Stapled peptide

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A cartoon depiction of a stapled peptide. The red coloring depicts a helix, and the green coloring denotes the hydrocarbon staple. Rendering based on PDB 4MZK . 4MZK stapled peptide.png
A cartoon depiction of a stapled peptide. The red coloring depicts a helix, and the green coloring denotes the hydrocarbon staple. Rendering based on PDB 4MZK ​.

A stapled peptide is a modified peptide (class A peptidomimetic), typically in an alpha-helical conformation, [2] that is constrained by a synthetic brace ("staple"). [3] The staple is formed by a covalent linkage between two amino acid side-chains, forming a peptide macrocycle. Staples, generally speaking, refer to a covalent linkage of two previously independent entities. Peptides with multiple, tandem staples are sometimes referred to as stitched peptides. [4] [5] Among other applications, peptide stapling is notably used to enhance the pharmacologic performance of peptides. [5]

Contents

Introduction

The two primary classes of therapeutics are small molecules and protein therapeutics. The design of small molecule inhibitors of protein-protein interactions has been impeded by issues such as the general lack of small-molecule starting points for drug design, the typical flatness of the interface, the difficulty of distinguishing real from artifactual binding, and the size and character of typical small-molecule libraries. [6] Meanwhile, the protein therapeutics that lack these issues are bedeviled by another problem, poor cell penetration due to an insufficient ability to diffuse across the cell membrane. Additionally, proteins and peptides are often subject to proteolytic degradation in vivo or if they do enter the cell. Furthermore, small peptides (such as single alpha-helices or α-helices) can lose helicity in solution due to entropic factors, which diminishes binding affinity. [5]

α-Helices are the most common protein secondary structure and play a key role in mediating many protein–protein interactions (PPIs) by serving as recognition motifs. [7] PPIs are frequently misregulated in disease, provides the long-running impetus to create alpha-helical peptides to inhibit disease-state PPIs for clinical applications, as well as for basic science applications. Introducing a synthetic brace (staple) helps to lock a peptide in a specific conformation, reducing conformational entropy. This approach can increase target affinity, increase cell penetration, and protect against proteolytic degradation. [5] [8] Various strategies have been employed for constraining α-helices, including the non-covalent and covalent stabilization techniques; however, the all-hydrocarbon covalent link, termed a peptide staple, has been shown to have improved stability and cell penetrability, making this stabilization strategy particularly relevant for clinical applications. [9]

Invention

Olefin terminated, non-natural amino acids used to as building blocks to form stapled peptides. R isomers shown, but S enantiomers may also be used. Alkene terminated amino acid.svg
Olefin terminated, non-natural amino acids used to as building blocks to form stapled peptides. R isomers shown, but S enantiomers may also be used.

Staples synthesized using ring-closing metathesis (RCM) are common. [8] This variation of olefin metathesis and its application to stapled peptides was developed by Nobel laureate Robert H. Grubbs and Helen Blackwell in the late 1990s, who used the Grubbs catalyst to cross-link O-allylserine residues in a covalent bond. [10] In 2000, Gregory Verdine and colleagues reported the first synthesis of an all-hydrocarbon cross-link for peptide α-helix stabilization, combining the principles of RCM with α,α-disubstitution of the amino acid chiral carbon and on-resin peptide synthesis. [11] [12] In collaboration with Edward Taylor of Princeton University, Loren Walensky, who was then a post-doc in Verdine's lab, subsequently demonstrated that stapling BH3 peptides enabled the synthetic peptides to retain their α-helical conformation, further demonstrating that these peptides were taken up by cancer cells and bound their physiologic BCL-2 family targets, which correlated with the induction of cell death. [13] It was discovered that the peptides side-stepped the membrane diffusion issue by crossing the membrane through active endosomal uptake, which deposited the peptides inside of the cell. [14] Since this first proof of principle, peptide stapling technology has been applied to numerous peptide templates, allowing the study of many other PPIs using stapled peptides including cancer targets such as p53, [15] MCL-1 BH3, [16] [17] PUMA BH3, Notch, [18] and beta-Catenin, [19] [20] as well as other therapeutic targets ranging from infectious diseases to metabolism. [21] [22]

