1
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Paquette AR, Boddy CN. Double Stranded DNA Binding Stapled Peptides: An Emerging Tool for Transcriptional Regulation. Chembiochem 2023; 24:e202300594. [PMID: 37750576 DOI: 10.1002/cbic.202300594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 09/27/2023]
Abstract
Stapled peptides have rapidly established themselves as a powerful technique to mimic α-helical interactions with a short peptide sequence. There are many examples of stapled peptides that successfully disrupt α-helix-mediated protein-protein interactions, with an example currently in clinical trials. DNA-protein interactions are also often mediated by α-helices and are involved in all transcriptional regulation processes. Unlike DNA-binding small molecules, which typically lack DNA sequence selectivity, DNA-binding proteins bind with high affinity and high selectivity. These are ideal candidates for the design DNA-binding stapled peptides. Despite the parallel to protein-protein interaction disrupting stapled peptides and the need for sequence specific DNA binders, there are very few DNA-binding stapled peptides. In this review we examine all the known DNA-binding stapled peptides. Their design concepts are compared to stapled peptides that disrupt protein-protein interactions and based on the few examples in the literature, DNA-binding stapled peptide trends are discussed.
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Affiliation(s)
- André R Paquette
- Department of Chemistry and Biomolecular Sciences, The University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, The University of Ottawa, Ottawa, ON, K1N 6N5, Canada
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2
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Xiao Q, Jones ZB, Hatfield SC, Ashton DS, Dalley NA, Dyer CD, Evangelista JL, Price JL. Structural guidelines for stabilization of α-helical coiled coils via PEG stapling. RSC Chem Biol 2022; 3:1096-1104. [PMID: 36128502 PMCID: PMC9428657 DOI: 10.1039/d1cb00237f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 07/01/2022] [Indexed: 11/24/2022] Open
Abstract
Macrocyclization or stapling is one of the most well-known and generally applicable strategies for enhancing peptide/protein conformational stability and target binding affinity. However, there are limited structure- or sequence-based guidelines for the incorporation of optimal interhelical staples within coiled coils: the location and length of an interhelical staple is either arbitrarily chosen or requires significant optimization. Here we explore the impact of interhelical PEG stapling on the conformational stability and proteolytic resistance of a model disulfide-bound heterodimeric coiled coil. We demonstrate that (1) interhelical PEG staples are more stabilizing when placed farther from an existing disulfide crosslink; (2) e/g′ staples are more stabilizing than f/b′ or b/c′ staples; (3) PEG staples between different positions have different optimal staple lengths; (4) PEG stapling tolerates variation in the structure of the PEG linker and in the mode of conjugation; and (5) the guidelines developed here enable the rational design of a stabilized PEG-stapled HER-2 affibody with enhanced conformational stability and proteolytic resistance. Here we identify key criteria for designing PEG-stapled coiled coils with increased conformational and proteolytic stability.![]()
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Affiliation(s)
- Qiang Xiao
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Zachary B. Jones
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Samantha C. Hatfield
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Dallin S. Ashton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Nicholas A. Dalley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Cody D. Dyer
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Judah L. Evangelista
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Joshua L. Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
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3
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Bechtler C, Lamers C. Macrocyclization strategies for cyclic peptides and peptidomimetics. RSC Med Chem 2021; 12:1325-1351. [PMID: 34447937 PMCID: PMC8372203 DOI: 10.1039/d1md00083g] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022] Open
Abstract
Peptides are a growing therapeutic class due to their unique spatial characteristics that can target traditionally "undruggable" protein-protein interactions and surfaces. Despite their advantages, peptides must overcome several key shortcomings to be considered as drug leads, including their high conformational flexibility and susceptibility to proteolytic cleavage. As a general approach for overcoming these challenges, macrocyclization of a linear peptide can usually improve these characteristics. Their synthetic accessibility makes peptide macrocycles very attractive, though traditional synthetic methods for macrocyclization can be challenging for peptides, especially for head-to-tail cyclization. This review provides an updated summary of the available macrocyclization chemistries, such as traditional lactam formation, azide-alkyne cycloadditions, ring-closing metathesis as well as unconventional cyclization reactions, and it is structured according to the obtained functional groups. Keeping peptide chemistry and screening in mind, the focus is given to reactions applicable in solution, on solid supports, and compatible with contemporary screening methods.
