IP Library Granted Patent US 12,398,178
Granted Patent B2
US 12,398,178 · App. 17/269,939 · Granted Aug 26, 2025

Collections of peptides, peptide agents, and methods of use thereof

Inventors: John Hanney McGee (Somerville, MA); Ty Matthew Thomson (Arlington, MA); Sebastian Christof Theodor Wahl (Zurich, CH); Gregory L. Verdine (Boston, MA); Raheleh Rezaei Araghi (Brookline, MA); Yue-Mei Zhang (Wellesley, MA); Mark Joseph Mulvihill (Sudbury, MA)
Assignee: Parabilis Medicines, Inc.
C07K7/08C07K14/001A61K38/00
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Quick Facts
Patent No.
US 12,398,178
App. No.
17/269,939
Granted
Aug 26, 2025
Kind
B2
Abstract

The present disclosure provides powerful technologies for the development, production, characterization, and/or use of stapled peptide compositions. Among other things, the present disclosure provides strategies for defining amino acid sequences particularly amenable or useful for stapling, as well as technologies, reagents, and systems for developing, producing, characterizing, and/or using stapled peptides having such amino acid sequences.

Claims (14)

1. A collection of stapled peptides, each of which independently comprises ADPAXXXCXXAAXXCXXX (SEQ ID NO: 3), wherein:

each X is independently an amino acid residue;

the two cysteine residues are covalently linked with one another via a linker having the structure of —S-L s2 -S—, where each S is independently a sulfur atom of one of the two cysteine residues; and

L s2 is

2. The collection of claim 1 , wherein each individual stapled peptide in the collection is covalently bound to a phage particle.

3. The collection of claim 1 , wherein each stapled peptide of the collection is discretely associated with an identifier so that the amino acid sequence of the stapled peptide can be independently identified.

4. The collection of claim 3 , wherein the identifier comprises a nucleic acid sequence that encodes the amino acid sequence of the stapled peptide or a portion thereof.

5. The collection of claim 4 , wherein the amino acid sequence of the stapled peptide is expressed by a system that comprises the identifier.

6. The collection of claim 2 , wherein each stapled peptide of the collection is discretely associated with an identifier so that the amino acid sequence of the stapled peptide can be independently identified.

7. The collection of claim 6 , wherein the identifier comprises a nucleic acid sequence that encodes the amino acid sequence of the stapled peptide or a portion thereof.

8. The collection of claim 7 , wherein the amino acid sequence is expressed by a phage system that comprises the identifier.