Clinical applications

In 2013, Aileron Therapeutics, which was co-founded by Verdine, Walensky and Taylor, completed the first stapled peptide clinical trial with their growth-hormone-releasing hormone agonist ALRN-5281. [23] As of 2019, Aileron Therapeutics is developing another candidate, sulanemadlin (ALRN-6924), in a Phase 2a trial that assesses the combination of sulanemadlin and Pfizer’s palbociclib for the treatment of patients with MDM2-amplified cancers, and a Phase 1b/2 clinical trial to evaluate sulanemadlin as a myelopreservative agent to protect against chemotherapy-induced toxicities. [24]

See also

Related Research Articles

<span class="mw-page-title-main">Alpha helix</span> Type of secondary structure of proteins

An alpha helix is a sequence of amino acids in a protein that are twisted into a coil.

<span class="mw-page-title-main">Hemoprotein</span> Protein containing a heme prosthetic group

A hemeprotein, or heme protein, is a protein that contains a heme prosthetic group. They are a very large class of metalloproteins. The heme group confers functionality, which can include oxygen carrying, oxygen reduction, electron transfer, and other processes. Heme is bound to the protein either covalently or noncovalently or both.

<span class="mw-page-title-main">Transmembrane protein</span> Protein spanning across a biological membrane

A transmembrane protein is a type of integral membrane protein that spans the entirety of the cell membrane. Many transmembrane proteins function as gateways to permit the transport of specific substances across the membrane. They frequently undergo significant conformational changes to move a substance through the membrane. They are usually highly hydrophobic and aggregate and precipitate in water. They require detergents or nonpolar solvents for extraction, although some of them (beta-barrels) can be also extracted using denaturing agents.

<span class="mw-page-title-main">Receptor (biochemistry)</span> Protein molecule receiving signals for a cell

In biochemistry and pharmacology, receptors are chemical structures, composed of protein, that receive and transduce signals that may be integrated into biological systems. These signals are typically chemical messengers which bind to a receptor and produce physiological responses such as change in the electrical activity of a cell. For example, GABA, an inhibitory neurotransmitter, inhibits electrical activity of neurons by binding to GABAA receptors. There are three main ways the action of the receptor can be classified: relay of signal, amplification, or integration. Relaying sends the signal onward, amplification increases the effect of a single ligand, and integration allows the signal to be incorporated into another biochemical pathway.

A coiled coil is a structural motif in proteins in which 2–7 alpha-helices are coiled together like the strands of a rope. They have been found in roughly 5-10% of proteins and have a variety of functions. They are one of the most widespread motifs found in protein-protein interactions. To aid protein study, several tools have been developed to predict coiled-coils in protein structures. Many coiled coil-type proteins are involved in important biological functions, such as the regulation of gene expression — e.g., transcription factors. Notable examples are the oncoproteins c-Fos and c-Jun, as well as the muscle protein tropomyosin.

Peptoids, or poly-N-substituted glycines, are a class of biochemicals known as biomimetics that replicate the behavior of biological molecules. Peptidomimetics are recognizable by side chains that are appended to the nitrogen atom of the peptide backbone, rather than to the α-carbons.

<span class="mw-page-title-main">Peptidomimetic</span> Class of compounds designed to mimic features of peptides

A peptidomimetic is a small protein-like chain designed to mimic a peptide. They typically arise either from modification of an existing peptide, or by designing similar systems that mimic peptides, such as peptoids and β-peptides. Irrespective of the approach, the altered chemical structure is designed to advantageously adjust the molecular properties such as stability or biological activity. This can have a role in the development of drug-like compounds from existing peptides. Peptidomimetics can be prepared by cyclization of linear peptides or coupling of stable unnatural amino acids. These modifications involve changes to the peptide that will not occur naturally. Unnatural amino acids can be generated from their native analogs via modifications such as amine alkylation, side chain substitution, structural bond extension cyclization, and isosteric replacements within the amino acid backbone. Based on their similarity with the precursor peptide, peptidomimetics can be grouped into four classes where A features the most and D the least similarities. Classes A and B involve peptide-like scaffolds, while classes C and D include small molecules.

