity relationship led to the identification of potent, cell permeable CyPPSs. In vitro assays revealed that CyPPSs stimulate degradation of highly disordered and misfolded proteins without affecting ordered proteins. Furthermore, using a novel flow-based assay for proteasome activity, several CyPPSs were found to stimulate the 20S CP in cellulo. Overall, this work describes the development of CyPPSs as chemical tools capable of stimulating the proteasome and provides strong support for proteasome stimulation as a therapeutic strategy for neurodegenerative diseases.
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Affiliation(s)
- Samantha Nelson
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47906, United States
| | - Timothy J. Harris
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California, 92697, United States
| | - Christine S. Muli
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47906, United States
| | - Marianne E. Maresch
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47906, United States
| | - Braden Baker
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
| | - Chloe Smith
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
| | - Chris Neumann
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
| | - Darci J. Trader
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California, 92697, United States
| | - Elizabeth I. Parkinson
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47906, United States
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
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5
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Li J, Tan YS, Verma CS. Dissecting the geometric and hydrophobic constraints of stapled peptides. Proteins 2024. [PMID: 38196284 DOI: 10.1002/prot.26662] [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: 09/20/2023] [Revised: 12/01/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Stapled peptides are a promising class of molecules with potential as highly specific probes of protein-protein interactions and as therapeutics. Hydrocarbon stapling affects the peptide properties through the interplay of two factors: enhancing the overall hydrophobicity and constraining the conformational flexibility. By constructing a series of virtual peptides, we study the role of each factor in modulating the structural properties of a hydrocarbon-stapled peptide PM2, which has been shown to enter cells, engage its target Mouse Double Minute 2 (MDM2), and activate p53. Hamiltonian replica exchange molecular dynamics (HREMD) simulations suggest that hydrocarbon stapling favors helical populations of PM2 through a combination of the geometric constraints and the enhanced hydrophobicity of the peptide. To further understand the conformational landscape of the stapled peptides along the binding pathway, we performed HREMD simulations by restraining the peptide at different distances from MDM2. When the peptide approaches MDM2, the binding pocket undergoes dehydration which appears to be greater in the presence of the stapled peptide compared with the linear peptide. In the binding pocket, the helicity of the stapled peptide is increased due to the favorable interactions between the peptide residues as well as the staple and the microenvironment of the binding pocket, contributing to enhanced affinity. The dissection of the multifaceted mechanism of hydrocarbon stapling into individual factors not only deepens fundamental understanding of peptide stapling, but also provides guidelines for the design of new stapled peptides.
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Affiliation(s)
- Jianguo Li
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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6
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Ricardo MG, Reuber EE, Yao L, Danglad-Flores J, Delbianco M, Seeberger PH. Design, Synthesis, and Characterization of Stapled Oligosaccharides. J Am Chem Soc 2022; 144:18429-18434. [PMID: 36173281 PMCID: PMC9562281 DOI: 10.1021/jacs.2c06882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Stapling short peptides
to lock specific conformations and thereby
obtain superior pharmacological properties is well established. However,
similar concepts have not been applied to oligosaccharides. Here,
we describe the design, synthesis, and characterization of the first
stapled oligosaccharides. Automated assembly of β-(1,6)-glucans
equipped with two alkenyl side chains was followed by on-resin Grubbs
metathesis for efficient ring closure with a variety of cross-linkers
of different sizes. Oligosaccharide stapling increases enzymatic stability
and cell penetration, therefore opening new opportunities for the
use of glycans in medicinal chemistry.
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Affiliation(s)
- Manuel G Ricardo
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Emelie E Reuber
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Ling Yao
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - José Danglad-Flores
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
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7
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Helical Foldamers and Stapled Peptides as New Modalities in Drug Discovery: Modulators of Protein-Protein Interactions. Processes (Basel) 2022. [DOI: 10.3390/pr10050924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A “foldamer” is an artificial oligomeric molecule with a regular secondary or tertiary structure consisting of various building blocks. A “stapled peptide” is a peptide with stabilized secondary structures, in particular, helical structures by intramolecular covalent side-chain cross-linking. Helical foldamers and stapled peptides are potential drug candidates that can target protein-protein interactions because they enable multipoint molecular recognition, which is difficult to achieve with low-molecular-weight compounds. This mini-review describes a variety of peptide-based foldamers and stapled peptides with a view to their applications in drug discovery, including our recent progress.
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8
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Lai Z, Yuan X, Chen H, Zhu Y, Dong N, Shan A. Strategies employed in the design of antimicrobial peptides with enhanced proteolytic stability. Biotechnol Adv 2022; 59:107962. [PMID: 35452776 DOI: 10.1016/j.biotechadv.2022.107962] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/14/2022] [Accepted: 04/13/2022] [Indexed: 12/12/2022]
Abstract
Due to the alarming developing rate of multidrug-resistant bacterial pathogens, the development and modification of antimicrobial peptides (AMPs) are unprecedentedly active. Despite the fact that considerable efforts have been expended on the discovery and design strategies of AMPs, the clinical translation of peptide antibiotics remains inadequate. A large number of articles and reviews credited the limited success of AMPs to their poor stability in the biological environment, particularly their poor proteolytic stability. In the past forty years, various design strategies have been used to improve the proteolytic stability of AMPs, such as sequence modification, cyclization, peptidomimetics, and nanotechnology. Herein, we focus our discussion on the progress made in improving the proteolytic stability of AMPs and the principle, successes, and limitations of various anti-proteolytic design strategies. It is of prospective significance to extend current insights into the degradation-related inactivation of AMPs and also alleviate/overcome the problem.
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Affiliation(s)
- Zhenheng Lai
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Xiaojie Yuan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Hongyu Chen
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Yunhui Zhu
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Na Dong
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Anshan Shan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China.
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9
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Taresh AB, Hutton CA. Backbone thioamide directed macrocyclisation: lactam stapling of peptides. Org Biomol Chem 2022; 20:1488-1492. [PMID: 35103273 DOI: 10.1039/d1ob02461b] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A novel method for lactam stapling of Asp/Lys-containing peptides has been developed that does not require coupling agents. A backbone thioamide is incorporated at the N-terminal side of the aspartate residue. Ag(I)-promoted activation of the thioamide in the vicinity of the Asp carboxylate generates a cyclic isoimide intermediate that is trapped by the Lys amine to generate the macrolactam. This method is suitable for generation of i,i+2, i,i+3, and i,i+4-spaced lactam-bridged peptides.
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Affiliation(s)
- Ameer B Taresh
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Craig A Hutton
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia.
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10
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Gruß H, Feiner RC, Mseya R, Schröder DC, Jewgiński M, Müller KM, Latajka R, Marion A, Sewald N. Peptide stapling by late-stage Suzuki–Miyaura cross-coupling. Beilstein J Org Chem 2022; 18:1-12. [PMID: 35047078 PMCID: PMC8744458 DOI: 10.3762/bjoc.18.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/09/2021] [Indexed: 12/19/2022] Open
Abstract
The development of peptide stapling techniques to stabilise α-helical secondary structure motifs of peptides led to the design of modulators of protein–protein interactions, which had been considered undruggable for a long time. We disclose a novel approach towards peptide stapling utilising macrocyclisation by late-stage Suzuki–Miyaura cross-coupling of bromotryptophan-containing peptides of the catenin-binding domain of axin. Optimisation of the linker length in order to find a compromise between both sufficient linker rigidity and flexibility resulted in a peptide with an increased α-helicity and enhanced binding affinity to its native binding partner β-catenin. An increased proteolytic stability against proteinase K has been demonstrated.