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Affiliation(s)
- Clément Bechtler
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
| | - Christina Lamers
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
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4
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Ahangarpour M, Kavianinia I, Harris PWR, Brimble MA. Photo-induced radical thiol-ene chemistry: a versatile toolbox for peptide-based drug design. Chem Soc Rev 2021; 50:898-944. [PMID: 33404559 DOI: 10.1039/d0cs00354a] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While the global market for peptide/protein-based therapeutics is witnessing significant growth, the development of peptide drugs remains challenging due to their low oral bioavailability, poor membrane permeability, and reduced metabolic stability. However, a toolbox of chemical approaches has been explored for peptide modification to overcome these obstacles. In recent years, there has been a revival of interest in photoinduced radical thiol-ene chemistry as a powerful tool for the construction of therapeutic peptides.
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Affiliation(s)
- Marzieh Ahangarpour
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand.
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5
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Lindsey‐Crosthwait A, Rodriguez‐Lema D, Walko M, Pask CM, Wilson AJ. Structural optimization of reversible dibromomaleimide peptide stapling. Pept Sci (Hoboken) 2021; 113:e24157. [PMID: 34938942 PMCID: PMC8650577 DOI: 10.1002/pep2.24157] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 01/05/2023]
Abstract
Methods to constrain peptides in a bioactive α-helical conformation for inhibition of protein-protein interactions represent an ongoing area of investigation in chemical biology. Recently, the first example of a reversible "stapling" methodology was described which exploits native cysteine or homocysteine residues spaced at the i and i + 4 positions in a peptide sequence together with the thiol selective reactivity of dibromomaleimides (a previous study). This manuscript reports on the optimization of the maleimide based constraint, focusing on the kinetics of macrocyclization and the extent to which helicity is promoted with different thiol containing amino acids. The study identified an optimal stapling combination of X 1 = L-Cys and X 5 = L-hCys in the context of the model peptide Ac-X1AAAX5-NH2, which should prove useful in implementing the dibromomaleimide stapling strategy in peptidomimetic ligand discovery programmes.
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Affiliation(s)
- Ayanna Lindsey‐Crosthwait
- School of Chemistry, University of LeedsLeedsUK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeedsUK
| | - Diana Rodriguez‐Lema
- School of Chemistry, University of LeedsLeedsUK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeedsUK
| | - Martin Walko
- School of Chemistry, University of LeedsLeedsUK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeedsUK
| | | | - Andrew J. Wilson
- School of Chemistry, University of LeedsLeedsUK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeedsUK
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6
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Bluntzer MTJ, O'Connell J, Baker TS, Michel J, Hulme AN. Designing stapled peptides to inhibit
protein‐protein
interactions: An analysis of successes in a rapidly changing field. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | | | | | - Julien Michel
- EaStChem School of Chemistry The University of Edinburgh Edinburgh UK
| | - Alison N. Hulme
- EaStChem School of Chemistry The University of Edinburgh Edinburgh UK
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7
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Cerulli RA, Shehaj L, Brown H, Pace J, Mei Y, Kritzer JA. Stapled Peptide Inhibitors of Autophagy Adapter LC3B. Chembiochem 2020; 21:2777-2785. [PMID: 32406996 PMCID: PMC7872222 DOI: 10.1002/cbic.202000212] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/09/2020] [Indexed: 12/12/2022]
Abstract
A growing body of evidence suggests that autophagy inhibition enhances the effectiveness of chemotherapy, especially in difficult-to-treat cancers. Existing autophagy inhibitors are primarily lysosomotropic agents. More specific autophagy inhibitors are highly sought-after. The microtubule-associated protein 1A/1B light chain 3B protein, LC3B, is an adapter protein that mediates key protein-protein interactions at several points in autophagy pathways. In this work, we used a known peptide ligand as a starting point to develop improved LC3B inhibitors. We obtained structure-activity relationships that quantify the binding contributions of peptide termini, individual charged residues, and hydrophobic interactions. Based on these data, we used artificial amino acids and diversity-oriented stapling to improve affinity and resistance to biological degradation, while maintaining or improving LC3B affinity and selectivity. These peptides represent the highest-affinity LC3B-selective ligands reported to date, and they will be useful tools for further elucidation of LC3B's role in autophagy and in cancer.