<span class="mw-page-title-main">Foldamer</span> Chain molecule which folds in predictable ways while in solution

In chemistry, a foldamer is a discrete chain molecule (oligomer) that folds into a conformationally ordered state in solution. They are artificial molecules that mimic the ability of proteins, nucleic acids, and polysaccharides to fold into well-defined conformations, such as α-helices and β-sheets. The structure of a foldamer is stabilized by noncovalent interactions between nonadjacent monomers. Foldamers are studied with the main goal of designing large molecules with predictable structures. The study of foldamers is related to the themes of molecular self-assembly, molecular recognition, and host–guest chemistry.

<span class="mw-page-title-main">Gp41</span> Subunit of the envelope protein complex of retroviruses

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3<sub>10</sub> helix Type of secondary structure

A 310 helix is a type of secondary structure found in proteins and polypeptides. Of the numerous protein secondary structures present, the 310-helix is the fourth most common type observed; following α-helices, β-sheets and reverse turns. 310-helices constitute nearly 10–15% of all helices in protein secondary structures, and are typically observed as extensions of α-helices found at either their N- or C- termini. Because of the α-helices tendency to consistently fold and unfold, it has been proposed that the 310-helix serves as an intermediary conformation of sorts, and provides insight into the initiation of α-helix folding.

Cell-penetrating peptides (CPPs) are short peptides that facilitate cellular intake and uptake of molecules ranging from nanosize particles to small chemical compounds to large fragments of DNA. The "cargo" is associated with the peptides either through chemical linkage via covalent bonds or through non-covalent interactions.

Affibody molecules are small, robust proteins engineered to bind to a large number of target proteins or peptides with high affinity, imitating monoclonal antibodies, and are therefore a member of the family of antibody mimetics. Affibody molecules are used in biochemical research and are being developed as potential new biopharmaceutical drugs. These molecules can be used for molecular recognition in diagnostic and therapeutic applications.

<span class="mw-page-title-main">Bcl-2 family</span>

The Bcl-2 family consists of a number of evolutionarily-conserved proteins that share Bcl-2 homology (BH) domains. The Bcl-2 family is most notable for their regulation of apoptosis, a form of programmed cell death, at the mitochondrion. The Bcl-2 family proteins consists of members that either promote or inhibit apoptosis, and control apoptosis by governing mitochondrial outer membrane permeabilization (MOMP), which is a key step in the intrinsic pathway of apoptosis. A total of 25 genes in the Bcl-2 family were identified by 2008.

<span class="mw-page-title-main">WALP peptide</span> Class of peptides used for studying lipid membranes

WALP peptides are a class of synthesized, membrane-spanning α-helices composed of tryptophan (W), alanine (A), and leucine (L) amino acids. They are designed to study properties of proteins in lipid membranes such as orientation, extent of insertion, and hydrophobic mismatch.

<span class="mw-page-title-main">Triple helix</span> Set of three congruent geometrical helices with the same axis

In the fields of geometry and biochemistry, a triple helix is a set of three congruent geometrical helices with the same axis, differing by a translation along the axis. This means that each of the helices keeps the same distance from the central axis. As with a single helix, a triple helix may be characterized by its pitch, diameter, and handedness. Examples of triple helices include triplex DNA, triplex RNA, the collagen helix, and collagen-like proteins.

Sortases are membrane anchored enzyme that sort these surface proteins onto the bacterial cell surface and anchor them to the peptidoglycan. There are different types of sortases and each catalyse the anchoring of different proteins to cell walls.