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Affiliation(s)
- Hendrik Gruß
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Rebecca C Feiner
- Department of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Ridhiwan Mseya
- Department of Chemistry, Middle East Technical University, 06800, Ankara, Turkey
| | - David C Schröder
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Michał Jewgiński
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wrocław, Poland
| | - Kristian M Müller
- Department of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Rafał Latajka
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wrocław, Poland
| | - Antoine Marion
- Department of Chemistry, Middle East Technical University, 06800, Ankara, Turkey
| | - Norbert Sewald
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
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11
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Sinclair JKL, Robertson WE, Mozumdar D, Quach K, Schepartz A. Allosteric Inhibition of the Epidermal Growth Factor Receptor. Biochemistry 2021; 60:500-512. [PMID: 33557518 DOI: 10.1021/acs.biochem.0c00978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We previously reported a family of hydrocarbon-stapled peptides designed to interact with the epidermal growth factor receptor (EGFR) juxtamembrane (JM) segment, blocking its ability to form a coiled coil dimer that is essential for receptor activation. These hydrocarbon-stapled peptides, most notably E1S, decreased the proliferation of cell lines that express wild-type EGFR (H2030 and A431) as well as those expressing the oncogenic mutants EGFR L858R (H3255) and L858R/T790M (H1975). Although our previous investigations provided evidence that E1S interacted with EGFR directly, the location and details of these interactions were not established. Here we apply biochemical and cross-linking mass spectrometry tools to better define the interactions between E1S and EGFR. Taken with previously reported structure-activity relationships, our results support a model in which E1S interacts simultaneously with both the JM and the C-lobe of the activator kinase, effectively displacing the JM of the receiver kinase. Our results also reveal potential interactions between E1S and the N-terminal region of the C-terminal tail. We propose a model in which E1S inhibits EGFR by both mimicking and inhibiting JM coiled coil formation. This model could be used to design novel, allosteric (and perhaps nonpeptidic) EGFR inhibitors.
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Affiliation(s)
- Julie K L Sinclair
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Wesley E Robertson
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, United States
| | - Deepto Mozumdar
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States.,Department of Chemistry, University of California, Berkeley, California 94705, United States
| | - Kim Quach
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, California 94705, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, California 94705, United States
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12
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Monty OBC, Simmons N, Chamakuri S, Matzuk MM, Young DW. Solution-Phase Fmoc-Based Peptide Synthesis for DNA-Encoded Chemical Libraries: Reaction Conditions, Protecting Group Strategies, and Pitfalls. ACS COMBINATORIAL SCIENCE 2020; 22:833-843. [PMID: 33074645 DOI: 10.1021/acscombsci.0c00144] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Peptide drug discovery has shown a resurgence since 2000, bringing 28 non-insulin therapeutics to the market compared to 56 since its first peptide drug, insulin, in 1923. While the main method of discovery has been biological display-phage, mRNA, and ribosome-the synthetic limitations of biological systems has restricted the depth of exploration of peptide chemical space. In contrast, DNA-encoded chemistry offers the synergy of large numbers and ribosome-independent synthetic flexibility for the fast and deeper exploration of the same space. Hence, as a bridge to building DNA-encoded chemical libraries (DECLs) of peptides, we have developed substrate-tolerant amide coupling reaction conditions for amino acid monomers, performed a coupling screen to illustrate such tolerance, developed protecting group strategies for relevant amino acids and reported the limitations thereof, developed a strategy for the coupling of α,α-disubstituted alkenyl amino acids relevant to all-hydrocarbon stapled peptide drug discovery, developed reaction conditions for the coupling of tripeptides likely to be used in DECL builds, and synthesized a fully deprotected DNA-decamer conjugate to illustrate the potency of the developed methodology for on-DNA peptide synthesis.
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Affiliation(s)
- Olivier B. C. Monty
- Center for Drug Discovery, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030 United States
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005 United States
| | - Nicholas Simmons
- Center for Drug Discovery, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030 United States
| | - Srinivas Chamakuri
- Center for Drug Discovery, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030 United States
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030 United States
| | - Martin M. Matzuk
- Center for Drug Discovery, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030 United States
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030 United States
| | - Damian W. Young
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030 United States
- Center for Drug Discovery, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030 United States
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030 United States
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005 United States
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13
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Hydrocarbon-Stapled Peptide Based-Nanoparticles for siRNA Delivery. NANOMATERIALS 2020; 10:nano10122334. [PMID: 33255624 PMCID: PMC7760004 DOI: 10.3390/nano10122334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/21/2020] [Indexed: 01/22/2023]
Abstract
Small interfering RNAs (siRNAs) are promising molecules for developing new therapies based on gene silencing; however, their delivery into cells remains an issue. In this study, we took advantage of stapled peptide technology that has emerged as a valuable strategy to render natural peptides more structured, resistant to protease degradation and more bioavailable, to develop short carriers for siRNA delivery. From the pool of stapled peptides that we have designed and synthesized, we identified non-toxic vectors that were able to efficiently encapsulate siRNA, transport them into the cell and induce gene silencing. Remarkably, the most efficient stapled peptide (JMV6582), is composed of only eight amino-acids and contains only two cationic charges.
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14
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Sindhikara D, Wagner M, Gkeka P, Güssregen S, Tiwari G, Hessler G, Yapici E, Li Z, Evers A. Automated Design of Macrocycles for Therapeutic Applications: From Small Molecules to Peptides and Proteins. J Med Chem 2020; 63:12100-12115. [PMID: 33017535 DOI: 10.1021/acs.jmedchem.0c01500] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Macrocycles and cyclic peptides are increasingly attractive therapeutic modalities as they often have improved affinity, are able to bind to extended protein surfaces, and otherwise have favorable properties. Macrocyclization of a known binder may stabilize its bioactive conformation and improve its metabolic stability, cell permeability, and in certain cases oral bioavailability. Herein, we present implementation and application of an approach that automatically generates, evaluates, and proposes cyclizations utilizing a library of well-established chemical reactions and reagents. Using the three-dimensional (3D) conformation of the linear molecule in complex with a target protein as the starting point, this approach identifies attachment points, generates linkers, evaluates their geometric compatibility, and ranks the resulting molecules with respect to their predicted conformational stability and interactions with the target protein. As we show here with prospective and retrospective case studies, this procedure can be applied for the macrocyclization of small molecules and peptides and even PROteolysis TArgeting Chimeras (PROTACs) and proteins.
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Affiliation(s)
- Dan Sindhikara
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Michael Wagner
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Paraskevi Gkeka
- Integrated Drug Discovery, Sanofi R&D, 1 Avenue Pierre Brossolette, 91385 Chilly-Mazarin, France
| | - Stefan Güssregen
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Garima Tiwari
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Gerhard Hessler
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Engin Yapici
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Ziyu Li
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Andreas Evers
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
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15
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Rodríguez J, Martínez-Calvo M. Transition-Metal-Mediated Modification of Biomolecules. Chemistry 2020; 26:9792-9813. [PMID: 32602145 DOI: 10.1002/chem.202001287] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/25/2020] [Indexed: 01/15/2023]
Abstract
The site-selective modification of biomolecules has grown spectacularly in recent years. The presence of a large number of functional groups in a biomolecule makes its chemo- and regioselective modification a challenging goal. In this context, transition-metal-mediated reactions are emerging as a powerful tool owing to their unique reactivity and good functional group compatibility, allowing highly efficient and selective bioconjugation reactions that operate under mild conditions. This Minireview focuses on the current state of organometallic chemistry for bioconjugation, highlighting the potential of transition metals for the development of chemoselective and site-specific methods for functionalization of peptides, proteins and nucleic acids. The importance of the selection of ligands attached to the transition metal for conferring the desired chemoselectivity will be highlighted.
