1
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DiGiorno MC, Vithanage N, Victorio CG, Kreitler DF, Outlaw VK, Sawyer N. Structural Characterization of Disulfide-Linked p53-Derived Peptide Dimers. RESEARCH SQUARE 2024:rs.3.rs-4644285. [PMID: 39070635 PMCID: PMC11275974 DOI: 10.21203/rs.3.rs-4644285/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Disulfide bonds provide a convenient method for chemoselective alteration of peptide and protein structure and function. We previously reported that mild oxidation of a p53-derived bisthiol peptide (CTFANLWRLLAQNC) under dilute non-denaturing conditions led to unexpected disulfide-linked dimers as the exclusive product. The dimers were antiparallel, significantly α-helical, resistant to protease degradation, and easily reduced back to the original bisthiol peptide. Here we examine the intrinsic factors influencing peptide dimerization using a combination of amino acid substitution, circular dichroism (CD) spectroscopy, and X-ray crystallography. CD analysis of peptide variants suggests critical roles for Leu6 and Leu10 in the formation of stable disulfide-linked dimers. The 1.0 Å resolution crystal structure of the peptide dimer supports these data, revealing a leucine-rich LxxLL dimer interface with canonical knobs-into-holes packing. Two levels of higher-order oligomerization are also observed in the crystal: an antiparallel "dimer of dimers" mediated by Phe3 and Trp7 residues in the asymmetric unit and a tetramer of dimers mediated by Trp7 and Leu10. In CD spectra of Trp-containing peptide variants, minima at 227 nm provide evidence for the dimer of dimers in dilute aqueous solution. Importantly, and in contrast to the original dimer model, the canonical leucine-rich core and robust dimerization of most peptide variants suggests a tunable molecular architecture to target various proteins and evaluate how folding and oligomerization impact various properties, such as cell permeability.
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2
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Mukherjee S, Saha G, Roy NS, Naiya G, Ghosh MK, Roy S. A small HDM2 antagonist peptide and a USP7 inhibitor synergistically inhibit the p53-HDM2-USP7 circuit. Chem Biol Drug Des 2023; 102:126-136. [PMID: 37105726 DOI: 10.1111/cbdd.14255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 02/28/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023]
Abstract
HDM2, an E3 ubiquitin ligase, is a crucial regulator of many proliferation-related pathways. It is also one of the primary regulators of p53. USP7, a deubiquitinase, also plays a key role in the regulation of both p53 and HDM2, thus forming a small regulatory network with them. This network has emerged as an important drug target. Development of a synergistic combination targeting both proteins is desirable and important for regulating this module. We have developed a small helically constrained peptide that potently inhibited p53-HDM2 interaction and exerted anti-proliferative effects on p53+/+ cells. A combination of this peptide-when attached to cell entry and nuclear localization tags-and a USP7 inhibitor showed synergistic anti-proliferative effects against cells harboring wild-type alleles of p53. Synergistic inhibition of two important drug targets may lead to novel therapeutic strategies.
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Affiliation(s)
| | - Gouranga Saha
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India
| | | | - Gitashri Naiya
- Department of Biophysics, Bose Institute, Kolkata, India
| | - Mrinal K Ghosh
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India
| | - Siddhartha Roy
- Department of Biophysics, Bose Institute, Kolkata, India
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3
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Pal S. Impact of Hydrogen‐Bond Surrogate Model on Helix Stabilization and Development of Protein‐Protein Interaction Inhibitors. ChemistrySelect 2023. [DOI: 10.1002/slct.202204207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Affiliation(s)
- Sunit Pal
- Chemical Genomics Centre of the Max Planck Society Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund Germany
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4
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Gupta S, Azadvari N, Hosseinzadeh P. Design of Protein Segments and Peptides for Binding to Protein Targets. BIODESIGN RESEARCH 2022; 2022:9783197. [PMID: 37850124 PMCID: PMC10521657 DOI: 10.34133/2022/9783197] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/16/2022] [Indexed: 10/19/2023] Open
Abstract
Recent years have witnessed a rise in methods for accurate prediction of structure and design of novel functional proteins. Design of functional protein fragments and peptides occupy a small, albeit unique, space within the general field of protein design. While the smaller size of these peptides allows for more exhaustive computational methods, flexibility in their structure and sparsity of data compared to proteins, as well as presence of noncanonical building blocks, add additional challenges to their design. This review summarizes the current advances in the design of protein fragments and peptides for binding to targets and discusses the challenges in the field, with an eye toward future directions.
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Affiliation(s)
- Suchetana Gupta
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Noora Azadvari
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Parisa Hosseinzadeh
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
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5
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Therapeutic peptides: current applications and future directions. Signal Transduct Target Ther 2022; 7:48. [PMID: 35165272 PMCID: PMC8844085 DOI: 10.1038/s41392-022-00904-4] [Citation(s) in RCA: 462] [Impact Index Per Article: 231.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/08/2023] Open
Abstract
Peptide drug development has made great progress in the last decade thanks to new production, modification, and analytic technologies. Peptides have been produced and modified using both chemical and biological methods, together with novel design and delivery strategies, which have helped to overcome the inherent drawbacks of peptides and have allowed the continued advancement of this field. A wide variety of natural and modified peptides have been obtained and studied, covering multiple therapeutic areas. This review summarizes the efforts and achievements in peptide drug discovery, production, and modification, and their current applications. We also discuss the value and challenges associated with future developments in therapeutic peptides.
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6
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Modell AE, Marrone F, Panigrahi NR, Zhang Y, Arora PS. Peptide Tethering: Pocket-Directed Fragment Screening for Peptidomimetic Inhibitor Discovery. J Am Chem Soc 2022; 144:1198-1204. [PMID: 35029987 PMCID: PMC8959088 DOI: 10.1021/jacs.1c09666] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Constrained peptides have proven to be a rich source of ligands for protein surfaces, but are often limited in their binding potency. Deployment of nonnatural side chains that access unoccupied crevices on the receptor surface offers a potential avenue to enhance binding affinity. We recently described a computational approach to create topographic maps of protein surfaces to guide the design of nonnatural side chains [J. Am. Chem. Soc. 2017, 139, 15560]. The computational method, AlphaSpace, was used to predict peptide ligands for the KIX domain of the p300/CBP coactivator. KIX has been the subject of numerous ligand discovery strategies, but potent inhibitors of its interaction with transcription factors remain difficult to access. Although the computational approach provided a significant enhancement in the binding affinity of the peptide, fine-tuning of nonnatural side chains required an experimental screening method. Here we implement a peptide-tethering strategy to screen fragments as nonnatural side chains on conformationally defined peptides. The combined computational-experimental approach offers a general framework for optimizing peptidomimetics as inhibitors of protein-protein interactions.