<span class="mw-page-title-main">Photoactivated peptide</span>

Photoactivated peptides are modified natural or synthetic peptides the functions of which can be activated with light. This can be done either irreversibly or in a reversible way. Caged peptides which contain photocleavable protecting groups belong to irreversibly activated peptides. Reversible activation/deactivation of peptide function are achieved by incorporation photo-controllable fragments in the side chains or in the backbone of peptide templates to get the photo-controlled peptides, which can reversibly change their structure upon irradiation with light of different wavelength. As the consequence, the properties, function and biological activity of the modified peptides can be controlled by light. Since light can be directed to specific areas, such peptides can be activated only at targeted sites. Azobenzenes, and diarylethenes can be used as the photoswitches. For therapeutic use, photoswitches with longer wavelengths or the use of two-photon excitation are required, coupled with improved methods for peptide delivery to live cells.

<span class="mw-page-title-main">Alphabody</span>

Alphabodies, also known as Cell-Penetrating Alphabodies or CPAB for short, are small 10 kDa proteins engineered to bind to a variety of antigens. Despite their name, they are not structurally similar to antibodies, which makes them a type of antibody mimetic. Alphabodies are different from many other antibody mimetics in their ability to reach and bind to intracellular protein targets. Their single chain alpha-helical structure is designed by computer modelling, inspired by naturally existing coiled-coil protein structures. Alphabodies are being developed by the Belgian biotechnology company Complix N.V. as potential new pharmaceutical drugs against cancer and autoimmune disease. In 2012, a collaboration agreement was signed with Monsanto to develop the technology for agricultural applications as well.

Coiled-coil drug delivery systems refer to drug delivery systems utilizing coiled-coil motifs capable of delivering disease-treating therapies, imaging agents, and vaccines to patients systemically or specifically. These systems are a form of peptide therapeutics and are capable of being engineered and finely tuned into different types of drug delivery vehicles based on the specific application required. The goal of a coiled-coil drug delivery system is to deliver cargo such as medication, imaging agents, biological molecules, or vaccines efficiently and specifically, in order to maximize the therapeutic efficacy and minimize unwanted side effects. This is achieved through fine-tuning the factors affecting the coiled coil’s oligomerization, resulting in modular systems that are highly specific for the intended application.

<span class="mw-page-title-main">Sulanemadlin</span> Chemical compound


Sulanemadlin is an experimental drug for the treatment of cancer. It is under development by Aileron Therapeutics, and has been studied in clinical trials for myelodysplastic syndrome and acute myeloid leukemia.