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Affiliation(s)
- Jessica Rodríguez
- Laboratoire Hétérochimie Fondamentale et Appliquée, Université Paul Sabatier/CNRS UMR 5069, 118 Route de Narbonne, 31062, Toulouse Cedex 09, France
| | - Miguel Martínez-Calvo
- Centro de Investigaciones Científicas Avanzadas (CICA), AE CICA-INIBIC, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, Campus de Elviña, 15071 A, Coruña, Galicia, Spain
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16
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Tan YS, Mhoumadi Y, Verma CS. Roles of computational modelling in understanding p53 structure, biology, and its therapeutic targeting. J Mol Cell Biol 2020; 11:306-316. [PMID: 30726928 PMCID: PMC6487789 DOI: 10.1093/jmcb/mjz009] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/14/2018] [Accepted: 01/31/2019] [Indexed: 12/21/2022] Open
Abstract
The transcription factor p53 plays pivotal roles in numerous biological processes, including the suppression of tumours. The rich availability of biophysical data aimed at understanding its structure–function relationships since the 1990s has enabled the application of a variety of computational modelling techniques towards the establishment of mechanistic models. Together they have provided deep insights into the structure, mechanics, energetics, and dynamics of p53. In parallel, the observation that mutations in p53 or changes in its associated pathways characterize several human cancers has resulted in a race to develop therapeutic modulators of p53, some of which have entered clinical trials. This review describes how computational modelling has played key roles in understanding structural-dynamic aspects of p53, formulating hypotheses about domains that are beyond current experimental investigations, and the development of therapeutic molecules that target the p53 pathway.
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Affiliation(s)
- Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore
| | - Yasmina Mhoumadi
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore
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17
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Reguera L, Rivera DG. Multicomponent Reaction Toolbox for Peptide Macrocyclization and Stapling. Chem Rev 2019; 119:9836-9860. [PMID: 30990310 DOI: 10.1021/acs.chemrev.8b00744] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In the past decade, multicomponent reactions have experienced a renaissance as powerful peptide macrocyclization tools enabling the rapid creation of skeletal complexity and diversity with low synthetic cost. This review provides both a historical and modern overview of the development of the peptide multicomponent macrocyclization as a strategy capable to compete with the classic peptide cyclization methods in terms of chemical efficiency and synthetic scope. We prove that the utilization of multicomponent reactions for cyclizing peptides by either their termini or side chains provides a key advantage over those more established methods; that is, the possibility to explore the cyclic peptide chemotype space not only at the amino acid sequence but also at the ring-forming moiety. Owing to its multicomponent nature, this type of peptide cyclization process is well-suited to generate diversity at both the endo- and exo-cyclic fragments formed during the ring-closing step, which stands as a distinctive and useful characteristic for the creation and screening of cyclic peptide libraries. Examples of the novel multicomponent peptide stapling approach and heterocycle ring-forming macrocyclizations are included, along with multicomponent methods incorporating macrocyclization handles and the one-pot syntheses of macromulticyclic peptide cages. Interesting applications of this strategy in the field of drug discovery and chemical biology are provided.
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Affiliation(s)
- Leslie Reguera
- Center for Natural Product Research, Faculty of Chemistry , University of Havana , Zapata y G , Havana 10400 , Cuba
| | - Daniel G Rivera
- Center for Natural Product Research, Faculty of Chemistry , University of Havana , Zapata y G , Havana 10400 , Cuba
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18
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Ricardo MG, Llanes D, Wessjohann LA, Rivera DG. Introducing the Petasis Reaction for Late‐Stage Multicomponent Diversification, Labeling, and Stapling of Peptides. Angew Chem Int Ed Engl 2019; 58:2700-2704. [DOI: 10.1002/anie.201812620] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/20/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Manuel G. Ricardo
- Department of Bioorganic ChemistryLeibniz Institute of Plant Biochemistry Weinberg 3 06120 Halle/Saale Germany
- Center for Natural Products ResearchFaculty of Chemistry University of Havana Zapata y G 10400 La Habana Cuba
| | - Dayma Llanes
- Center for Natural Products ResearchFaculty of Chemistry University of Havana Zapata y G 10400 La Habana Cuba
| | - Ludger A. Wessjohann
- Department of Bioorganic ChemistryLeibniz Institute of Plant Biochemistry Weinberg 3 06120 Halle/Saale Germany
| | - Daniel G. Rivera
- Department of Bioorganic ChemistryLeibniz Institute of Plant Biochemistry Weinberg 3 06120 Halle/Saale Germany
- Center for Natural Products ResearchFaculty of Chemistry University of Havana Zapata y G 10400 La Habana Cuba
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19
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Ricardo MG, Llanes D, Wessjohann LA, Rivera DG. Introducing the Petasis Reaction for Late‐Stage Multicomponent Diversification, Labeling, and Stapling of Peptides. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812620] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Manuel G. Ricardo
- Department of Bioorganic ChemistryLeibniz Institute of Plant Biochemistry Weinberg 3 06120 Halle/Saale Germany
- Center for Natural Products ResearchFaculty of Chemistry University of Havana Zapata y G 10400 La Habana Cuba
| | - Dayma Llanes
- Center for Natural Products ResearchFaculty of Chemistry University of Havana Zapata y G 10400 La Habana Cuba
| | - Ludger A. Wessjohann
- Department of Bioorganic ChemistryLeibniz Institute of Plant Biochemistry Weinberg 3 06120 Halle/Saale Germany
| | - Daniel G. Rivera
- Department of Bioorganic ChemistryLeibniz Institute of Plant Biochemistry Weinberg 3 06120 Halle/Saale Germany
- Center for Natural Products ResearchFaculty of Chemistry University of Havana Zapata y G 10400 La Habana Cuba
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20
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Ricardo MG, Marrrero JF, Valdés O, Rivera DG, Wessjohann LA. A Peptide Backbone Stapling Strategy Enabled by the Multicomponent Incorporation of Amide N-Substituents. Chemistry 2018; 25:769-774. [PMID: 30412333 DOI: 10.1002/chem.201805318] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Indexed: 12/12/2022]
Abstract
The multicomponent backbone N-modification of peptides on solid-phase is presented as a powerful and general method to enable peptide stapling at the backbone instead of the side chains. This work shows that a variety of functionalized N-substituents suitable for backbone stapling can be readily introduced by means of on-resin Ugi multicomponent reactions conducted during solid-phase peptide synthesis. Diverse macrocyclization chemistries were implemented with such backbone N-substituents, including the ring-closing metathesis, lactamization, and thiol alkylation. The backbone N-modification method was also applied to the synthesis of α-helical peptides by linking N-substituents to the peptide N-terminus, thus featuring hydrogen-bond surrogate structures. Overall, the strategy proves useful for peptide backbone macrocyclization approaches that show promise in peptide drug discovery.