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Affiliation(s)
- Robert A Cerulli
- Cell, Molecular and Developmental Biology Program Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Livia Shehaj
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | - Hawley Brown
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | - Jennifer Pace
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | - Yang Mei
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
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8
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Li X, Chen S, Zhang WD, Hu HG. Stapled Helical Peptides Bearing Different Anchoring Residues. Chem Rev 2020; 120:10079-10144. [DOI: 10.1021/acs.chemrev.0c00532] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiang Li
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Insititute of Translational Medicine, Shanghai University, Shanghai, China
| | - Si Chen
- School of Medicine, Shanghai University, Shanghai, China
| | - Wei-Dong Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hong-Gang Hu
- Insititute of Translational Medicine, Shanghai University, Shanghai, China
- Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
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9
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Xiao Q, Ashton DS, Jones ZB, Thompson KP, Price JL. Long-range PEG Stapling: Macrocyclization for Increased Protein Conformational Stability and Resistance to Proteolysis. RSC Chem Biol 2020; 1:273-280. [PMID: 33796855 PMCID: PMC8009319 DOI: 10.1039/d0cb00075b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We previously showed that long-range stapling of two Asn-linked O-allyl PEG oligomers via olefin metathesis substantially increases the conformational stability of the WW domain through an entropic effect. The impact of stapling was more favorable when the staple connected positions that were far apart in primary sequence but close in the folded tertiary structure. Here we validate these criteria by identifying new stabilizing PEG-stapling sites within the WW domain and the SH3 domain, both β-sheet proteins. We find that stapling via olefin metathesis vs. the copper(i)-catalyzed azide/alkyne cycloaddition (CuAAC) results in similar energetic benefits, suggesting that olefin and triazole staples can be used interchangeably. Proteolysis assays of selected WW variants reveal that the observed staple-based increases in conformational stability lead to enhanced proteolytic resistance. Finally, we find that an intermolecular staple dramatically increases the quaternary structural stability of an α-helical GCN4 coiled-coil heterodimer. Long-range stapling of two Asn-linked PEG oligomers via olefin metathesis substantially increases the conformational stability of the WW and SH3 domain tertiary structures and the GCN4 coiled-coil quaternary structure.![]()
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Affiliation(s)
- Qiang Xiao
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Dallin S Ashton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Zachary B Jones
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Katherine P Thompson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Joshua L Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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10
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Hetherington K, Hegedus Z, Edwards TA, Sessions RB, Nelson A, Wilson AJ. Stapled Peptides as HIF-1α/p300 Inhibitors: Helicity Enhancement in the Bound State Increases Inhibitory Potency. Chemistry 2020; 26:7638-7646. [PMID: 32307728 PMCID: PMC7318359 DOI: 10.1002/chem.202000417] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/13/2020] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions (PPIs) control virtually all cellular processes and have thus emerged as potential targets for development of molecular therapeutics. Peptide-based inhibitors of PPIs are attractive given that they offer recognition potency and selectivity features that are ideal for function, yet, they do not predominantly populate the bioactive conformation, frequently suffer from poor cellular uptake and are easily degraded, for example, by proteases. The constraint of peptides in a bioactive conformation has emerged as a promising strategy to mitigate against these liabilities. In this work, using peptides derived from hypoxia-inducible factor 1 (HIF-1α) together with dibromomaleimide stapling, we identify constrained peptide inhibitors of the HIF-1α/p300 interaction that are more potent than their unconstrained sequences. Contrary to expectation, the increased potency does not correlate with an increased population of an α-helical conformation in the unbound state as demonstrated by experimental circular dichroism analysis. Rather, the ability of the peptide to adopt a bioactive α-helical conformation in the p300 bound state is better supported in the constrained variant as demonstrated by molecular dynamics simulations and circular dichroism difference spectra.