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Affiliation(s)
- Ashley E Modell
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Frank Marrone
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Nihar R Panigrahi
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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7
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Adpressa DA, Reibarkh M, Jiang Y, Saurí J, Makarov AA. Interrogation of solution conformation of complex macrocyclic peptides utilizing a combined SEC-HDX-MS, circular dichroism, and NMR workflow. Analyst 2021; 147:325-332. [PMID: 34927633 DOI: 10.1039/d1an01619a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Recent technological and synthetic advances have led to a resurgence in the exploration of peptides as potential therapeutics. Understanding peptide conformation in both free and protein-bound states remains one of the most critical areas for successful development of peptide drugs. In this study it was demonstrated that the combination of Size-Exclusion Chromatography with Hydrogen-Deuterium Exchange Mass Spectrometry (SEC-HDX-MS) and Circular Dichroism Spectroscopy (CD) can be used to guide the selection of peptides for further NMR analysis. Moreover, the insights from this workflow guide the choice of the best biologically relevant conditions for NMR conformational studies of peptide ligands in a free state in solution. Combined information about solution conformation character and stability across temperatures and co-solvent compositions greatly expedites selection of optimal conditions for NMR analysis. In total, the combination of SEC-HDX-MS, CD, and NMR into a single complementary workflow greatly accelerates conformational analysis of peptides in the drug discovery lead optimization process.
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Affiliation(s)
- Donovon A Adpressa
- Analytical Research & Development, Merck & Co. Inc., Boston, Massachusetts 02115, USA.
| | - Mikhail Reibarkh
- Analytical Research & Development, Merck & Co. Inc., Rahway, New Jersey 07065, USA.
| | - Yuan Jiang
- Analytical Research & Development, Merck & Co. Inc., Boston, Massachusetts 02115, USA.
| | - Josep Saurí
- Analytical Research & Development, Merck & Co. Inc., Boston, Massachusetts 02115, USA.
| | - Alexey A Makarov
- Analytical Research & Development, Merck & Co. Inc., Boston, Massachusetts 02115, USA.
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8
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Torner JM, Yang Y, Rooklin D, Zhang Y, Arora PS. Identification of Secondary Binding Sites on Protein Surfaces for Rational Elaboration of Synthetic Protein Mimics. ACS Chem Biol 2021; 16:1179-1183. [PMID: 34228913 DOI: 10.1021/acschembio.1c00418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Minimal mimics of protein conformations provide rationally designed ligands to modulate protein function. The advantage of minimal mimics is that they can be chemically synthesized and coaxed to be proteolytically resistant; a key disadvantage is that minimization of the protein binding epitope may be associated with loss of affinity and specificity. Several approaches to overcome this challenge may be envisioned, including deployment of covalent warheads and use of nonnatural residues to improve contacts with the binding surface. Herein, we describe our computational and experimental efforts to enhance the minimal protein mimics with fragments that can contact undiscovered binding pockets on Mdm2 and MdmX-two well-studied protein partners of p53.
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Affiliation(s)
- Justin M. Torner
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Yuwei Yang
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - David Rooklin
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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9
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Jedhe GS, Arora PS. Hydrogen bond surrogate helices as minimal mimics of protein α-helices. Methods Enzymol 2021; 656:1-25. [PMID: 34325784 DOI: 10.1016/bs.mie.2021.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Examination of complexes of proteins with biomolecular ligands reveals that proteins tend to interact with partners via folded sub-domains, in which the backbone possesses secondary structure. α-Helices comprising the largest class of protein secondary structures, play fundamental roles in a multitude of highly specific protein-protein and protein-nucleic acid interactions. We have demonstrated a unique strategy for stabilization of the α-helical conformation that involves replacement of one of the main chain i and i+4 hydrogen bonds in the target α-helix with a covalent bond. We termed this synthetic strategy a hydrogen bond surrogate (HBS) approach. Two salient features of this approach are: (1) the internal placement of the crosslink allows development of helices such that none of the solvent-exposed surfaces are blocked by the constraining element, i.e., all side chains of the constrained helices remain available for molecular recognition. (2) This approach can be deployed to constrain very short peptides (<10 amino acid residues) into highly stable α-helices. This chapter presents the biophysical basis for the development of the hydrogen bond surrogate approach, as well as methods for the synthesis and conformational analysis of the artificial helices.
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Affiliation(s)
- Ganesh S Jedhe
- Department of Chemistry, New York University, New York, NY, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY, United States.
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10
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Wang X, Ni D, Liu Y, Lu S. Rational Design of Peptide-Based Inhibitors Disrupting Protein-Protein Interactions. Front Chem 2021; 9:682675. [PMID: 34017824 PMCID: PMC8128998 DOI: 10.3389/fchem.2021.682675] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/09/2021] [Indexed: 12/12/2022] Open
Abstract
Protein-protein interactions (PPIs) are well-established as a class of promising drug targets for their implications in a wide range of biological processes. However, drug development toward PPIs is inevitably hampered by their flat and wide interfaces, which generally lack suitable pockets for ligand binding, rendering most PPI systems "undruggable." Here, we summarized drug design strategies for developing peptide-based PPI inhibitors. Importantly, several quintessential examples toward well-established PPI targets such as Bcl-2 family members, p53-MDM2, as well as APC-Asef are presented to illustrate the detailed schemes for peptide-based PPI inhibitor development and optimizations. This review supplies a comprehensive overview of recent progresses in drug discovery targeting PPIs through peptides or peptidomimetics, and will shed light on future therapeutic agent development toward the historically "intractable" PPI systems.
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Affiliation(s)
- Xuefei Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Duan Ni
- The Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Yaqin Liu
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Shaoyong Lu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
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11
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Liu Y, Hu K, Yin F, Li Z. Facile Chemoselective Modification of Thioethers Generates Chiral Center-Induced Helical Peptides. Methods Mol Biol 2021; 2355:301-322. [PMID: 34386967 DOI: 10.1007/978-1-0716-1617-8_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The modulation of protein-protein interactions (PPIs) is a promising way for interrogating disease. Stapled peptides that stabilize peptides into a fixed α-helical conformation via chemical means are important representative compounds for regulating PPIs. The effect of the secondary conformation of peptides on the biophysical properties has not been explicitly elucidated due to the difficulty of obtaining peptide epimers with the same chemical composition but different conformations. Herein, we systematically designed and demonstrated the concept of "Chiral Center-Induced Helicity" (CIH) to stabilize the secondary structure of peptides. By introducing a precise R-configuration chiral center on the side-ring of a peptide, researchers can decisively regulate the secondary structure of peptides. Through the study of CIH peptides, we found that increasing the helicity can significantly enhance the stability of peptides and improve the cell membrane penetrating capability of the peptides. Moreover, the substitution group in the chiral center could contribute to additional interactions with the binding groove, which shows great significance for fragment-based drug design. This chapter will focus on the method involved in this research, including specific protocols of the synthesis and basic characterization of CIH peptides in Subheading 3.1. In addition, we have also extended the concept of CIH to dual-chiral center systems, including sulfoxide-based and sulfonium-based in-tether chiral center peptides, which we will introduce in Subheadings 3.2 and 3.3.
