Landscaping Macrocyclic Peptides: Stapling HDM2-binding Peptides for Helicity, Protein Affinity, Proteolytic Stability and Cell Uptake

Overview

Journal RSC Chem Biol

Publisher Royal Society of Chemistry

Specialty Biology

Date 2022 Jul 22

PMID 35866171

Authors

Aline D de Araujo

Junxian Lim

Kai-Chen Wu

Huy N Hoang

Huy T Nguyen

David P Fairlie

Affiliations

Soon will be listed here.

Abstract

Cyclic peptides that modulate protein-protein interactions can be valuable therapeutic candidates if they can be delivered intact to their target proteins in cells. Here we systematically compare the effects of different helix-inducing cyclization constraints on the capacity of a macrocyclic peptide component to confer α-helicity, protein-binding affinity, resistance to degradative proteases and cell uptake to a 12-residue peptide fragment of tumor suppressor protein p53. We varied the helix-inducing constraint (hydrocarbon, lactam, aliphatic or aromatic thioether, ) and the position of the cyclization linker ( to + 4 or to + 7 bridges) in order to sculpt the macrocyclic size, stabilize its structure, and promote cell uptake. We find that rigidifying the macrocycle leads to higher alpha helicity, target affinity and proteolytic stability to different extents, whereas cell uptake of compounds shown here is mostly driven by hydrophobicity and aromaticity of the macrocycle.

Citing Articles

Squaric esters as peptide stapling reagents.

Wayment A, Johnson N, Moreno M, Stewart C, Felix B, Lambert I Tetrahedron Lett. 2024; 140.

PMID: 38736688 PMC: 11087058. DOI: 10.1016/j.tetlet.2024.155010.

Design-rules for stapled peptides with in vivo activity and their application to Mdm2/X antagonists.

Chandramohan A, Josien H, Yuen T, Duggal R, Spiegelberg D, Yan L Nat Commun. 2024; 15(1):489.

PMID: 38216578 PMC: 10786919. DOI: 10.1038/s41467-023-43346-4.

An overview of descriptors to capture protein properties - Tools and perspectives in the context of QSAR modeling.

Emonts J, Buyel J Comput Struct Biotechnol J. 2024; 21:3234-3247.

PMID: 38213891 PMC: 10781719. DOI: 10.1016/j.csbj.2023.05.022.

Comparative Analysis of Cyclization Techniques in Stapled Peptides: Structural Insights into Protein-Protein Interactions in a SARS-CoV-2 Spike RBD/hACE2 Model System.

Ferkova S, Froehlich U, Nepveu-Traversy M, Murza A, Azad T, Grandbois M Int J Mol Sci. 2024; 25(1).

PMID: 38203338 PMC: 10778704. DOI: 10.3390/ijms25010166.

Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR.

Kuschert S, Stroet M, Chin Y, Conibear A, Jia X, Lee T Magn Reson (Gott). 2023; 4(1):57-72.

PMID: 37904802 PMC: 10583272. DOI: 10.5194/mr-4-57-2023.

References

Perell G, Staebell R, Hairani M, Cembran A, Pomerantz W . Tuning Sulfur Oxidation States on Thioether-Bridged Peptide Macrocycles for Modulation of Protein Interactions. Chembiochem. 2017; 18(18):1836-1844. DOI: 10.1002/cbic.201700222. View

Spokoyny A, Zou Y, Ling J, Yu H, Lin Y, Pentelute B . A perfluoroaryl-cysteine S(N)Ar chemistry approach to unprotected peptide stapling. J Am Chem Soc. 2013; 135(16):5946-9. PMC: 3675880. DOI: 10.1021/ja400119t. View

de Araujo A, Lim J, Wu K, Xiang Y, Good A, Skerlj R . Bicyclic Helical Peptides as Dual Inhibitors Selective for Bcl2A1 and Mcl-1 Proteins. J Med Chem. 2018; 61(7):2962-2972. DOI: 10.1021/acs.jmedchem.8b00010. View

Shepherd N, Hoang H, Abbenante G, Fairlie D . Single turn peptide alpha helices with exceptional stability in water. J Am Chem Soc. 2005; 127(9):2974-83. DOI: 10.1021/ja0456003. View

Fadzen C, Wolfe J, Cho C, Chiocca E, Lawler S, Pentelute B . Perfluoroarene-Based Peptide Macrocycles to Enhance Penetration Across the Blood-Brain Barrier. J Am Chem Soc. 2017; 139(44):15628-15631. PMC: 5818988. DOI: 10.1021/jacs.7b09790. View