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Affiliation(s)
- Kristina Hetherington
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Zsofia Hegedus
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Thomas A. Edwards
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Richard B. Sessions
- School of BiochemistryUniversity of BristolMedical Sciences Building, University WalkBristolBS8 1TDUK
- BrisSynBioUniversity of Bristol, Life Sciences BuildingTyndall AvenueBristolBS8 1TQUK
| | - Adam Nelson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Andrew J. Wilson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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11
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Brož B, Marek A. Tritiodefluorination of alkyl C-F groups. J Labelled Comp Radiopharm 2019; 62:743-750. [PMID: 31267564 DOI: 10.1002/jlcr.3782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/10/2019] [Accepted: 06/28/2019] [Indexed: 11/09/2022]
Abstract
A straightforward methodology of fluorine substitution by tritium/deuterium is reported. The described method is selective towards the F─C (sp3 ) group and leaves both the aromatic F─C (sp2 ) and F2 ─C (sp3 ) moieties unaffected. Alkylfluorides, readily synthesized from appropriate alcohols by treatment with diethylaminosulfur trifluoride (DAST) reagent in an overall yield up to 76%, undergoes activation with the boron-based Lewis acid B(C6 F5 )3 , and stoichiometric in situ reduction with a tritide/deuteride reagent-the [TMP2(3) H][2(3) HB(C6 F5 )3 ] system of frustrated Lewis pair. This methodology provides an isolated yield of up to 93% of regio-specifically labeled small organic compounds with superior 2 H-enrichment of over 95%. The specific activity of prepared 1-(2-[3 H]-ethyl)naphthalene was determined at 29.0 Ci/mmol. The site selectivity of the Lewis acid/ [TMP2(3) H][2(3) HB(C6 F5 )3 ] approach is orthogonal to currently used methods and allows for isotopic labeling of complementary positions in molecules. Reported labeling methodology proceeds well at ultra-mild reaction conditions (220 mbar of T2 ), allowing very low consumption of the radioactive source (4.2 Ci/156 GBq), and producing limited amount of radioactive waste.
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Affiliation(s)
- Břetislav Brož
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic
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12
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Doubková S, Marek A. Frustrated Lewis pairs: A real alternative to deuteride/tritide reductions. J Labelled Comp Radiopharm 2019; 62:729-742. [PMID: 31170318 DOI: 10.1002/jlcr.3774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 11/11/2022]
Abstract
Deuterium- and tritium-labeled compounds play a principal role in tracing of biologically active molecules in complicated biochemical systems. The state-of-the-art techniques using noble metal catalysts or strong reducing agents often suffers from low functional group tolerances, poor selectivity, tricky or multistep synthesis of reagents, and low specific activity of the labeled product. Herein, we demonstrate a mild and nonmetallic technique of deuteration and tritiation of polarized double bonds, such as carbonyl compounds, yielding labeled alcohols of high specific activities. This one-pot synthesis uses carrier-free hydrogen gas in situ activated by a freshly prepared frustrated Lewis pair, generating reducing reagents. This labeling strategy shows better selectivity and functional group tolerances compared with current reductive methods. Reported is an example of the selective reduction of the aldehyde moiety of 3-acetylbenzaldehyde. What makes this technology groundbreaking is its mildness, selectivity, and generation of limited amount of radioactive waste as almost no byproducts were generated after use of (B(C6 F5 )3 3 H)(3 HTMP) reducing reagent. Radiochemical purity of desired 3 H-labeled product in a crude reaction mixture was determined of over 94%. This work provides, to the community of radiochemists, a practical protocol for frustrated Lewis pairs (FLP)-assisted deuterium/tritium labeling technology.
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Affiliation(s)
- Sabina Doubková
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic
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13
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Iegre J, Brear P, Baker DJ, Tan YS, Atkinson EL, Sore HF, O' Donovan DH, Verma CS, Hyvönen M, Spring DR. Efficient development of stable and highly functionalised peptides targeting the CK2α/CK2β protein-protein interaction. Chem Sci 2019; 10:5056-5063. [PMID: 31183056 PMCID: PMC6530537 DOI: 10.1039/c9sc00798a] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/11/2019] [Indexed: 12/15/2022] Open
Abstract
The discovery of new Protein-Protein Interaction (PPI) modulators is currently limited by the difficulties associated with the design and synthesis of selective small molecule inhibitors. Peptides are a potential solution for disrupting PPIs; however, they typically suffer from poor stability in vivo and limited tissue penetration hampering their wide spread use as new chemical biology tools and potential therapeutics. In this work, a combination of CuAAC chemistry, molecular modelling, X-ray crystallography, and biological validation allowed us to develop highly functionalised peptide PPI inhibitors of the protein CK2. The lead peptide, CAM7117, prevents the formation of the holoenzyme assembly in vitro, slows down proliferation, induces apoptosis in cancer cells and is stable in human serum. CAM7117 could aid the development of novel CK2 inhibitors acting at the interface and help to fully understand the intracellular pathways involving CK2. Importantly, the approach adopted herein could be applied to many PPI targets and has the potential to ease the study of PPIs by efficiently providing access to functionalised peptides.