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Affiliation(s)
- Yinghuan Liu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Kuan Hu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Feng Yin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, China.
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12
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Yoo DY, Barros SA, Brown GC, Rabot C, Bar-Sagi D, Arora PS. Macropinocytosis as a Key Determinant of Peptidomimetic Uptake in Cancer Cells. J Am Chem Soc 2020; 142:14461-14471. [PMID: 32786217 DOI: 10.1021/jacs.0c02109] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peptides and peptidomimetics represent the middle space between small molecules and large proteins-they retain the relatively small size and synthetic accessibility of small molecules while providing high binding specificity for biomolecular partners typically observed with proteins. During the course of our efforts to target intracellular protein-protein interactions in cancer, we observed that the cellular uptake of peptides is critically determined by the cell line-specifically, we noted that peptides show better uptake in cancer cells with enhanced macropinocytic indices. Here, we describe the results of our analysis of cellular penetration by different classes of conformationally stabilized peptides. We tested the uptake of linear peptides, peptide macrocycles, stabilized helices, β-hairpin peptides, and cross-linked helix dimers in 11 different cell lines. Efficient uptake of these conformationally defined constructs directly correlated with the macropinocytic activity of each cell line: high uptake of compounds was observed in cells with mutations in certain signaling pathways. Significantly, the study shows that constrained peptides follow the same uptake mechanism as proteins in macropinocytic cells, but unlike proteins, peptide mimics can be readily designed to resist denaturation and proteolytic degradation. Our findings expand the current understanding of cellular uptake in cancer cells by designed peptidomimetics and suggest that cancer cells with certain mutations are suitable mediums for the study of biological pathways with peptide leads.
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Affiliation(s)
- Daniel Y Yoo
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Stephanie A Barros
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Gordon C Brown
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Christian Rabot
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Dafna Bar-Sagi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, New York 10003, United States
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13
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Kannan S, Aronica PGA, Ng S, Gek Lian DT, Frosi Y, Chee S, Shimin J, Yuen TY, Sadruddin A, Kaan HYK, Chandramohan A, Wong JH, Tan YS, Chang ZW, Ferrer-Gago FJ, Arumugam P, Han Y, Chen S, Rénia L, Brown CJ, Johannes CW, Henry B, Lane DP, Sawyer TK, Verma CS, Partridge AW. Macrocyclization of an all-d linear α-helical peptide imparts cellular permeability. Chem Sci 2020; 11:5577-5591. [PMID: 32874502 PMCID: PMC7441689 DOI: 10.1039/c9sc06383h] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/08/2020] [Indexed: 12/13/2022] Open
Abstract
Peptide-based molecules hold great potential as targeted inhibitors of intracellular protein-protein interactions (PPIs). Indeed, the vast diversity of chemical space conferred through their primary, secondary and tertiary structures allows these molecules to be applied to targets that are typically deemed intractable via small molecules. However, the development of peptide therapeutics has been hindered by their limited conformational stability, proteolytic sensitivity and cell permeability. Several contemporary peptide design strategies are aimed at addressing these issues. Strategic macrocyclization through optimally placed chemical braces such as olefinic hydrocarbon crosslinks, commonly referred to as staples, may improve peptide properties by (i) restricting conformational freedom to improve target affinities, (ii) improving proteolytic resistance, and (iii) enhancing cell permeability. As a second strategy, molecules constructed entirely from d-amino acids are hyper-resistant to proteolytic cleavage, but generally lack conformational stability and membrane permeability. Since neither approach is a complete solution, we have combined these strategies to identify the first examples of all-d α-helical stapled and stitched peptides. As a template, we used a recently reported all d-linear peptide that is a potent inhibitor of the p53-Mdm2 interaction, but is devoid of cellular activity. To design both stapled and stitched all-d-peptide analogues, we used computational modelling to predict optimal staple placement. The resultant novel macrocyclic all d-peptide was determined to exhibit increased α-helicity, improved target binding, complete proteolytic stability and, most notably, cellular activity.
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Affiliation(s)
- Srinivasaraghavan Kannan
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore . ; ; ; Tel: +65 6478 8353 ; Tel: +65 6478 8273
| | - Pietro G A Aronica
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore . ; ; ; Tel: +65 6478 8353 ; Tel: +65 6478 8273
| | - Simon Ng
- p53 Laboratory , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648
| | - Dawn Thean Gek Lian
- p53 Laboratory , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648
| | - Yuri Frosi
- p53 Laboratory , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648
| | - Sharon Chee
- p53 Laboratory , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648
| | - Jiang Shimin
- p53 Laboratory , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648
| | - Tsz Ying Yuen
- Institute of Chemical & Engineering Science , Agency for Science, Technology and Research (ASTAR) , 8 Biomedical Grove, #07, Neuros Building , Singapore 138665
| | - Ahmad Sadruddin
- MSD International , Translation Medicine Research Centre , 8 Biomedical Grove, #04-01/05 Neuros Building , Singapore , 138665 , Singapore .
| | - Hung Yi Kristal Kaan
- MSD International , Translation Medicine Research Centre , 8 Biomedical Grove, #04-01/05 Neuros Building , Singapore , 138665 , Singapore .
| | - Arun Chandramohan
- MSD International , Translation Medicine Research Centre , 8 Biomedical Grove, #04-01/05 Neuros Building , Singapore , 138665 , Singapore .
| | - Jin Huei Wong
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore . ; ; ; Tel: +65 6478 8353 ; Tel: +65 6478 8273
| | - Yaw Sing Tan
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore . ; ; ; Tel: +65 6478 8353 ; Tel: +65 6478 8273
| | - Zi Wei Chang
- Singapore Immunology Network (SIgN) , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #03-06, Immunos , Singapore 138648
| | - Fernando J Ferrer-Gago
- p53 Laboratory , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648
| | - Prakash Arumugam
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore . ; ; ; Tel: +65 6478 8353 ; Tel: +65 6478 8273
| | - Yi Han
- Merck & Co., Inc. , Kenilworth , New Jersey , USA
| | - Shiying Chen
- Merck & Co., Inc. , Kenilworth , New Jersey , USA
| | - Laurent Rénia
- Singapore Immunology Network (SIgN) , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #03-06, Immunos , Singapore 138648
| | - Christopher J Brown
- p53 Laboratory , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648
| | - Charles W Johannes
- Institute of Chemical & Engineering Science , Agency for Science, Technology and Research (ASTAR) , 8 Biomedical Grove, #07, Neuros Building , Singapore 138665
| | - Brian Henry
- MSD International , Translation Medicine Research Centre , 8 Biomedical Grove, #04-01/05 Neuros Building , Singapore , 138665 , Singapore .
| | - David P Lane
- p53 Laboratory , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648
| | | | - Chandra S Verma
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore . ; ; ; Tel: +65 6478 8353 ; Tel: +65 6478 8273
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
- Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543
| | - Anthony W Partridge
- MSD International , Translation Medicine Research Centre , 8 Biomedical Grove, #04-01/05 Neuros Building , Singapore , 138665 , Singapore .