Lau Y, Wu Y, Rossmann M, Tan B, de Andrade P, Sing Tan Y . Double Strain-Promoted Macrocyclization for the Rapid Selection of Cell-Active Stapled Peptides. Angew Chem Int Ed Engl. 2016; 54(51):15410-3. PMC: 5868729. DOI: 10.1002/anie.201508416. View

Kelso M, Beyer R, Hoang H, Lakdawala A, Snyder J, Oliver W . Alpha-turn mimetics: short peptide alpha-helices composed of cyclic metallopentapeptide modules. J Am Chem Soc. 2004; 126(15):4828-42. DOI: 10.1021/ja037980i. View

Bird G, Mazzola E, Opoku-Nsiah K, Lammert M, Godes M, Neuberg D . Biophysical determinants for cellular uptake of hydrocarbon-stapled peptide helices. Nat Chem Biol. 2016; 12(10):845-52. PMC: 5055751. DOI: 10.1038/nchembio.2153. View

Pelay-Gimeno M, Glas A, Koch O, Grossmann T . Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. Angew Chem Int Ed Engl. 2015; 54(31):8896-927. PMC: 4557054. DOI: 10.1002/anie.201412070. View

10.

Walensky L, Bird G . Hydrocarbon-stapled peptides: principles, practice, and progress. J Med Chem. 2014; 57(15):6275-88. PMC: 4136684. DOI: 10.1021/jm4011675. View

11.

Philippe G, Huang Y, Cheneval O, Lawrence N, Zhang Z, Fairlie D . Development of cell-penetrating peptide-based drug leads to inhibit MDMX:p53 and MDM2:p53 interactions. Biopolymers. 2016; 106(6):853-863. DOI: 10.1002/bip.22893. View

12.

Yoo D, Barros S, Brown G, Rabot C, Bar-Sagi D, Arora P . Macropinocytosis as a Key Determinant of Peptidomimetic Uptake in Cancer Cells. J Am Chem Soc. 2020; 142(34):14461-14471. PMC: 7755425. DOI: 10.1021/jacs.0c02109. View

13.

Chang Y, Graves B, Guerlavais V, Tovar C, Packman K, To K . Stapled α-helical peptide drug development: a potent dual inhibitor of MDM2 and MDMX for p53-dependent cancer therapy. Proc Natl Acad Sci U S A. 2013; 110(36):E3445-54. PMC: 3767549. DOI: 10.1073/pnas.1303002110. View

14.

Fairlie D, Tyndall J, Reid R, Wong A, Abbenante G, Scanlon M . Conformational selection of inhibitors and substrates by proteolytic enzymes: implications for drug design and polypeptide processing. J Med Chem. 2001; 43(7):1271-81. DOI: 10.1021/jm990315t. View

15.

Tyndall J, Fairlie D . Conformational homogeneity in molecular recognition by proteolytic enzymes. J Mol Recognit. 1999; 12(6):363-70. DOI: 10.1002/(SICI)1099-1352(199911/12)12:6<363::AID-JMR478>3.0.CO;2-M. View

16.

Lu H, Zhou Q, He J, Jiang Z, Peng C, Tong R . Recent advances in the development of protein-protein interactions modulators: mechanisms and clinical trials. Signal Transduct Target Ther. 2020; 5(1):213. PMC: 7511340. DOI: 10.1038/s41392-020-00315-3. View

17.

Bernal F, Tyler A, Korsmeyer S, Walensky L, Verdine G . Reactivation of the p53 tumor suppressor pathway by a stapled p53 peptide. J Am Chem Soc. 2007; 129(9):2456-7. PMC: 6333086. DOI: 10.1021/ja0693587. View

18.

Philippe G, Mittermeier A, Lawrence N, Huang Y, Condon N, Loewer A . Angler Peptides: Macrocyclic Conjugates Inhibit p53:MDM2/X Interactions and Activate Apoptosis in Cancer Cells. ACS Chem Biol. 2021; 16(2):414-428. DOI: 10.1021/acschembio.0c00988. View

19.

Saleh M, Patel M, Bauer T, Goel S, Falchook G, Shapiro G . Phase 1 Trial of ALRN-6924, a Dual Inhibitor of MDMX and MDM2, in Patients with Solid Tumors and Lymphomas Bearing Wild-type TP53. Clin Cancer Res. 2021; 27(19):5236-5247. PMC: 9401461. DOI: 10.1158/1078-0432.CCR-21-0715. View

20.

Zhang G, Barragan F, Wilson K, Levy N, Herskovits A, Sapozhnikov M . A Solid-Phase Approach to Accessing Bisthioether-Stapled Peptides Resulting in a Potent Inhibitor of PRC2 Catalytic Activity. Angew Chem Int Ed Engl. 2018; 57(52):17073-17078. DOI: 10.1002/anie.201810007. View