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Affiliation(s)
- Jessica Iegre
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK .
| | - Paul Brear
- Department of Biochemistry , University of Cambridge , Tennis Court Road , CB2 1GA , Cambridge , UK .
| | - David J Baker
- Discovery Sciences , IMED Biotech Unit , AstraZeneca , Cambridge , UK
| | - Yaw Sing Tan
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671
| | - Eleanor L Atkinson
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK .
| | - Hannah F Sore
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK .
| | | | - Chandra S Verma
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 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
| | - Marko Hyvönen
- Department of Biochemistry , University of Cambridge , Tennis Court Road , CB2 1GA , Cambridge , UK .
| | - David R Spring
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK .
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14
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Xiao Q, Bécar NA, Brown NP, Smith MS, Stern KL, Draper SRE, Thompson KP, Price JL. Stapling of two PEGylated side chains increases the conformational stability of the WW domain via an entropic effect. Org Biomol Chem 2019; 16:8933-8939. [PMID: 30444518 DOI: 10.1039/c8ob02535e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Hydrocarbon stapling and PEGylation are distinct strategies for enhancing the conformational stability and/or pharmacokinetic properties of peptide and protein drugs. Here we combine these approaches by incorporating asparagine-linked O-allyl PEG oligomers at two positions within the β-sheet protein WW, followed by stapling of the PEGs via olefin metathesis. The impact of stapling two sites that are close in primary sequence is small relative to the impact of PEGylation alone and depends strongly on PEG length. In contrast, stapling of two PEGs that are far apart in primary sequence but close in tertiary structure provides substantially more stabilization, derived mostly from an entropic effect. Comparison of PEGylation + stapling vs. alkylation + stapling at the same positions in WW reveals that both approaches provide similar overall levels of conformational stability.
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Affiliation(s)
- Qiang Xiao
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
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15
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Wu Y, Kaur A, Fowler E, Wiedmann MM, Young R, Galloway WRJD, Olsen L, Sore HF, Chattopadhyay A, Kwan TTL, Xu W, Walsh SJ, de Andrade P, Janecek M, Arumugam S, Itzhaki LS, Lau YH, Spring DR. Toolbox of Diverse Linkers for Navigating the Cellular Efficacy Landscape of Stapled Peptides. ACS Chem Biol 2019; 14:526-533. [PMID: 30702850 DOI: 10.1021/acschembio.9b00063] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Stapled peptides have great potential as modulators of protein-protein interactions (PPIs). However, there is a vast landscape of chemical features that can be varied for any given peptide, and identifying a set of features that maximizes cellular uptake and subsequent target engagement remains a key challenge. Herein, we present a systematic analysis of staple functionality on the peptide bioactivity landscape in cellular assays. Through application of a "toolbox" of diversified dialkynyl linkers to the stapling of MDM2-binding peptides via a double-click approach, we conducted a study of cellular uptake and p53 activation as a function of the linker. Minor changes in the linker motif and the specific pairing of linker with peptide sequence can lead to substantial differences in bioactivity, a finding which may have important design implications for peptide-based inhibitors of other PPIs. Given the complexity of the structure-activity relationships involved, the toolbox approach represents a generalizable strategy for optimization when progressing from in vitro binding assays to cellular efficacy studies.