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14
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Sang P, Shi Y, Lu J, Chen L, Yang L, Borcherds W, Abdulkadir S, Li Q, Daughdrill G, Chen J, Cai J. α-Helix-Mimicking Sulfono-γ-AApeptide Inhibitors for p53-MDM2/MDMX Protein-Protein Interactions. J Med Chem 2020; 63:975-986. [PMID: 31971801 PMCID: PMC7025332 DOI: 10.1021/acs.jmedchem.9b00993] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The use of peptidomimetic scaffolds is a promising strategy for the inhibition of protein-protein interactions (PPIs). Herein, we demonstrate that sulfono-γ-AApeptides can be rationally designed to mimic the p53 α-helix and inhibit p53-MDM2 PPIs. The best inhibitor, with Kd and IC50 values of 26 nM and 0.891 μM toward MDM2, respectively, is among the most potent unnatural peptidomimetic inhibitors disrupting the p53-MDM2/MDMX interaction. Using fluorescence polarization assays, circular dichroism, nuclear magnetic resonance spectroscopy, and computational simulations, we demonstrate that sulfono-γ-AApeptides adopt helical structures resembling p53 and competitively inhibit the p53-MDM2 interaction by binding to the hydrophobic cleft of MDM2. Intriguingly, the stapled sulfono-γ-AApeptides showed promising cellular activity by enhancing p53 transcriptional activity and inducing expression of MDM2 and p21. Moreover, sulfono-γ-AApeptides exhibited remarkable resistance to proteolysis, augmenting their biological potential. Our results suggest that sulfono-γ-AApeptides are a new class of unnatural helical foldamers that disrupt PPIs.
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Affiliation(s)
- Peng Sang
- Department of Chemistry , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Yan Shi
- Department of Chemistry , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Junhao Lu
- Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612 , United States
| | - Lihong Chen
- Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612 , United States
| | - Leixiang Yang
- Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612 , United States
| | - Wade Borcherds
- Department of Cell Biology, Microbiology and Molecular Biology , University of South Florida , Tampa , Florida 33620 , United States
| | - Sami Abdulkadir
- Department of Chemistry , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Qi Li
- Department of Medical Oncology , Shuguang Hospital, Shanghai University of Traditional Chinese Medicine , Shanghai 201203 , China
| | - Gary Daughdrill
- Department of Cell Biology, Microbiology and Molecular Biology , University of South Florida , Tampa , Florida 33620 , United States
| | - Jiandong Chen
- Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612 , United States
| | - Jianfeng Cai
- Department of Chemistry , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
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15
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Merritt HI, Sawyer N, Arora PS. Bent Into Shape: Folded Peptides to Mimic Protein Structure and Modulate Protein Function. Pept Sci (Hoboken) 2020; 112:e24145. [PMID: 33575525 PMCID: PMC7875438 DOI: 10.1002/pep2.24145] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 12/11/2019] [Indexed: 12/16/2022]
Abstract
Protein secondary and tertiary structure mimics have served as model systems to probe biophysical parameters that guide protein folding and as attractive reagents to modulate protein interactions. Here we review contemporary methods to reproduce loop, helix, sheet and coiled-coil conformations in short peptides.
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Affiliation(s)
| | | | - Paramjit S. Arora
- Department of Chemistry New York University, New York, New York 10003, United States
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16
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Design and Synthetic Strategies for Helical Peptides. Methods Mol Biol 2019; 2001:107-131. [PMID: 31134570 DOI: 10.1007/978-1-4939-9504-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Abnormal protein-protein interactions (PPIs) are the basis of multiple diseases, and the large and shallow PPI interfaces make the target "undruggable" for traditional small molecules. Peptides, emerging as a new therapeutic modality, can efficiently mimic PPIs with their large scaffolds. Natural peptides are flexible and usually have poor serum stability and cell permeability, features that limit their further biological applications. To satisfy the clinical application of peptide inhibitors, many strategies have been developed to constrain peptides in their bioactive conformation. In this report, we describe several classic methods used to constrain peptides into a fixed secondary structure which could significantly improve their biophysical properties.
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17
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Guarracino DA, Riordan JA, Barreto GM, Oldfield AL, Kouba CM, Agrinsoni D. Macrocyclic Control in Helix Mimetics. Chem Rev 2019; 119:9915-9949. [DOI: 10.1021/acs.chemrev.8b00623] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Danielle A. Guarracino
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Jacob A. Riordan
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Gianna M. Barreto
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Alexis L. Oldfield
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Christopher M. Kouba
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Desiree Agrinsoni
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
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18
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Yu Z, Liu Y, Zhu J, Han J, Tian X, Han W, Zhao L. Insights from molecular dynamics simulations and steered molecular dynamics simulations to exploit new trends of the interaction between HIF-1α and p300. J Biomol Struct Dyn 2019; 38:1-12. [DOI: 10.1080/07391102.2019.1580616] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Zhengfei Yu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Ye Liu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Jingxuan Zhu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Jiarui Han
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Xiaopian Tian
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Li Zhao
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
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19
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Peptidomimetics: A Synthetic Tool for Inhibiting Protein–Protein Interactions in Cancer. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09831-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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20
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Arachchige D, Holub JM. Synthesis and Biological Activity of Scyllatoxin-Based BH3 Domain Mimetics Containing Two Disulfide Linkages. Protein J 2018; 37:428-443. [PMID: 30128635 DOI: 10.1007/s10930-018-9791-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The B cell lymphoma 2 (BCL2) proteins are a family of evolutionarily related proteins that act as positive or negative regulators of the intrinsic apoptosis pathway. Overexpression of anti-apoptotic BCL2 proteins in cells is associated with apoptotic resistance, which can result in cancerous phenotypes and pathogenic cell survival. Consequently, anti-apoptotic BCL2 proteins have attracted considerable interest as therapeutic targets. We recently reported the development of a novel class of synthetic protein based on scyllatoxin (ScTx) designed to mimic the helical BH3 interaction domain of the pro-apoptotic BCL2 protein Bax. These studies showed that the number and position of native disulfide linkages contained within the ScTx-Bax structure significantly influences the ability for these constructs to target anti-apoptotic BCL2 proteins in vitro. The goal of the present study is to investigate the contribution of two disulfide linkages in the folding and biological activity of ScTx-Bax proteins. Here, we report the full chemical synthesis of three ScTx-Bax sequence variants, each presenting two native disulfide linkages at different positions within the folded structure. It was observed that two disulfide linkages were sufficient to fold ScTx-Bax proteins into native-like architectures reminiscent of wild-type ScTx. Furthermore, we show that select (bis)disulfide ScTx-Bax variants can target Bcl-2 (proper) in vitro and that the position of the disulfide bonds significantly influences binding affinity. Despite exhibiting only modest binding to Bcl-2, the successful synthesis of ScTx-Bax proteins containing two disulfide linkages represents a viable route to ScTx-based BH3 domain mimetics that preserve native-like conformations. Finally, structural models of ScTx-Bax proteins in complex with Bcl-2 indicate that these helical mimetics bind in similar configurations as wild-type Bax BH3 domains. Taken together, these results suggest that ScTx-Bax proteins may serve as potent lead compounds that expand the repertoire of "druggable" protein-protein interactions.