References

  1. ↑ Douse, CH; Maas, SJ; Thomas, JC; Garnett, JA; Sun, Y; Cota, E; Tate, EW (17 October 2014). "Crystal structures of stapled and hydrogen bond surrogate peptides targeting a fully buried protein-helix interaction". ACS Chemical Biology. 9 (10): 2204–9. doi: 10.1021/cb500271c . PMID   25084543.
  2. ↑ Lau, Yu Heng; Andrade, Peterson de; Wu, Yuteng; Spring, David R. (2014-12-08). "Peptide stapling techniques based on different macrocyclisation chemistries". Chemical Society Reviews. 44 (1): 91–102. doi:10.1039/C4CS00246F. ISSN   1460-4744. PMID   25199043.
  3. ↑ Kim, Young-Woo; Grossmann, Tom N.; Verdine, Gregory L. (2011). "Synthesis of all-hydrocarbon stapled α-helical peptides by ring-closing olefin metathesis". Nature Protocols. 6 (6): 761–771. doi:10.1038/nprot.2011.324. ISSN   1750-2799. PMID   21637196. S2CID   45832954.
  4. ↑ Hilinski, Gerard J.; Kim, Young-Woo; Hong, Jooyeon; Kutchukian, Peter S.; Crenshaw, Charisse M.; Berkovitch, Shaunna S.; Chang, Andrew; Ham, Sihyun; Verdine, Gregory L. (2014-09-03). "Stitched α-Helical Peptides via Bis Ring-Closing Metathesis". Journal of the American Chemical Society. 136 (35): 12314–12322. doi:10.1021/ja505141j. ISSN   0002-7863. PMID   25105213.
  5. 1 2 3 4 Verdine, GL; Hilinski, GJ (2012). "Stapled Peptides for Intracellular Drug Targets". Protein Engineering for Therapeutics, Part B. Methods in Enzymology. Vol. 503. pp. 3–33. doi:10.1016/B978-0-12-396962-0.00001-X. ISBN   9780123969620. PMID   22230563.
  6. ↑ Arkin, Michelle R.; Wells, James A. (April 2004). "Small-molecule inhibitors of protein–protein interactions: progressing towards the dream". Nature Reviews Drug Discovery. 3 (4): 301–317. doi:10.1038/nrd1343. PMC   4179228 . PMID   15060526.
  7. ↑ Moon, Heejo; Lim, Hyun-Suk (2015-02-01). "Synthesis and screening of small-molecule α-helix mimetic libraries targeting protein–protein interactions". Current Opinion in Chemical Biology. Omics. 24: 38–47. doi:10.1016/j.cbpa.2014.10.023. ISSN   1367-5931. PMID   25461722.
  8. 1 2 3 Walensky, LD; Bird, GH (14 August 2014). "Hydrocarbon-stapled peptides: principles, practice, and progress". Journal of Medicinal Chemistry. 57 (15): 6275–88. doi:10.1021/jm4011675. PMC   4136684 . PMID   24601557.
  9. ↑ Roy, Siddhartha; Ghosh, Piya; Ahmed, Israr; Chakraborty, Madhumita; Naiya, Gitashri; Ghosh, Basusree (December 2018). "Constrained α-Helical Peptides as Inhibitors of Protein-Protein and Protein-DNA Interactions". Biomedicines. 6 (4): 118. doi: 10.3390/biomedicines6040118 . PMC   6315407 . PMID   30567318.
  10. ↑ Blackwell, Helen E.; Grubbs, Robert H. (17 December 1998). "Highly Efficient Synthesis of Covalently Cross-Linked Peptide Helices by Ring-Closing Metathesis". Angewandte Chemie International Edition. 37 (23): 3281–3284. doi:10.1002/(SICI)1521-3773(19981217)37:23<3281::AID-ANIE3281>3.0.CO;2-V. PMID   29711420.
  11. ↑ Schafmeister, Christian E.; Po, Julia; Verdine, Gregory L. (June 2000). "An All-Hydrocarbon Cross-Linking System for Enhancing the Helicity and Metabolic Stability of Peptides". Journal of the American Chemical Society. 122 (24): 5891–5892. doi:10.1021/ja000563a. ISSN   0002-7863.
  12. ↑ Walensky, Loren D.; Bird, Gregory H. (2014-08-14). "Hydrocarbon-Stapled Peptides: Principles, Practice, and Progress". Journal of Medicinal Chemistry. 57 (15): 6275–6288. doi:10.1021/jm4011675. ISSN   0022-2623. PMC   4136684 . PMID   24601557.