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Affiliation(s)
- Yuteng Wu
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Amandeep Kaur
- European Molecular Biology Laboratory Australia Node for Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences , University of New South Wales , Sydney , NSW 2052 , Australia
| | - Elaine Fowler
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Mareike M Wiedmann
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Reginald Young
- School of Chemistry , The University of Sydney , Eastern Avenue , Sydney , NSW 2006 , Australia
| | - Warren R J D Galloway
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Lasse Olsen
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Hannah F Sore
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Anasuya Chattopadhyay
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , United Kingdom
| | - Terence T-L Kwan
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Wenshu Xu
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , United Kingdom
| | - Stephen J Walsh
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Peterson de Andrade
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Matej Janecek
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Senthil Arumugam
- European Molecular Biology Laboratory Australia Node for Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences , University of New South Wales , Sydney , NSW 2052 , Australia
| | - Laura S Itzhaki
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , United Kingdom
| | - Yu Heng Lau
- School of Chemistry , The University of Sydney , Eastern Avenue , Sydney , NSW 2006 , Australia
| | - David R Spring
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
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16
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Iegre J, Gaynord JS, Robertson NS, Sore HF, Hyvönen M, Spring DR. Two-Component Stapling of Biologically Active and Conformationally Constrained Peptides: Past, Present, and Future. ADVANCED THERAPEUTICS 2018. [DOI: 10.1002/adtp.201800052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jessica Iegre
- Department of Chemistry; University of Cambridge; Cambridge CB2 1EW UK
| | | | | | - Hannah F. Sore
- Department of Chemistry; University of Cambridge; Cambridge CB2 1EW UK
| | - Marko Hyvönen
- Department of Biochemistry; University of Cambridge; Cambridge CB2 1GA UK
| | - David R. Spring
- Department of Chemistry; University of Cambridge; Cambridge CB2 1EW UK
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17
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Robertson NS, Spring DR. Using Peptidomimetics and Constrained Peptides as Valuable Tools for Inhibiting Protein⁻Protein Interactions. Molecules 2018; 23:molecules23040959. [PMID: 29671834 PMCID: PMC6017787 DOI: 10.3390/molecules23040959] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/16/2018] [Accepted: 04/18/2018] [Indexed: 02/07/2023] Open
Abstract
Protein–protein interactions (PPIs) are tremendously important for the function of many biological processes. However, because of the structure of many protein–protein interfaces (flat, featureless and relatively large), they have largely been overlooked as potential drug targets. In this review, we highlight the current tools used to study the molecular recognition of PPIs through the use of different peptidomimetics, from small molecules and scaffolds to peptides. Then, we focus on constrained peptides, and in particular, ways to constrain α-helices through stapling using both one- and two-component techniques.
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Affiliation(s)
- Naomi S Robertson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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18
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Boyhus LE, Danielsen M, Bengtson NS, Ben Achim Kunze M, Kubiak X, Sminia TJ, Løper JH, Tran PT, Lindorff-Larsen K, Rasmussen SGF, Mathiesen JM, Pedersen DS. Gs protein peptidomimetics as allosteric modulators of the β2-adrenergic receptor. RSC Adv 2018; 8:2219-2228. [PMID: 35542596 PMCID: PMC9077236 DOI: 10.1039/c7ra11713b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/04/2017] [Indexed: 11/21/2022] Open
Abstract
A series of Gs protein peptidomimetics were designed and synthesised based on the published X-ray crystal structure of the active state β2-adrenergic receptor (β2AR) in complex with the Gs protein (PDB 3SN6). We hypothesised that such peptidomimetics may function as allosteric modulators that target the intracellular Gs protein binding site of the β2AR. Peptidomimetics were designed to mimic the 15 residue C-terminal α-helix of the Gs protein and were pre-organised in a helical conformation by (i, i + 4)-stapling using copper catalysed azide alkyne cycloaddition. Linear and stapled peptidomimetics were analysed by circular dichroism (CD) and characterised in a membrane-based cAMP accumulation assay and in a bimane fluorescence assay on purified β2AR. Several peptidomimetics inhibited agonist isoproterenol (ISO) induced cAMP formation by lowering the ISO maximal efficacy up to 61%. Moreover, some peptidomimetics were found to significantly decrease the potency of ISO up to 39-fold. In the bimane fluorescence assay none of the tested peptidomimetics could stabilise an active-like conformation of β2AR. Overall, the obtained pharmacological data suggest that some of the peptidomimetics may be able to compete with the native Gs protein for the intracellular binding site to block ISO-induced cAMP formation, but are unable to stabilise an active-like receptor conformation. A series of Gs protein peptidomimetics were designed and synthesised based on the published X-ray crystal structure of the active state β2-adrenergic receptor (β2AR) in complex with the Gs protein (PDB 3SN6).![]()