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Affiliation(s)
- Danushka Arachchige
- Department of Chemistry and Biochemistry, Ohio University, Biochemistry Research Facility 108, 350 W. State St., Athens, OH, 45701, USA
| | - Justin M Holub
- Department of Chemistry and Biochemistry, Ohio University, Biochemistry Research Facility 108, 350 W. State St., Athens, OH, 45701, USA.
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA.
- Edison Biotechnology Institute, Ohio University, Athens, OH, 45701, USA.
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21
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Abstract
Peptide secondary and tertiary structure motifs frequently serve as inspiration for the development of protein-protein interaction (PPI) inhibitors. While a wide variety of strategies have been used to stabilize or imitate α-helices, similar strategies for β-sheet stabilization are more limited. Synthetic scaffolds that stabilize reverse turns and cross-strand interactions have provided important insights into β-sheet stability and folding. However, these templates occupy regions of the β-sheet that might impact the β-sheet's ability to bind at a PPI interface. Here, we present the hydrogen bond surrogate (HBS) approach for stabilization of β-hairpin peptides. The HBS linkage replaces a cross-strand hydrogen bond with a covalent linkage, conferring significant conformational and proteolytic resistance. Importantly, this approach introduces the stabilizing linkage in the buried β-sheet interior, retains all side chains for further functionalization, and allows efficient solid-phase macrocyclization. We anticipate that HBS stabilization of PPI β-sheets will enhance the development of β-sheet PPI inhibitors and expand the repertoire of druggable PPIs.
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Affiliation(s)
- Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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22
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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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23
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Klein M. Stabilized helical peptides: overview of the technologies and its impact on drug discovery. Expert Opin Drug Discov 2017; 12:1117-1125. [PMID: 28889766 DOI: 10.1080/17460441.2017.1372745] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Protein-protein interactions are predominant in the workings of all cells. Until now, there have been a few successes in targeting protein-protein interactions with small molecules. Peptides may overcome some of the challenges of small molecules in disrupting protein-protein interactions. However, peptides present a new set of challenges in drug discovery. Thus, the study of the stabilization of helical peptides has been extensive. Areas covered: Several technological approaches to helical peptide stabilization have been studied. In this review, stapled peptides, foldamers, and hydrogen bond surrogates are discussed. Issues regarding design principles are also discussed. Furthermore, this review introduces select computational techniques used to aid peptide design and discusses clinical trials of peptides in a more advanced stage of development. Expert opinion: Stabilized helical peptides hold great promise in a wide array of diseases. However, the field is still relatively new and new design principles are emerging. The possibilities of peptide modification are quite extensive and expanding, so the design of stabilized peptides requires great attention to detail in order to avoid a large number of failed lead peptides. The start of clinical trials with stapled peptides is a promising sign for the future.
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Affiliation(s)
- Mark Klein
- a Division of Hematology, Oncology, and Transplantation , University of Minnesota , Minneapolis , MN , USA.,b Hematology/Oncology Section , Minneapolis VA Healthcare System , Minneapolis , MN , USA
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24
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Marshall GR, Ballante F. Limiting Assumptions in the Design of Peptidomimetics. Drug Dev Res 2017; 78:245-267. [DOI: 10.1002/ddr.21406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
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25
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Ibrahim MIA, Zhou Z, Deng C, Didierjean C, Vanderesse R, Bodiguel J, Averlant-Petit MC, Jamart-Grégoire B. Impact of Cα
-Chirality on Supramolecular Self-Assembly in Cyclo-2:1-[α/aza]-Hexamers (d
/l
-Phe-azaPhe-Ala)2. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700555] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mohamed Ibrahim Abdelmoneim Ibrahim
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM); UMR 7375; CNRS; Université de Lorraine; 1 rue Grandville, BP 20451 54001 Nancy France
- Marine Chemistry Department; National Institute of Oceanography and Fisheries (NIOF); Qayet-Bey, El-Anfoushy 21557 Alexandria Egypt
| | - Zhou Zhou
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM); UMR 7375; CNRS; Université de Lorraine; 1 rue Grandville, BP 20451 54001 Nancy France
| | - Cheng Deng
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM); UMR 7375; CNRS; Université de Lorraine; 1 rue Grandville, BP 20451 54001 Nancy France
| | - Claude Didierjean
- Laboratoire de Cristallographie; Résonance Magnétique et Modélisation (CRM2); UMR 7036; CNRS; Université de Lorraine; Boulevard des Aiguillettes 56506 Vandoeuvre-lès-Nancy France
| | - Régis Vanderesse
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM); UMR 7375; CNRS; Université de Lorraine; 1 rue Grandville, BP 20451 54001 Nancy France
| | - Jacques Bodiguel
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM); UMR 7375; CNRS; Université de Lorraine; 1 rue Grandville, BP 20451 54001 Nancy France
| | - Marie-Christine Averlant-Petit
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM); UMR 7375; CNRS; Université de Lorraine; 1 rue Grandville, BP 20451 54001 Nancy France
| | - Brigitte Jamart-Grégoire
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM); UMR 7375; CNRS; Université de Lorraine; 1 rue Grandville, BP 20451 54001 Nancy France
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26
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Sawyer N, Watkins AM, Arora PS. Protein Domain Mimics as Modulators of Protein-Protein Interactions. Acc Chem Res 2017; 50:1313-1322. [PMID: 28561588 DOI: 10.1021/acs.accounts.7b00130] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein-protein interactions (PPIs) are ubiquitous in biological systems and often misregulated in disease. As such, specific PPI modulators are desirable to unravel complex PPI pathways and expand the number of druggable targets available for therapeutic intervention. However, the large size and relative flatness of PPI interfaces make them challenging molecular targets. This Account describes our systematic approach using secondary and tertiary protein domain mimics (PDMs) to specifically modulate PPIs. Our strategy focuses on mimicry of regular secondary and tertiary structure elements from one of the PPI partners to inspire rational PDM design. We have compiled three databases (HIPPDB, SIPPDB, and DIPPDB) of secondary and tertiary structures at PPI interfaces to guide our designs and better understand the energetics of PPI secondary and tertiary structures. Our efforts have focused on three of the most common secondary and tertiary structures: α-helices, β-strands, and helix dimers (e.g., coiled coils). To mimic α-helices, we designed the hydrogen bond surrogate (HBS) as an isosteric PDM and the oligooxopiperazine helix mimetic (OHM) as a topographical PDM. The nucleus of the HBS approach is a peptide macrocycle in which the N-terminal i, i + 4 main-chain hydrogen bond is replaced with a covalent carbon-carbon bond. In mimicking a main-chain hydrogen bond, the HBS