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Affiliation(s)
- Manuel G Ricardo
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle/Saale, Germany.,Center for Natural Products Research, Faculty of Chemistry, University of Havana, Zapata y G, 10400, La Habana, Cuba
| | - Javiel F Marrrero
- Center for Natural Products Research, Faculty of Chemistry, University of Havana, Zapata y G, 10400, La Habana, Cuba
| | - Oscar Valdés
- Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca, 3460000, Chile
| | - Daniel G Rivera
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle/Saale, Germany.,Center for Natural Products Research, Faculty of Chemistry, University of Havana, Zapata y G, 10400, La Habana, Cuba
| | - Ludger A Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle/Saale, Germany
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21
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Almeida JR, Palacios ALV, Patiño RSP, Mendes B, Teixeira CAS, Gomes P, da Silva SL. Harnessing snake venom phospholipases A 2 to novel approaches for overcoming antibiotic resistance. Drug Dev Res 2018; 80:68-85. [PMID: 30255943 DOI: 10.1002/ddr.21456] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/25/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022]
Abstract
The emergence of antibiotic resistance drives an essential race against time to reveal new molecular structures capable of addressing this alarming global health problem. Snake venoms are natural catalogs of multifunctional toxins and privileged frameworks, which serve as potential templates for the inspiration of novel treatment strategies for combating antibiotic resistant bacteria. Phospholipases A2 (PLA2 s) are one of the main classes of antibacterial biomolecules, with recognized therapeutic value, found in these valuable secretions. Recently, a number of biomimetic oligopeptides based on small fragments of primary structure from PLA2 toxins has emerged as a meaningful opportunity to overcome multidrug-resistant clinical isolates. Thus, this review will highlight the biochemical and structural properties of antibacterial PLA2 s and peptides thereof, as well as their possible molecular mechanisms of action and key roles in development of effective therapeutic strategies. Chemical strategies possibly useful to convert antibacterial peptides from PLA2 s to efficient drugs will be equally addressed.
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Affiliation(s)
| | | | | | - Bruno Mendes
- Departamento de Biologia Animal, Instituto de Biologia, Universidade de Campinas (UNICAMP), Campinas, Brazil
| | - Cátia A S Teixeira
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Paula Gomes
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Saulo L da Silva
- Facultad de Ciencias Química, Universidad de Cuenca - Cuenca/Azuay - Ecuador
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22
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The role of the gap junction perinexus in cardiac conduction: Potential as a novel anti-arrhythmic drug target. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 144:41-50. [PMID: 30241906 DOI: 10.1016/j.pbiomolbio.2018.08.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/09/2018] [Accepted: 08/10/2018] [Indexed: 12/16/2022]
Abstract
Cardiovascular disease remains the single largest cause of natural death in the United States, with a significant cause of mortality associated with cardiac arrhythmias. Presently, options for treating and preventing myocardial electrical dysfunction, including sudden cardiac death, are limited. Recent studies have indicated that conduction of electrical activation in the heart may have an ephaptic component, wherein intercellular coupling occurs via electrochemical signaling across narrow extracellular clefts between cardiomyocytes. The perinexus is a 100-200 nm-wide stretch of closely apposed membrane directly adjacent to connexin 43 gap junctions. Electron and super-resolution microscopy studies, as well as biochemical analyses, have provided evidence that perinexal nanodomains may be candidate structures for facilitating ephaptic coupling. This work has included characterization of the perinexus as a region of close inter-membrane contact between cardiomyocytes (<30 nm) containing dense clusters of voltage-gated sodium channels. Here, we review what is known about perinexal structure and function and the potential that the perinexus may have novel and pivotal roles in disorders of cardiac conduction. Of particular interest is the prospect that cell adhesion mediated by the cardiac sodium channel β subunit (Scn1b) may be a novel anti-arrhythmic target.
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23
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Guo Y, Fu L, Fan X, Shi X. Stapled SC34EK fusion inhibitors with high potency against HIV-1 and improved protease resistance. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.03.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Jiang Y, Hu K, Shi X, Tang Q, Wang Z, Ye X, Li Z. Switching substitution groups on the in-tether chiral centre influences backbone peptides' permeability and target binding affinity. Org Biomol Chem 2018; 15:541-544. [PMID: 27929189 DOI: 10.1039/c6ob02289h] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Different substitution groups on the in-tether chiral centre of chirality-induced helical peptides (CIH peptides) showed distinguishable effects on the peptides' cellular uptakes and binding affinities with the estrogen receptor α(ER-α). This study proves that in-tether chiral centres are a valuable modification site for constructing peptide ligands with preferable biophysical properties.
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Affiliation(s)
- Yixiang Jiang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Kuan Hu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Xiaodong Shi
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Qingzhuang Tang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - ZiChen Wang
- Shenzhen Middle School, Shenzhen 518001, China
| | - Xiyang Ye
- Department of Gynecology, Shenzhen People's Hospital, Shenzhen 518055, China
| | - Zigang Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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25
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Sawyer TK, Partridge AW, Kaan HYK, Juang YC, Lim S, Johannes C, Yuen TY, Verma C, Kannan S, Aronica P, Tan YS, Sherborne B, Ha S, Hochman J, Chen S, Surdi L, Peier A, Sauvagnat B, Dandliker PJ, Brown CJ, Ng S, Ferrer F, Lane DP. Macrocyclic α helical peptide therapeutic modality: A perspective of learnings and challenges. Bioorg Med Chem 2018; 26:2807-2815. [PMID: 29598901 DOI: 10.1016/j.bmc.2018.03.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/03/2018] [Accepted: 03/06/2018] [Indexed: 12/20/2022]
Abstract
Macrocyclic α-helical peptides have emerged as a compelling new therapeutic modality to tackle targets confined to the intracellular compartment. Within the scope of hydrocarbon-stapling there has been significant progress to date, including the first stapled α-helical peptide to enter into clinical trials. The principal design concept of stapled α-helical peptides is to mimic a cognate (protein) ligand relative to binding its target via an α-helical interface. However, it was the proclivity of such stapled α-helical peptides to exhibit cell permeability and proteolytic stability that underscored their promise as unique macrocyclic peptide drugs for intracellular targets. This perspective highlights key learnings as well as challenges in basic research with respect to structure-based design, innovative chemistry, cell permeability and proteolytic stability that are essential to fulfill the promise of stapled α-helical peptide drug development.
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26
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KleinJan A, Tindemans I, Montgomery JE, Lukkes M, de Bruijn MJW, van Nimwegen M, Bergen I, Moellering RE, Hoogsteden HC, Boon L, Amsen D, Hendriks RW. The Notch pathway inhibitor stapled α-helical peptide derived from mastermind-like 1 (SAHM1) abrogates the hallmarks of allergic asthma. J Allergy Clin Immunol 2017; 142:76-85.e8. [PMID: 29111218 DOI: 10.1016/j.jaci.2017.08.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 07/12/2017] [Accepted: 08/24/2017] [Indexed: 01/07/2023]
Abstract
BACKGROUND The Notch signaling pathway has been implicated in the pathogenesis of allergic airway inflammation. Targeting the active Notch transactivation complex by using the cell-permeable, hydrocarbon-stapled synthetic peptide stapled α-helical peptide derived from mastermind-like 1 (SAHM1) resulted in genome-wide suppression of Notch-activated genes in leukemic cells and other models. However, the efficacy of SAHM1 in allergic asthma models has remained unexplored. OBJECTIVE We aimed to investigate the therapeutic efficacy of SAHM1 in a house dust mite (HDM)-driven asthma model. METHODS Topical therapeutic intervention with SAHM1 or a control peptide was performed during sensitization, challenge, or both with HDM in mice. Airway inflammation was assessed by using multicolor flow cytometry, and bronchial hyperreactivity was studied. Additionally, SAHM1 therapy was investigated in mice with established allergic airway inflammation and in a model in which we neutralized IFN-γ during HDM challenge to support the TH2 response and exacerbate asthma. RESULTS SAHM1 treatment during the challenge phase led to a marked reduction of eosinophil and T cell numbers in bronchoalveolar lavage fluid compared with those in diluent-treated or control peptide-treated mice. Likewise, T-cell cytokine content and bronchial hyperreactivity were reduced. SAHM1 treatment dampened TH2 inflammation during ongoing HDM challenge and enhanced recovery after established asthma. Additionally, in the presence of anti-IFN-γ antibodies, SAHM1 downregulated expression of the key TH2 transcription factor GATA3 and intracellular IL-4 in bronchoalveolar lavage fluid T cells, but expression of the TH17 transcription factor retinoic acid-related orphan receptor γt or intracellular IL-17 was not affected. SAHM1 therapy also reduced serum IgE levels. CONCLUSIONS Therapeutic intervention of Notch signaling by SAHM1 inhibits allergic airway inflammation in mice and is therefore an interesting new topical treatment opportunity in asthmatic patients.