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Affiliation(s)
- Lotte-Emilie Boyhus
- Department of Drug Design and Pharmacology
- University of Copenhagen
- 2100 Copenhagen
- Denmark
| | - Mia Danielsen
- Department of Drug Design and Pharmacology
- University of Copenhagen
- 2100 Copenhagen
- Denmark
| | - Nina Smidt Bengtson
- Department of Drug Design and Pharmacology
- University of Copenhagen
- 2100 Copenhagen
- Denmark
| | - Micha Ben Achim Kunze
- Structural Biology and NMR Laboratory
- Department of Biology
- University of Copenhagen
- 2200 Copenhagen
- Denmark
| | - Xavier Kubiak
- Department of Neuroscience
- University of Copenhagen
- 2200 Copenhagen
- Denmark
| | - Tjerk J. Sminia
- Department of Drug Design and Pharmacology
- University of Copenhagen
- 2100 Copenhagen
- Denmark
| | - Jacob Hartvig Løper
- Department of Drug Design and Pharmacology
- University of Copenhagen
- 2100 Copenhagen
- Denmark
| | - Phuong Thu Tran
- Department of Drug Design and Pharmacology
- University of Copenhagen
- 2100 Copenhagen
- Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory
- Department of Biology
- University of Copenhagen
- 2200 Copenhagen
- Denmark
| | | | | | - Daniel Sejer Pedersen
- Department of Drug Design and Pharmacology
- University of Copenhagen
- 2100 Copenhagen
- Denmark
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19
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Hu K, Sun C, Li Z. Reversible and Versatile On-Tether Modification of Chiral-Center-Induced Helical Peptides. Bioconjug Chem 2017. [PMID: 28650634 DOI: 10.1021/acs.bioconjchem.7b00321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Modification of the cross-linker of constrained peptides has recently received considerable attention. Here, we present a versatile approach to modifing the cross-linking tether of chiral-center-induced helical (CIH) peptides via the S-alkylation reaction. The alkylation process displayed high conversion efficiency, selectivity, and substrate tolerance. Notably, although on-tether S-alkylation could lead to a pair of peptide epimers, the major alkylated product retained the helical structure of its helical precursor peptide. This S-alkylation was readily reversible under reductive conditions, which provides a simple method for traceless modification. In addition to expanding the chemical space of CIH peptides, this strategy is the first on-tether modification platform with known retention of the peptides' original helicity.
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Affiliation(s)
- Kuan Hu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, Guangdong 518055, China
| | - Chengjie Sun
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, Guangdong 518055, China
| | - Zigang Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, Guangdong 518055, China
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20
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Grison CM, Burslem GM, Miles JA, Pilsl LKA, Yeo DJ, Imani Z, Warriner SL, Webb ME, Wilson AJ. Double quick, double click reversible peptide "stapling". Chem Sci 2017; 8:5166-5171. [PMID: 28970902 PMCID: PMC5618791 DOI: 10.1039/c7sc01342f] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/11/2017] [Indexed: 12/23/2022] Open
Abstract
A versatile, rapid and reversible approach to constrain peptides in a bioactive helical conformation and bearing a functional handle for inhibition of protein–protein interactions is described.
The development of constrained peptides for inhibition of protein–protein interactions is an emerging strategy in chemical biology and drug discovery. This manuscript introduces a versatile, rapid and reversible approach to constrain peptides in a bioactive helical conformation using BID and RNase S peptides as models. Dibromomaleimide is used to constrain BID and RNase S peptide sequence variants bearing cysteine (Cys) or homocysteine (hCys) amino acids spaced at i and i + 4 positions by double substitution. The constraint can be readily removed by displacement of the maleimide using excess thiol. This new constraining methodology results in enhanced α-helical conformation (BID and RNase S peptide) as demonstrated by circular dichroism and molecular dynamics simulations, resistance to proteolysis (BID) as demonstrated by trypsin proteolysis experiments and retained or enhanced potency of inhibition for Bcl-2 family protein–protein interactions (BID), or greater capability to restore the hydrolytic activity of the RNAse S protein (RNase S peptide). Finally, use of a dibromomaleimide functionalized with an alkyne permits further divergent functionalization through alkyne–azide cycloaddition chemistry on the constrained peptide with fluorescein, oligoethylene glycol or biotin groups to facilitate biophysical and cellular analyses. Hence this methodology may extend the scope and accessibility of peptide stapling.
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Affiliation(s)
- Claire M Grison
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - George M Burslem
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Jennifer A Miles
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Ludwig K A Pilsl
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - David J Yeo
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Zeynab Imani
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Stuart L Warriner
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Michael E Webb
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
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