approach stabilizes the α-helical conformation while leaving all helical faces available for functionalization to tune binding affinity and specificity. The OHM approach, in contrast, envisions a tetrapeptide to mimic one face of a two-turn helix. We anticipated that placement of ethylene bridges between adjacent amides constrains the tetrapeptide backbone to mimic the i, i + 4, and i + 7 side chains on one face of an α-helix. For β-strands, we developed triazolamers, a topographical PDM where the peptide bonds are replaced by triazoles. The triazoles simultaneously stabilize the extended, zigzag conformation of β-strands and transform an otherwise ideal protease substrate into a stable molecule by replacement of the peptide bonds. We turned to a salt bridge surrogate (SBS) approach as a means for stabilizing very short helix dimers. As with the HBS approach, the SBS strategy replaces a noncovalent interaction with a covalent bond. Specifically, we used a bis-triazole linkage that mimics a salt bridge interaction to drive helix association and folding. Using this approach, we were able to stabilize helix dimers that are less than half of the length required to form a coiled coil from two independent strands. In addition to demonstrating the stabilization of desired structures, we have also shown that our designed PDMs specifically modulate target PPIs in vitro and in vivo. Examples of PPIs successfully targeted include HIF1α/p300, p53/MDM2, Bcl-xL/Bak, Ras/Sos, and HIV gp41. The PPI databases and designed PDMs created in these studies will aid development of a versatile set of molecules to probe complex PPI functions and, potentially, PPI-based therapeutics.
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Affiliation(s)
- Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Andrew M. Watkins
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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27
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28
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Abstract
Bio-inspired synthetic backbones leading to foldamers can provide effective biopolymer mimics with new and improved properties in a physiological environment, and in turn could serve as useful tools to study biology and lead to practical applications in the areas of diagnostics or therapeutics. Remarkable progress has been accomplished over the past 20 years with the discovery of many potent bioactive foldamers originating from diverse backbones and targeting a whole spectrum of bio(macro)molecules such as membranes, protein surfaces, and nucleic acids. These current achievements, future opportunities, and key challenges that remain are discussed in this article.
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29
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Watkins AM, Bonneau R, Arora PS. Modeling and Design of Peptidomimetics to Modulate Protein-Protein Interactions. Methods Mol Biol 2017; 1561:291-307. [PMID: 28236245 DOI: 10.1007/978-1-4939-6798-8_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We describe a modular approach to identify and inhibit protein-protein interactions (PPIs) that are mediated by protein secondary and tertiary structures with rationally designed peptidomimetics. Our analysis begins with entries of high-resolution complexes in the Protein Data Bank and utilizes conformational sampling, scoring, and design capabilities of advanced biomolecular modeling software to develop peptidomimetics.
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Affiliation(s)
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, 29 Washington Place, Brown Bldg., Room 360, New York, NY, USA.
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30
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Abstract
Substitution of a main chain i → i + 4 hydrogen bond with a covalent bond can nucleate and stabilize the α-helical conformation in peptides. Herein we describe the potential of different alkene isosteres to mimic intramolecular hydrogen bonds and stabilize α-helices in diverse peptide sequences.
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Affiliation(s)
- Stephen T Joy
- Department of Chemistry, New York University, New York, NY 10003, USA.
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA.
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31
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Fouché M, Schäfer M, Berghausen J, Desrayaud S, Blatter M, Piéchon P, Dix I, Martin Garcia A, Roth HJ. Design and Development of a Cyclic Decapeptide Scaffold with Suitable Properties for Bioavailability and Oral Exposure. ChemMedChem 2016; 11:1048-59. [DOI: 10.1002/cmdc.201600082] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 03/09/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Marianne Fouché
- Global Discovery Chemistry/Macrocycles; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Michael Schäfer
- Global Discovery Chemistry/CADD; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Jörg Berghausen
- Metabolism and Pharmacokinetics; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Sandrine Desrayaud
- Metabolism and Pharmacokinetics; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Markus Blatter
- Global Discovery Chemistry/Analytics (NMR); Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Philippe Piéchon
- Global Discovery Chemistry/Analytics (Crystallography); Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Ina Dix
- Global Discovery Chemistry/Analytics (Crystallography); Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Aimar Martin Garcia
- The University of the Basque Country-Euskal Herriko Unibertsitatea; Campus de Leioa 48949 Leioa Spain
| | - Hans-Jörg Roth
- Global Discovery Chemistry/Macrocycles; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
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32
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Nguyen LT, Luong HX, Kim YW. Helix Nucleation via Hydrocarbon Cross-link MimickingN-capping Box. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.10727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Huy Xuan Luong
- College of Pharmacy; Dongguk University; Seoul 04620 Korea
| | - Young-Woo Kim
- College of Pharmacy; Dongguk University; Seoul 04620 Korea
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33
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Tian Y, Wang D, Li J, Shi C, Zhao H, Niu X, Li Z. A proline-derived transannular N-cap for nucleation of short α-helical peptides. Chem Commun (Camb) 2016; 52:9275-8. [DOI: 10.1039/c6cc04672j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report herein a simple and practical proline-derived transannular N-cap as a helix nucleating template in diverse bio-related peptide sequences via macrolactamization on resin.
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Affiliation(s)
- Yuan Tian
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Dongyuan Wang
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Jingxu Li
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Chuan Shi
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Hui Zhao
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering
- Beijing Nuclear Magnetic Resonance Center
- Peking University
- Beijing
- China
| | - Zigang Li
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
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34
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Lanning ME, Fletcher S. Multi-Facial, Non-Peptidic α-Helix Mimetics. BIOLOGY 2015; 4:540-55. [PMID: 26404384 PMCID: PMC4588149 DOI: 10.3390/biology4030540] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/11/2015] [Accepted: 08/14/2015] [Indexed: 01/13/2023]
Abstract
α-Helices often recognize their target proteins at protein–protein interfaces through more than one recognition face. This review describes the state-of-the-art in the design of non-peptidic α-helix mimetics that reproduce functionality from multiple faces of an α-helix.