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Affiliation(s)
- Alex KleinJan
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands.
| | - Irma Tindemans
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Jeffrey E Montgomery
- Department of Chemistry, University of Chicago, Chicago, Ill; Institute for Genomics and Systems Biology, University of Chicago, Chicago, Ill
| | - Melanie Lukkes
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands
| | | | - Menno van Nimwegen
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Ingrid Bergen
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Raymond E Moellering
- Department of Chemistry, University of Chicago, Chicago, Ill; Institute for Genomics and Systems Biology, University of Chicago, Chicago, Ill
| | - Henk C Hoogsteden
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Louis Boon
- Epirus Biopharmaceuticals Netherlands, Utrecht, The Netherlands
| | | | - R W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands
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27
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Protein epitope mimetic macrocycles as biopharmaceuticals. Curr Opin Chem Biol 2017; 38:45-51. [DOI: 10.1016/j.cbpa.2017.02.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/02/2017] [Accepted: 02/06/2017] [Indexed: 01/13/2023]
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28
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Wang Y, Bruno BJ, Cornillie S, Nogieira JM, Chen D, Cheatham TE, Lim CS, Chou DHC. Application of Thiol-yne/Thiol-ene Reactions for Peptide and Protein Macrocyclizations. Chemistry 2017; 23:7087-7092. [DOI: 10.1002/chem.201700572] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Yuanxiang Wang
- Department of Biochemistry; University of Utah; 15 N, Medical Drive East 4100 Salt Lake City UT 84112 USA
| | - Benjamin J. Bruno
- Department of Pharmaceutics and Pharmaceutical Chemistry; University of Utah; 30 S 2000 E, Rm 2916 Salt Lake City UT 84112 USA
| | - Sean Cornillie
- Department of Medicinal Chemistry; University of Utah; 30 S 2000 E, Rm 4914 Salt Lake City UT 84112 USA
| | - Jason M. Nogieira
- Department of Biochemistry; University of Utah; 15 N, Medical Drive East 4100 Salt Lake City UT 84112 USA
| | - Diao Chen
- Department of Biochemistry; University of Utah; 15 N, Medical Drive East 4100 Salt Lake City UT 84112 USA
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry; University of Utah; 30 S 2000 E, Rm 4914 Salt Lake City UT 84112 USA
| | - Carol S. Lim
- Department of Pharmaceutics and Pharmaceutical Chemistry; University of Utah; 30 S 2000 E, Rm 2916 Salt Lake City UT 84112 USA
| | - Danny Hung-Chieh Chou
- Department of Biochemistry; University of Utah; 15 N, Medical Drive East 4100 Salt Lake City UT 84112 USA
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29
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García-Pindado J, Royo S, Teixidó M, Giralt E. Bike peptides: a ride through the membrane. J Pept Sci 2017; 23:294-302. [DOI: 10.1002/psc.2993] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 02/20/2017] [Accepted: 02/22/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Júlia García-Pindado
- Institute for Research in Biomedicine (IRB Barcelona); Barcelona Institute of Science and Technology (BIST); 08028 Barcelona Spain
| | - Soledad Royo
- Institute for Research in Biomedicine (IRB Barcelona); Barcelona Institute of Science and Technology (BIST); 08028 Barcelona Spain
| | - Meritxell Teixidó
- Institute for Research in Biomedicine (IRB Barcelona); Barcelona Institute of Science and Technology (BIST); 08028 Barcelona Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona); Barcelona Institute of Science and Technology (BIST); 08028 Barcelona Spain
- Department of Organic Chemistry; University of Barcelona; 08028 Barcelona Spain
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30
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Tian Y, Yang D, Ye X, Li Z. Thioether-derived Macrocycle for Peptide Secondary Structure Fixation. CHEM REC 2017; 17:874-885. [DOI: 10.1002/tcr.201600137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Yuan Tian
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 P. R. China
- School of Life Science and Engineering; Southwest Jiaotong University; Chengdu 611756 P. R. China
| | - Dan Yang
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 P. R. China
| | - Xiyang Ye
- Department of Gynecology, Second Clinical Medical College; Jinan University, Shenzhen People's Hospital; 1017 Dongmen North Road, Luohu District Shenzhen 518020 P. R. China
| | - Zigang Li
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 P. R. China
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31
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Tran PT, Larsen CØ, Røndbjerg T, De Foresta M, Kunze MBA, Marek A, Løper JH, Boyhus LE, Knuhtsen A, Lindorff-Larsen K, Pedersen DS. Diversity-Oriented Peptide Stapling: A Third Generation Copper-Catalysed Azide-Alkyne Cycloaddition Stapling and Functionalisation Strategy. Chemistry 2017; 23:3490-3495. [DOI: 10.1002/chem.201700128] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Phuong Thu Tran
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Christian Ørnbøl Larsen
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Tobias Røndbjerg
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Martina De Foresta
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Micha B. A. Kunze
- Structural Biology and NMR Laboratory; Department of Biology; University of Copenhagen; Ole Maaloes Vej 5 2200 Copenhagen Denmark
| | - Ales Marek
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; 16610 Prague 6 Czech Republic
| | - Jacob Hartvig Løper
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Lotte-Emilie Boyhus
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Astrid Knuhtsen
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory; Department of Biology; University of Copenhagen; Ole Maaloes Vej 5 2200 Copenhagen Denmark
| | - Daniel Sejer Pedersen
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
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32
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Acar H, Srivastava S, Chung EJ, Schnorenberg MR, Barrett JC, LaBelle JL, Tirrell M. Self-assembling peptide-based building blocks in medical applications. Adv Drug Deliv Rev 2017; 110-111:65-79. [PMID: 27535485 PMCID: PMC5922461 DOI: 10.1016/j.addr.2016.08.006] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/01/2016] [Accepted: 08/05/2016] [Indexed: 12/22/2022]
Abstract
Peptides and peptide-conjugates, comprising natural and synthetic building blocks, are an increasingly popular class of biomaterials. Self-assembled nanostructures based on peptides and peptide-conjugates offer advantages such as precise selectivity and multifunctionality that can address challenges and limitations in the clinic. In this review article, we discuss recent developments in the design and self-assembly of various nanomaterials based on peptides and peptide-conjugates for medical applications, and categorize them into two themes based on the driving forces of molecular self-assembly. First, we present the self-assembled nanostructures driven by the supramolecular interactions between the peptides, with or without the presence of conjugates. The studies where nanoassembly is driven by the interactions between the conjugates of peptide-conjugates are then presented. Particular emphasis is given to in vivo studies focusing on therapeutics, diagnostics, immune modulation and regenerative medicine. Finally, challenges and future perspectives are presented.