  13. ↑ Walensky, Loren D.; Kung, Andrew L.; Escher, Iris; Malia, Thomas J.; Barbuto, Scott; Wright, Renee D.; Wagner, Gerhard; Verdine, Gregory L.; Korsmeyer, Stanley J. (2004-09-03). "Activation of Apoptosis in Vivo by a Hydrocarbon-Stapled BH3 Helix". Science. 305 (5689): 1466–1470. Bibcode:2004Sci...305.1466W. doi:10.1126/science.1099191. ISSN   0036-8075. PMC   1360987 . PMID   15353804.
  14. ↑ Wolfson, Wendy (2009-09-25). "Aileron Staples Peptides". Chemistry & Biology. 16 (9): 910–912. doi: 10.1016/j.chembiol.2009.09.008 . ISSN   1074-5521. PMID   19778714.
  15. ↑ Chang, Yong S.; Graves, Bradford; Guerlavais, Vincent; Tovar, Christian; Packman, Kathryn; To, Kwong-Him; Olson, Karen A.; Kesavan, Kamala; Gangurde, Pranoti; Mukherjee, Aditi; Baker, Theresa; Darlak, Krzysztof; Elkin, Carl; Filipovic, Zoran; Qureshi, Farooq Z. (2013-09-03). "Stapled α−helical peptide drug development: A potent dual inhibitor of MDM2 and MDMX for p53-dependent cancer therapy". Proceedings of the National Academy of Sciences. 110 (36): E3445-54. Bibcode:2013PNAS..110E3445C. doi: 10.1073/pnas.1303002110 . ISSN   0027-8424. PMC   3767549 . PMID   23946421.
  16. ↑ Stewart, Michelle L.; Fire, Emiko; Keating, Amy E.; Walensky, Loren D. (2010). "The MCL-1 BH3 helix is an exclusive MCL-1 inhibitor and apoptosis sensitizer". Nature Chemical Biology. 6 (8): 595–601. doi:10.1038/nchembio.391. ISSN   1552-4469. PMC   3033224 . PMID   20562877.
  17. ↑ Cohen, Nicole A.; Stewart, Michelle L.; Gavathiotis, Evripidis; Tepper, Jared L.; Bruekner, Susanne R.; Koss, Brian; Opferman, Joseph T.; Walensky, Loren D. (2012-09-21). "A Competitive Stapled Peptide Screen Identifies a Selective Small Molecule that Overcomes MCL-1-Dependent Leukemia Cell Survival". Chemistry & Biology. 19 (9): 1175–1186. doi:10.1016/j.chembiol.2012.07.018. ISSN   1074-5521. PMC   3582387 . PMID   22999885.
  18. ↑ Moellering, Raymond E.; Cornejo, Melanie; Davis, Tina N.; Bianco, Cristina Del; Aster, Jon C.; Blacklow, Stephen C.; Kung, Andrew L.; Gilliland, D. Gary; Verdine, Gregory L.; Bradner, James E. (2009). "Direct inhibition of the NOTCH transcription factor complex". Nature. 462 (7270): 182–188. Bibcode:2009Natur.462..182M. doi:10.1038/nature08543. ISSN   1476-4687. PMC   2951323 . PMID   19907488.
  19. ↑ Grossmann, Tom N.; Yeh, Johannes T.-H.; Bowman, Brian R.; Chu, Qian; Moellering, Raymond E.; Verdine, Gregory L. (2012). "Inhibition of oncogenic Wnt signaling through direct targeting of β-catenin". Proceedings of the National Academy of Sciences. 109 (44): 17942–17947. Bibcode:2012PNAS..10917942G. doi: 10.1073/pnas.1208396109 . ISSN   0027-8424. PMC   3497784 . PMID   23071338.
  20. ↑ Dietrich, Laura; Rathmer, Bernd; Ewan, Kenneth; Bange, Tanja; Heinrichs, Stefan; Dale, Trevor C.; Schade, Dennis; Grossmann, Tom N. (2017). "Cell Permeable Stapled Peptide Inhibitor of Wnt Signaling that Targets β-Catenin Protein-Protein Interactions". Cell Chemical Biology. 24 (8): 958–968.e5. doi:10.1016/j.chembiol.2017.06.013. hdl: 1871.1/31abdd1f-19a6-44d7-845b-a0b6e97c5cf8 . ISSN   2451-9456. PMID   28757184.
  21. ↑ Robertson, Naomi S.; Jamieson, Andrew G. (2015-08-12). "Regulation of protein–protein interactions using stapled peptides". Reports in Organic Chemistry. 5: 65–74. doi: 10.2147/ROC.S68161 . Retrieved 2019-11-04.
  22. ↑ Cromm, Philipp M.; Spiegel, Jochen; Grossmann, Tom N. (2015-06-19). "Hydrocarbon Stapled Peptides as Modulators of Biological Function". ACS Chemical Biology. 10 (6): 1362–1375. doi:10.1021/cb501020r. ISSN   1554-8929. PMID   25798993.
  23. ↑ "Phase 1 Safety Study of ALRN-5281 in Healthy Subjects". ClinicalTrials. U.S. National Institutes of Health. Retrieved 23 July 2015.
  24. ↑ "Pipeline". Aileron Therapeutics. Retrieved 2019-11-04.
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