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Affiliation(s)
- Maryanna E Lanning
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA.
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA.
- University of Maryland Greenebaum Cancer Center, 22 S. Greene St., Baltimore, MD 21201, USA.
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Frost JR, Jacob NT, Papa LJ, Owens AE, Fasan R. Ribosomal Synthesis of Macrocyclic Peptides in Vitro and in Vivo Mediated by Genetically Encoded Aminothiol Unnatural Amino Acids. ACS Chem Biol 2015; 10:1805-16. [PMID: 25933125 DOI: 10.1021/acschembio.5b00119] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A versatile method for orchestrating the formation of side chain-to-tail cyclic peptides from ribosomally derived polypeptide precursors is reported. Upon ribosomal incorporation into intein-containing precursor proteins, designer unnatural amino acids bearing side chain 1,3- or 1,2-aminothiol functionalities are able to promote the cyclization of a downstream target peptide sequence via a C-terminal ligation/ring contraction mechanism. Using this approach, peptide macrocycles of variable size and composition could be generated in a pH-triggered manner in vitro or directly in living bacterial cells. This methodology furnishes a new platform for the creation and screening of genetically encoded libraries of conformationally constrained peptides. This strategy was applied to identify and isolate a low-micromolar streptavidin binder (KD = 1.1 μM) from a library of cyclic peptides produced in Escherichia coli, thereby illustrating its potential toward aiding the discovery of functional peptide macrocycles.
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Affiliation(s)
- John R. Frost
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Nicholas T. Jacob
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Louis J. Papa
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Andrew E. Owens
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
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36
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. Angew Chem Int Ed Engl 2015; 54:8896-927. [PMID: 26119925 PMCID: PMC4557054 DOI: 10.1002/anie.201412070] [Citation(s) in RCA: 496] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A-D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices.
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Affiliation(s)
- Marta Pelay-Gimeno
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Adrian Glas
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Oliver Koch
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
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Fahs S, Patil-Sen Y, Snape TJ. Foldamers as Anticancer Therapeutics: Targeting Protein-Protein Interactions and the Cell Membrane. Chembiochem 2015; 16:1840-1853. [DOI: 10.1002/cbic.201500188] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Indexed: 01/10/2023]
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38
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Strukturbasierte Entwicklung von Protein-Protein-Interaktionsinhibitoren: Stabilisierung und Nachahmung von Peptidliganden. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412070] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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39
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Rohrbacher F, Deniau G, Luther A, Bode JW. Spontaneous head-to-tail cyclization of unprotected linear peptides with the KAHA ligation. Chem Sci 2015; 6:4889-4896. [PMID: 29142720 PMCID: PMC5664356 DOI: 10.1039/c5sc01774b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/05/2015] [Indexed: 12/03/2022] Open
Abstract
The α-ketoacid–hydroxylamine (KAHA) ligation enables the direct cyclization of unprotected peptides upon cleavage, without coupling reagents or purification of precursors. We report the synthesis of a library of 24 cyclic peptides and a detailed mechanistic study.
The α-ketoacid–hydroxylamine (KAHA) ligation with 5-oxaproline enables the direct cyclization of peptides upon cleavage from a solid support, without coupling reagents, protecting groups, or purification of the linear precursors. This Fmoc SPPS-based method was applied to the synthesis of a library of 24 homoserine-containing cyclic peptides and was compared side-by-side with the synthesis of the same products using a standard method for cyclizing side-chain protected substrates. A detailed mechanistic study including 2H and 18O labeling experiments and the characterization of reaction intermediates by NMR and mass spectrometry is reported.
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Affiliation(s)
- Florian Rohrbacher
- Laboratorium für Organische Chemie , Department of Chemistry and Applied Biosciences , ETH Zürich , 8093 Zürich , Switzerland . ; http://www.bode.ethz.ch
| | - Gildas Deniau
- Polyphor Ltd. , Hegenheimermattweg 125 , 4123 Allschwil , Switzerland . http://www.polyphor.com
| | - Anatol Luther
- Polyphor Ltd. , Hegenheimermattweg 125 , 4123 Allschwil , Switzerland . http://www.polyphor.com
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie , Department of Chemistry and Applied Biosciences , ETH Zürich , 8093 Zürich , Switzerland . ; http://www.bode.ethz.ch.,Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan . http://www.itbm.nagoya-u.ac.jp
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40
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Campbell ST, Carlson KJ, Buchholz CJ, Helmers MR, Ghosh I. Mapping the BH3 Binding Interface of Bcl-xL, Bcl-2, and Mcl-1 Using Split-Luciferase Reassembly. Biochemistry 2015; 54:2632-43. [PMID: 25844633 DOI: 10.1021/bi501505y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The recognition of helical BH3 domains by Bcl-2 homology (BH) receptors plays a central role in apoptosis. The residues that determine specificity or promiscuity in this interactome are difficult to predict from structural and computational data. Using a cell free split-luciferase system, we have generated a 276 pairwise interaction map for 12 alanine mutations at the binding interface for three receptors, Bcl-xL, Bcl-2, and Mcl-1, and interrogated them against BH3 helices derived from Bad, Bak, Bid, Bik, Bim, Bmf, Hrk, and Puma. This panel, in conjunction with previous structural and functional studies, starts to provide a more comprehensive portrait of this interactome, explains promiscuity, and uncovers surprising details; for example, the Bcl-xL R139A mutation disrupts binding to all helices but the Bad-BH3 peptide, and Mcl-1 binding is particularly perturbed by only four mutations of the 12 tested (V220A, N260A, R263A, and F319A), while Bcl-xL and Bcl-2 have a more diverse set of important residues depending on the bound helix.
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Affiliation(s)
- Sean T Campbell
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Kevin J Carlson
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Carl J Buchholz
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Mark R Helmers
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Indraneel Ghosh
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
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Zhao DS, Chen YX, Li YM. Rational design of an orthosteric regulator of hIAPP aggregation. Chem Commun (Camb) 2015; 51:2095-8. [DOI: 10.1039/c4cc06739h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Compounds that can block hIAPP toxic oligomer but not fibril formation have been rationally designed based on the helix aggregation mechanism.
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Affiliation(s)
- De-Sheng Zhao
- Department of Chemistry
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)
- Tsinghua University
- Beijing 10084
- P. R. China
| | - Yong-Xiang Chen
- Department of Chemistry
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)
- Tsinghua University
- Beijing 10084
- P. R. China
| | - Yan-Mei Li
- Department of Chemistry
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)
- Tsinghua University
- Beijing 10084
- P. R. China
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42
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Tumminakatti S, Reddy DN, Prabhakaran EN. Exploring the consequences of a representative "disallowed" conformation of Aib on a 3₁₀-helical fold. Biopolymers 2014; 104:21-36. [PMID: 25488434 DOI: 10.1002/bip.22599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 11/28/2014] [Accepted: 12/01/2014] [Indexed: 01/24/2023]
Abstract
The structural effects of a representative "disallowed" conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D ((1)H, (13)C) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)-helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib*-Oxa) of 2, in a conformation (ϕ, ψ = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)-helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations.