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Affiliation(s)
- Handan Acar
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, USA; Department of Pediatrics, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA.
| | - Samanvaya Srivastava
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, USA; Institute for Molecular Engineering, Argonne National Laboratory, Argonne, IL 60439, USA.
| | - Eun Ji Chung
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, USA; Department of Biomedical Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Mathew R Schnorenberg
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, USA; Department of Pediatrics, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA; Medical Scientist Training Program, University of Chicago, Chicago, IL 60637, USA.
| | - John C Barrett
- Biophysical Sciences Graduate Program, University of Chicago, Chicago, IL 60637, USA.
| | - James L LaBelle
- Department of Pediatrics, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA.
| | - Matthew Tirrell
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, USA; Institute for Molecular Engineering, Argonne National Laboratory, Argonne, IL 60439, USA.
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33
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Stapled peptide design: principles and roles of computation. Drug Discov Today 2016; 21:1642-1653. [DOI: 10.1016/j.drudis.2016.06.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/11/2016] [Accepted: 06/13/2016] [Indexed: 12/23/2022]
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34
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Tan YS, Reeks J, Brown CJ, Thean D, Ferrer
Gago FJ, Yuen TY, Goh EL, Lee XEC, Jennings CE, Joseph TL, Lakshminarayanan R, Lane DP, Noble MEM, Verma CS. Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design. J Phys Chem Lett 2016; 7:3452-7. [PMID: 27532490 PMCID: PMC5515508 DOI: 10.1021/acs.jpclett.6b01525] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Protein flexibility poses a major challenge in binding site identification. Several computational pocket detection methods that utilize small-molecule probes in molecular dynamics (MD) simulations have been developed to address this issue. Although they have proven hugely successful at reproducing experimental structural data, their ability to predict new binding sites that are yet to be identified and characterized has not been demonstrated. Here, we report the use of benzenes as probe molecules in ligand-mapping MD (LMMD) simulations to predict the existence of two novel binding sites on the surface of the oncoprotein MDM2. One of them was serendipitously confirmed by biophysical assays and X-ray crystallography to be important for the binding of a new family of hydrocarbon stapled peptides that were specifically designed to target the other putative site. These results highlight the predictive power of LMMD and suggest that predictions derived from LMMD simulations can serve as a reliable basis for the identification of novel ligand binding sites in structure-based drug design.
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Affiliation(s)
- Yaw Sing Tan
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Judith Reeks
- Northern
Institute for Cancer Research, Newcastle
University, Framlington
Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Christopher J. Brown
- p53
Laboratory, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
| | - Dawn Thean
- p53
Laboratory, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
| | | | - Tsz Ying Yuen
- Institute
of Chemical & Engineering Sciences, A*STAR, 8 Biomedical
Grove, #07-01 Neuros, Singapore 138665
| | - Eunice
Tze Leng Goh
- Singapore
Eye Research Institute, 11 Third Hospital Avenue, Singapore 168751
| | - Xue Er Cheryl Lee
- p53
Laboratory, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
| | - Claire E. Jennings
- Northern
Institute for Cancer Research, Newcastle
University, Framlington
Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Thomas L. Joseph
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | | | - David P. Lane
- p53
Laboratory, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
- E-mail:
| | - Martin E. M. Noble
- Northern
Institute for Cancer Research, Newcastle
University, Framlington
Place, Newcastle upon Tyne NE2 4HH, U.K.
- E-mail:
| | - Chandra S. Verma
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- Department
of Biological Sciences, National University
of Singapore, 14 Science
Drive 4, Singapore 117543
- School
of Biological Sciences, Nanyang Technological
University, 60 Nanyang
Drive, Singapore 637551
- E-mail:
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35
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Tian Y, Li J, Zhao H, Zeng X, Wang D, Liu Q, Niu X, Huang X, Xu N, Li Z. Stapling of unprotected helical peptides via photo-induced intramolecular thiol-yne hydrothiolation. Chem Sci 2016; 7:3325-3330. [PMID: 29997825 PMCID: PMC6006495 DOI: 10.1039/c6sc00106h] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/03/2016] [Indexed: 12/27/2022] Open
Abstract
Peptide stapling emerged as a versatile strategy to recapitulate the bioactive helical conformation of unstructured short peptides in water to improve their therapeutic properties in targeting intracellular "undruggable" targets. Here, we describe the development of photo-induced intramolecular thiol-yne macrocyclization for rapid access to short stapled peptides with enhanced biophysical properties. This new peptide stapling technique provides rapid access to conformationally constrained helices with satisfying functional group tolerance. Notably, the vinyl sulfide linkage shows distinct lipophilicity with reduced membrane toxicity compared to the corresponding all-hydrocarbon analogue. As a proof of principle, we constructed stabilized helices modulating intracellular estrogen receptor (ER)-coactivator interactions with a nanomolar binding affinity, enhanced serum stability, a diffuse cellular distribution and selective cytotoxicity towards ER-positive MCF-7 cells.
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Affiliation(s)
- Yuan Tian
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
| | - Jingxu Li
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
| | - Hui Zhao
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
| | - Xiangze Zeng
- Department of Chemistry , Center of Systems Biology and Human Health , School of Science and Institute for Advance Study , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon , Hong Kong , China
| | - Dongyuan Wang
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
| | - Qisong Liu
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering , Beijing Nuclear Magnetic Resonance Center , Peking University , Beijing , 100871 , China
| | - Xuhui Huang
- Department of Chemistry , Center of Systems Biology and Human Health , School of Science and Institute for Advance Study , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon , Hong Kong , China
| | - Naihan Xu
- Key Lab in Healthy Science and Technology , Division of Life Science , Shenzhen Graduate School of Tsinghua University , Shenzhen , 518055 , China .
| | - Zigang Li
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
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36
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Gunnoo SB, Madder A. Bioconjugation – using selective chemistry to enhance the properties of proteins and peptides as therapeutics and carriers. Org Biomol Chem 2016; 14:8002-13. [DOI: 10.1039/c6ob00808a] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Both peptide and protein therapeutics are becoming increasingly important for treating a wide range of diseases. Functionalisation of theseviasite-selective chemical modification leads to enhancement of their therapeutic properties.
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Affiliation(s)
- Smita B. Gunnoo
- Organic and Biomimetic Chemistry Research Group
- Department of Organic and Macromolecular Chemistry
- Ghent University
- Ghent
- Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group
- Department of Organic and Macromolecular Chemistry
- Ghent University
- Ghent
- Belgium
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37
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Wang ZA, Ding XZ, Tian CL, Zheng JS. Protein/peptide secondary structural mimics: design, characterization, and modulation of protein–protein interactions. RSC Adv 2016. [DOI: 10.1039/c6ra13976k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This review discusses general aspects of novel artificial peptide secondary structure mimics for modulation of PPIs, their therapeutic applications and future prospects.
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Affiliation(s)
- Zhipeng A. Wang
- School of Life Sciences
- University of Science and Technology of China
- Hefei 230026
- China
- Department of Chemistry
| | - Xiaozhe Z. Ding
- School of Life Sciences
- Tsinghua University
- Beijing 100084
- China
- Department of Bioengineering
| | - Chang-Lin Tian
- School of Life Sciences
- University of Science and Technology of China
- Hefei 230026
- China
| | - Ji-Shen Zheng
- School of Life Sciences
- University of Science and Technology of China
- Hefei 230026
- China
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38
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Liao GP, Abdelraheem EMM, Neochoritis CG, Kurpiewska K, Kalinowska-Tłuścik J, McGowan DC, Dömling A. Versatile Multicomponent Reaction Macrocycle Synthesis Using α-Isocyano-ω-carboxylic Acids. Org Lett 2015; 17:4980-3. [PMID: 26439710 DOI: 10.1021/acs.orglett.5b02419] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The direct macrocycle synthesis of α-isocyano-ω-carboxylic acids via an Ugi multicomponent reaction is introduced. This multicomponent reaction (MCR) protocol differs by being especially short, convergent, and versatile, giving access to 12-22 membered rings.
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Affiliation(s)
- George P Liao
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Eman M M Abdelraheem
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Chemistry Department, Faculty of Science, Sohag University , Sohag 82524, Egypt
| | - Constantinos G Neochoritis
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University , 3 Ingardena Street, 30-060 Kraków, Poland
| | | | - David C McGowan
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Alexander Dömling
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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39
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Tan YS, Spring DR, Abell C, Verma CS. The Application of Ligand-Mapping Molecular Dynamics Simulations to the Rational Design of Peptidic Modulators of Protein-Protein Interactions. J Chem Theory Comput 2015; 11:3199-210. [PMID: 26575757 DOI: 10.1021/ct5010577] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A computational ligand-mapping approach to detect protein surface pockets that interact with hydrophobic moieties is presented. In this method, we incorporated benzene molecules into explicit solvent molecular dynamics simulations of various protein targets. The benzene molecules successfully identified the binding locations of hydrophobic hot-spot residues and all-hydrocarbon cross-links from known peptidic ligands. They also unveiled cryptic binding sites that are occluded by side chains and the protein backbone. Our results demonstrate that ligand-mapping molecular dynamics simulations hold immense promise to guide the rational design of peptidic modulators of protein-protein interactions, including that of stapled peptides, which show promise as an exciting new class of cell-penetrating therapeutic molecules.
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Affiliation(s)
- Yaw Sing Tan
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom.,Bioinformatics Institute (A*STAR) , 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - David R Spring
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Chandra S Verma
- Bioinformatics Institute (A*STAR) , 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,Department of Biological Sciences, National University of Singapore , 14 Science Drive 4, Singapore 117543.,School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551
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40
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Cromm PM, Spiegel J, Grossmann TN. Hydrocarbon stapled peptides as modulators of biological function. ACS Chem Biol 2015; 10:1362-75. [PMID: 25798993 DOI: 10.1021/cb501020r] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peptide-based drug discovery has experienced a significant upturn within the past decade since the introduction of chemical modifications and unnatural amino acids has allowed for overcoming some of the drawbacks associated with peptide therapeutics. Strengthened by such features, modified peptides become capable of occupying a niche that emerges between the two major classes of today's therapeutics-small molecules (<500 Da) and biologics (>5000 Da). Stabilized α-helices have proven particularly successful at impairing disease-relevant PPIs previously considered "undruggable." Among those, hydrocarbon stapled α-helical peptides have emerged as a novel class of potential peptide therapeutics. This review provides a comprehensive overview of the development and applications of hydrocarbon stapled peptides discussing the benefits and limitations of this technique.
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Affiliation(s)
- Philipp M. Cromm
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
- Technical University Dortmund, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Jochen Spiegel
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
- Technical University Dortmund, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Tom N. Grossmann
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
- Technical University Dortmund, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
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41
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Flaherty BR, Wang Y, Trope EC, Ho TG, Muralidharan V, Kennedy EJ, Peterson DS. The Stapled AKAP Disruptor Peptide STAD-2 Displays Antimalarial Activity through a PKA-Independent Mechanism. PLoS One 2015; 10:e0129239. [PMID: 26010880 PMCID: PMC4444124 DOI: 10.1371/journal.pone.0129239] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/06/2015] [Indexed: 11/19/2022] Open
Abstract
Drug resistance poses a significant threat to ongoing malaria control efforts. Coupled with lack of a malaria vaccine, there is an urgent need for the development of new antimalarials with novel mechanisms of action and low susceptibility to parasite drug resistance. Protein Kinase A (PKA) has been implicated as a critical regulator of pathogenesis in malaria. Therefore, we sought to investigate the effects of disrupted PKA signaling as a possible strategy for inhibition of parasite replication. Host PKA activity is partly regulated by a class of proteins called A Kinase Anchoring Proteins (AKAPs), and interaction between HsPKA and AKAP can be inhibited by the stapled peptide Stapled AKAP Disruptor 2 (STAD-2). STAD-2 was tested for permeability to and activity against Plasmodium falciparum blood stage parasites in vitro. The compound was selectively permeable only to infected red blood cells (iRBC) and demonstrated rapid antiplasmodial activity, possibly via iRBC lysis (IC50 ≈ 1 μM). STAD-2 localized within the parasite almost immediately post-treatment but showed no evidence of direct association with PKA, indicating that STAD-2 acts via a PKA-independent mechanism. Furosemide-insensitive parasite permeability pathways in the iRBC were largely responsible for uptake of STAD-2. Further, peptide import was highly specific to STAD-2 as evidenced by low permeability of control stapled peptides. Selective uptake and antiplasmodial activity of STAD-2 provides important groundwork for the development of stapled peptides as potential antimalarials. Such peptides may also offer an alternative strategy for studying protein-protein interactions critical to parasite development and pathogenesis.
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Affiliation(s)
- Briana R. Flaherty
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, United States of America
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Yuxiao Wang
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, United States of America
| | - Edward C. Trope
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, United States of America
| | - Tienhuei G. Ho
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, United States of America
| | - Vasant Muralidharan
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Eileen J. Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, United States of America
- * E-mail: (EK); David Peterson: (DP)
| | - David S. Peterson
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, United States of America
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
- * E-mail: (EK); David Peterson: (DP)
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42
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Tsomaia N. Peptide therapeutics: Targeting the undruggable space. Eur J Med Chem 2015; 94:459-70. [DOI: 10.1016/j.ejmech.2015.01.014] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 01/04/2023]
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43
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Brown SP, Smith AB. Peptide/protein stapling and unstapling: introduction of s-tetrazine, photochemical release, and regeneration of the peptide/protein. J Am Chem Soc 2015; 137:4034-7. [PMID: 25793939 PMCID: PMC4394111 DOI: 10.1021/ja512880g] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Protocols have been achieved that
permit facile introduction of s-tetrazine into unprotected
peptides and the protein, thioredoxin,
between two cysteine sulfhydryl groups (i.e., staple), followed
by photochemical release (i.e., unstaple) and regeneration of
the peptide/protein upon removal of the cyano groups from
the derived bisthiocyanate. The S,S-tetrazine
macrocycles in turn provide a convenient handle for probe introduction
by exploiting the inverse electron demand Diels–Alder reactivity
of the tetrazine.