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Affiliation(s)
- Shama Tumminakatti
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
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43
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Sawyer TK, Guerlavais V, Darlak K, Feyfant E. Macrocyclic α-Helical Peptide Drug Discovery. MACROCYCLES IN DRUG DISCOVERY 2014. [DOI: 10.1039/9781782623113-00339] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Macrocyclic α-helical peptides have emerged as a promising new drug class and within the scope of hydrocarbon-stapled peptides such molecules have advanced into the clinic. The overarching concept of designing proteomimetics of an α-helical ‘ligand’ which binds its cognate ‘target’ relative to α-helical interfacing protein-protein interactions has been well-validated and expanded through numerous investigations for a plethora of therapeutic targets oftentimes referred to as “undruggable” with respect to other modalities (e.g., small-molecule or proteins). This chapter highlights the evolution of macrocyclic α-helical peptides in terms of target space, biophysical and computational chemistry, structural diversity and synthesis, drug design and chemical biology. It is noteworthy that hydrocarbon-stapled peptides have successfully risen to the summit of such drug discovery campaigns.
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Smith JM, Hill NC, Krasniak PJ, Fasan R. Synthesis of bicyclic organo-peptide hybrids via oxime/intein-mediated macrocyclization followed by disulfide bond formation. Org Biomol Chem 2014; 12:1135-42. [PMID: 24395107 DOI: 10.1039/c3ob42222d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A new strategy is described to generate bicyclic peptides that incorporate non-peptidic backbone elements starting from recombinant polypeptide precursors. These compounds are produced via a one-pot, two-step sequence, in which peptide macrocyclization by means of a bifunctional oxyamine/1,3-amino-thiol synthetic precursor is followed by intramolecular disulfide formation between the synthetic precursor-borne thiol and a cysteine embedded in the peptide sequence. This approach was found to be compatible with the cysteine residue occupying different positions within 8mer and 10mer target peptide sequences and across different synthetic precursor scaffolds, thereby enabling the formation of a variety of diverse bicyclic scaffolds.
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Affiliation(s)
- Jessica M Smith
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA.
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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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46
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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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47
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Zhang Q, Shi X, Jiang Y, Li Z. Influence of α-methylation in constructing stapled peptides with olefin metathesis. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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48
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Kumar EA, Chen Q, Kizhake S, Kolar C, Kang M, Chang CEA, Borgstahl GEO, Natarajan A. The paradox of conformational constraint in the design of Cbl(TKB)-binding peptides. Sci Rep 2014; 3:1639. [PMID: 23572190 PMCID: PMC3965358 DOI: 10.1038/srep01639] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 03/22/2013] [Indexed: 02/06/2023] Open
Abstract
Solving the crystal structure of Cbl(TKB) in complex with a pentapeptide, pYTPEP, revealed that the PEP region adopted a poly-L-proline type II (PPII) helix. An unnatural amino acid termed a proline-templated glutamic acid (ptE) that constrained both the backbone and sidechain to the bound conformation was synthesized and incorporated into the pYTPXP peptide. We estimated imposing structural constraints onto the backbone and sidechain of the peptide and preorganize it to the bound conformation in solution will yield nearly an order of magnitude improvement in activity. NMR studies confirmed that the ptE-containing peptide adopts the PPII conformation, however, competitive binding studies showed an order of magnitude loss of activity. Given the emphasis that is placed on imposing structural constraints, we provide an example to support the contrary. These results point to conformational flexibility at the interface, which have implications in the design of potent Cbl(TKB)-binding peptides.
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Affiliation(s)
- Eric A Kumar
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68022, United States
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Miller SE, Thomson PF, Arora PS. Synthesis of hydrogen-bond surrogate α-helices as inhibitors of protein-protein interactions. ACTA ACUST UNITED AC 2014; 6:101-116. [PMID: 24903885 DOI: 10.1002/9780470559277.ch130202] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The α-helix is a prevalent secondary structure in proteins and is critical in mediating protein-protein interactions (PPIs). Peptide mimetics that adopt stable helices have become powerful tools for the modulation of PPIs in vitro and in vivo. Hydrogen-bond surrogate (HBS) α-helices utilize a covalent bond in place of an N-terminal i to i+4 hydrogen bond and have been used to target and disrupt PPIs that become dysregulated in disease states. These compounds have improved conformational stability and cellular uptake as compared to their linear peptide counterparts. The protocol presented here describes current methodology for the synthesis of HBS α-helical mimetics. The solid-phase synthesis of HBS helices involves solid-phase peptide synthesis with three key steps involving incorporation of N-allyl functionality within the backbone of the peptide, coupling of a secondary amine, and a ring-closing metathesis step.
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Affiliation(s)
- Stephen E Miller
- Department of Chemistry, New York University, New York, New York
| | - Paul F Thomson
- Department of Chemistry, New York University, New York, New York
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, New York
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50
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Lao BB, Drew K, Guarracino DA, Brewer TF, Heindel DW, Bonneau R, Arora PS. Rational design of topographical helix mimics as potent inhibitors of protein-protein interactions. J Am Chem Soc 2014; 136:7877-88. [PMID: 24972345 PMCID: PMC4353027 DOI: 10.1021/ja502310r] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
Protein–protein
interactions encompass large surface areas, but
often a handful of key residues dominate the binding energy landscape.
Rationally designed small molecule scaffolds that reproduce the relative
positioning and disposition of important binding residues, termed
“hotspot residues”, have been shown to successfully
inhibit specific protein complexes. Although this strategy has led
to development of novel synthetic inhibitors of protein complexes,
often direct mimicry of natural amino acid residues does not lead
to potent inhibitors. Experimental screening of focused compound libraries
is used to further optimize inhibitors but the number of possible
designs that can be efficiently synthesized and experimentally tested
in academic settings is limited. We have applied the principles of
computational protein design to optimization of nonpeptidic helix
mimics as ligands for protein complexes. We describe the development
of computational tools to design helix mimetics from canonical and
noncanonical residue libraries and their application to two therapeutically
important protein–protein interactions: p53-MDM2 and p300-HIF1α.
The overall study provides a streamlined approach for discovering
potent peptidomimetic inhibitors of protein–protein interactions.
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Affiliation(s)
- Brooke Bullock Lao
- Department of Chemistry and ‡Departments of Biology and Computer Science, New York University , New York, New York 10003, United States
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