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Affiliation(s)
- Stephen P Brown
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Amos B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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44
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Sim AYL, Verma C. How does a hydrocarbon staple affect peptide hydrophobicity? J Comput Chem 2015; 36:773-84. [DOI: 10.1002/jcc.23859] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/06/2015] [Accepted: 01/19/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Adelene Y. L. Sim
- Bioinformatics Institute (A*STAR); 30 Biopolis Street #07-01 Matrix 138671 Singapore
| | - Chandra Verma
- Bioinformatics Institute (A*STAR); 30 Biopolis Street #07-01 Matrix 138671 Singapore
- School of Biological Sciences, Nanyang Technological University; 60 Nanyang Drive 637551 Singapore
- Department of Biological Sciences; National University of Singapore; 14 Science Drive 4 Singapore 117543
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45
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Insights into the molecular mechanisms of action of bioportides: a strategy to target protein-protein interactions. Expert Rev Mol Med 2015; 17:e1. [DOI: 10.1017/erm.2014.24] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cell-penetrating peptides (CPPs) are reliable vehicles for the target-selective intracellular delivery of therapeutic agents. The identification and application of numerous intrinsically bioactive CPPs, now designated as bioportides, is further endorsement of the tremendous clinical potential of CPP technologies. The refinement of proteomimetic bioportides, particularly sequences that mimic cationic α-helical domains involved in protein-protein interactions (PPIs), provides tremendous opportunities to modulate this emergent drug modality in a clinical setting. Thus, a number of CPP-based constructs are currently undergoing clinical trials as human therapeutics, with a particular focus upon anti-cancer agents. A well-characterised array of synthetic modifications, compatible with modern solid-phase synthesis, can be utilised to improve the biophysical and pharmacological properties of bioportides and so achieve cell-and tissue-selective targeting in vivo. Moreover, considering the recent successful development of stapled α-helical peptides as anti-cancer agents, we hypothesise that similar structural modifications are applicable to the design of bioportides that more effectively modulate the many interactomes known to underlie human diseases. Thus, we propose that stapled-helical bioportides could satisfy all of the clinical requirements for metabolically stable, intrinsically cell-permeable agents capable of regulating discrete PPIs by a dominant negative mode of action with minimal toxicity.
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46
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Ma X, Jia J, Cao R, Wang X, Fei H. Histidine-iridium(III) coordination-based peptide luminogenic cyclization and cyclo-RGD peptides for cancer-cell targeting. J Am Chem Soc 2014; 136:17734-7. [PMID: 25486120 DOI: 10.1021/ja511656q] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In the field of peptide drug discovery, structural constraining and fluorescent labeling are two sought-after techniques important for both basic research and pharmaceutical development. In this work, we describe an easy-to-use approach for simultaneous peptide cyclization and luminescent labeling based on iridium(III)-histidine coordination (Ir-HH cyclization). Using a series of model peptides with histidine flanking each terminus, the binding activity and reaction kinetics of Ir-HH cyclization of different ring sizes were characterized. In the series, Ir-HAnH (n = 2, 3) with moderate ring sizes provides appropriate flexibility and proper distance between histidines for cyclic formation, which leads to the best binding affinity and structural stability in physiological conditions, as compared to other Ir-HH-cyclized peptides with smaller (n = 0, 1) or larger (n = 4, 5) ring sizes. Ir-HRGDH, an Ir-HH-cyclized peptide containing integrin targeting motif Arg-Gly-Asp (RGD), showed better targeting affinity than its linear form and enhanced membrane permeability in comparison with fluorescein-labeled cyclic RGDyK peptide. Cell death inducing peptide KLA-linked Ir-HRGDH (Ir-HRGDH-KLA) showed dramatically enhanced cytotoxicity and high selectivity for cancer cells versus noncancer cells. These data demonstrate that the method conveniently combines structural constraining of peptides with luminescent imaging capabilities, which facilitates functional and intracellular characterization of potential peptide-based drug leads, thus introducing a new tool to meet emerging needs in medicinal research.
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Affiliation(s)
- Xiaochuan Ma
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory for Nanotheranostics, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123, China
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47
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Constraining cyclic peptides to mimic protein structure motifs. Angew Chem Int Ed Engl 2014; 53:13020-41. [PMID: 25287434 DOI: 10.1002/anie.201401058] [Citation(s) in RCA: 306] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/02/2013] [Indexed: 12/18/2022]
Abstract
Many proteins exert their biological activities through small exposed surface regions called epitopes that are folded peptides of well-defined three-dimensional structures. Short synthetic peptide sequences corresponding to these bioactive protein surfaces do not form thermodynamically stable protein-like structures in water. However, short peptides can be induced to fold into protein-like bioactive conformations (strands, helices, turns) by cyclization, in conjunction with the use of other molecular constraints, that helps to fine-tune three-dimensional structure. Such constrained cyclic peptides can have protein-like biological activities and potencies, enabling their uses as biological probes and leads to therapeutics, diagnostics and vaccines. This Review highlights examples of cyclic peptides that mimic three-dimensional structures of strand, turn or helical segments of peptides and proteins, and identifies some additional restraints incorporated into natural product cyclic peptides and synthetic macrocyclic peptidomimetics that refine peptide structure and confer biological properties.
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Affiliation(s)
- Timothy A Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072 (Australia)
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48
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Fixierung cyclischer Peptide: Mimetika von Proteinstrukturmotiven. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401058] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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49
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Sinclair JL, Schepartz A. Influence of macrocyclization on allosteric, juxtamembrane-derived, stapled peptide inhibitors of the epidermal growth factor receptor (EGFR). Org Lett 2014; 16:4916-9. [PMID: 25207804 PMCID: PMC4168776 DOI: 10.1021/ol502426b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Indexed: 01/18/2023]
Abstract
The hydrocarbon-stapled peptide E1(S) allosterically inhibits the kinase activity of the epidermal growth factor receptor (EGFR) by blocking a distant but essential protein-protein interaction: a coiled coil formed from the juxtamembrane segment (JM) of each member of the dimeric partnership.1 Macrocyclization is not required for activity: the analogous unstapled (but alkene-bearing) peptide is equipotent in cell viability, immunoblot, and bipartite display experiments to detect coiled coil formation on the cell surface.
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Affiliation(s)
- Julie
K.-L. Sinclair
- Department of Chemistry and Department of
Molecular, Cellular and Developmental
Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Alanna Schepartz
- Department of Chemistry and Department of
Molecular, Cellular and Developmental
Biology, Yale University, New Haven, Connecticut 06520-8107, United States
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50
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Hilinski GJ, Kim YW, Hong J, Kutchukian PS, Crenshaw CM, Berkovitch SS, Chang A, Ham S, Verdine GL. Stitched α-helical peptides via bis ring-closing metathesis. J Am Chem Soc 2014; 136:12314-22. [PMID: 25105213 DOI: 10.1021/ja505141j] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Conformationally stabilized α-helical peptides are capable of inhibiting disease-relevant intracellular or extracellular protein-protein interactions in vivo. We have previously reported that the employment of ring-closing metathesis to introduce a single all-hydrocarbon staple along one face of an α-helical peptide greatly increases α-helical content, binding affinity to a target protein, cell penetration through active transport, and resistance to proteolytic degradation. In an effort to improve upon this technology for stabilizing a peptide in a bioactive α-helical conformation, we report the discovery of an efficient and selective bis ring-closing metathesis reaction leading to peptides bearing multiple contiguous staples connected by a central spiro ring junction. Circular dichroism spectroscopy, NMR, and computational analyses have been used to investigate the conformation of these "stitched" peptides, which are shown to exhibit remarkable thermal stabilities. Likewise, trypsin proteolysis assays confirm the achievement of a structural rigidity unmatched by peptides bearing a single staple. Furthermore, fluorescence-activated cell sorting (FACS) and confocal microscopy assays demonstrate that stitched peptides display superior cell penetrating ability compared to their stapled counterparts, suggesting that this technology may be useful not only in the context of enhancing the drug-like properties of α-helical peptides but also in producing potent agents for the intracellular delivery of proteins and oligonucleotides.
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Affiliation(s)
- Gerard J Hilinski
- Department of Chemistry and Chemical Biology and Department of Stem Cell and Regenerative Biology, Harvard University , Cambridge, Massachusetts 02138, United States
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