9. The collection of claim 1 , wherein the stapled peptides of the collection are each fused to a phage protein.

10. The collection of claim 8 , wherein the stapled peptides of the collection are each fused to a phage protein.

11. The collection of claim 5 , wherein the stapled peptides of the collection are each fused to a phage protein.

Assignments (4)
CHANGE OF NAME Recorded Jan 23, 2025
From: FOG PHARMACEUTICALS, INC.
To: PARABILIS MEDICINES, INC.
Reel/Frame 070001/0829 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jun 4, 2021
From: REZAEI ARAGHI, RAHELEH; ZHANG, YUE-MEI
To: FOG PHARMACEUTICALS, INC.
Reel/Frame 056444/0192 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jun 4, 2021
From: MCGEE, JOHN HANNEY; THOMSON, TY MATTHEW; WAHL, SEBASTIAN CHRISTOF THEODOR; VERDINE, GREGORY L.
To: FOG PHARMACEUTICALS, INC.
Reel/Frame 056444/0229 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jun 4, 2021
From: MULVIHILL, MARK JOSEPH
To: FOG PHARMACEUTICALS, INC.
Reel/Frame 056444/0249 →
Continuity (2)
Provisional Application 62719996 · Aug 20, 2018
Related Publication 20210179665A1 · Jun 17, 2021
References Cited (175)
US 7723469B2 · Walensky et al. · 2010 [cited by applicant]
US 8198405B2 · Walensky et al. · 2012 [cited by applicant]
US 8592377B2 · Verdine et al. · 2013 [cited by applicant]
US 8796418B2 · Walensky et al. · 2014 [cited by applicant]
US 8889632B2 · Bernal et al. · 2014 [cited by applicant]
US 8921323B2 · Walensky et al. · 2014 [cited by applicant]
US 8957026B2 · Verdine et al. · 2015 [cited by applicant]
US 9074009B2 · Bradner et al. · 2015 [cited by applicant]
US 9079970B2 · Walensky et al. · 2015 [cited by applicant]
US 9163330B2 · Verdine et al. · 2015 [cited by applicant]
US 9273099B2 · Walensky et al. · 2016 [cited by applicant]
US 9290545B2 · Walensky et al. · 2016 [cited by applicant]
US 9296805B2 · Walensky et al. · 2016 [cited by applicant]
US 9303024B2 · Walensky et al. · 2016 [cited by applicant]
US 9458189B2 · Verdine et al. · 2016 [cited by applicant]
US 9464115B2 · Walensky et al. · 2016 [cited by applicant]
US 9487562B2 · Moellering et al. · 2016 [cited by applicant]
US 9505816B2 · Walensky et al. · 2016 [cited by applicant]
US 9527896B2 · Bernal et al. · 2016 [cited by applicant]
US 9556227B2 · Verdine et al. · 2017 [cited by applicant]
US 9617309B2 · Verdine et al. · 2017 [cited by applicant]
US 9695224B2 · Walensky et al. · 2017 [cited by applicant]
US 9822165B2 · Walensky et al. · 2017 [cited by applicant]
US 9926306B2 · Walensky · 2018 [cited by applicant]
US 10000478B2 · Walensky et al. · 2018 [cited by applicant]
US 10000511B2 · Walensky et al. · 2018 [cited by applicant]
US 10077290B2 · Walensky et al. · 2018 [cited by applicant]
US 10081654B2 · Verdine et al. · 2018 [cited by applicant]
US 10087215B2 · Leshchiner et al. · 2018 [cited by applicant]
US 10106590B2 · Walensky et al. · 2018 [cited by applicant]
US 10202431B2 · Bernal et al. · 2019 [cited by applicant]
US 10227390B2 · Verdine et al. · 2019 [cited by applicant]
US 10259848B2 · Walensky et al. · 2019 [cited by applicant]
US 10273290B2 · Walensky et al. · 2019 [cited by applicant]
US 10301351B2 · Verdine et al. · 2019 [cited by applicant]
US 10308926B2 · Walensky et al. · 2019 [cited by applicant]
US 10351554B2 · Walensky et al. · 2019 [cited by applicant]
US 10464975B2 · Walensky et al. · 2019 [cited by applicant]
US 10487129B2 · Walensky et al. · 2019 [cited by applicant]
US 10533039B2 · Verdine et al. · 2020 [cited by applicant]
US 10703785B2 · Walensky et al. · 2020 [cited by applicant]
US 10716828B2 · Danial et al. · 2020 [cited by applicant]
US 10822374B2 · Walensky et al. · 2020 [cited by applicant]
US 10844053B2 · Walensky et al. · 2020 [cited by applicant]
US 11198713B2 · Hilinski et al. · 2021 [cited by applicant]
US 11332496B2 · Verdine et al. · 2022 [cited by applicant]
US 11377476B2 · Verdine et al. · 2022 [cited by applicant]
US 20100184628A1 · Nash · 2010 [cited by applicant]
US 20110218155A1 · Walensky et al. · 2011 [cited by applicant]
US 20130035304A1 · Walensky et al. · 2013 [cited by applicant]
US 20140256912A1 · Moellering et al. · 2014 [cited by applicant]
US 20150225471A1 · Liang et al. · 2015 [cited by applicant]
US 20150284437A1 · Verdine et al. · 2015 [cited by applicant]
US 20160122405A1 · Palchaudhuri et al. · 2016 [cited by applicant]
US 20160152667A1 · Walensky et al. · 2016 [cited by applicant]
US 20160171150A1 · Walensky et al. · 2016 [cited by applicant]
US 20160244494A1 · Verdine et al. · 2016 [cited by applicant]
US 20160257725A1 · Verdine et al. · 2016 [cited by applicant]
US 20170008930A1 · Walensky et al. · 2017 [cited by applicant]
US 20180009847A1 · Verdine et al. · 2018 [cited by applicant]
US 20180010001A1 · Hersam et al. · 2018 [cited by applicant]
US 20180057565A1 · Liang et al. · 2018 [cited by applicant]
US 20180100001A1 · Verdine et al. · 2018 [cited by applicant]
US 20180201658A1 · Rezaei-Araghi et al. · 2018 [cited by applicant]
US 20180265524A1 · Walensky et al. · 2018 [cited by applicant]
US 20190002506A1 · Walensky et al. · 2019 [cited by applicant]
US 20190002514A1 · Walensky et al. · 2019 [cited by applicant]
US 20190092822A1 · Walensky et al. · 2019 [cited by applicant]
US 20190202862A1 · Verdine et al. · 2019 [cited by applicant]
US 20200231638A1 · Walensky et al. · 2020 [cited by applicant]
US 20200239533A1 · Verdine et al. · 2020 [cited by applicant]
US 20200247858A1 · Hilinski et al. · 2020 [cited by applicant]
US 20210002336A1 · Walensky et al. · 2021 [cited by applicant]
US 20210032234A1 · Walensky et al. · 2021 [cited by applicant]
US 20220177522A1 · Verdine et al. · 2022 [cited by applicant]
US 20220213154A1 · Hilinski et al. · 2022 [cited by applicant]
US 20220306708A1 · Verdine et al. · 2022 [cited by applicant]
US 20220372075A1 · Verdine et al. · 2022 [cited by applicant]
US 20230046728A1 · Chandhoke et al. · 2023 [cited by applicant]
US 20230137773A1 · Verdine et al. · 2023 [cited by applicant]
US 20230271917A1 · Jewett et al. · 2023 [cited by applicant]
US 20230357320A1 · Verdine et al. · 2023 [cited by applicant]
US 20240376151A1 · Tokareva et al. · 2024 [cited by applicant]
WO WO2008121767A2 · 2008 [cited by applicant]
WO WO2011008260A2 · 2011 [cited by applicant]
WO WO2012040459A2 · 2012 [cited by examiner]
WO WO2014052647A2 · 2014 [cited by applicant]
WO WO2014055564A1 · 2014 [cited by applicant]
WO WO2014159969A1 · 2014 [cited by applicant]
WO WO2014201370A1 · 2014 [cited by applicant]
WO WO2015051030A2 · 2015 [cited by applicant]
WO WO2015095406A1 · 2015 [cited by applicant]
WO WO2015179635A2 · 2015 [cited by applicant]
WO WO2016209978A2 · 2016 [cited by applicant]
WO WO2018017485A1 · 2018 [cited by examiner]
WO WO2019051327A2 · 2019 [cited by applicant]
WO WO2020041270A1 · 2020 [cited by applicant]
WO WO2020041270A9 · 2020 [cited by applicant]
WO WO2021119537A1 · 2021 [cited by applicant]
WO WO2021188659A1 · 2021 [cited by applicant]
WO WO2022020651A1 · 2022 [cited by applicant]
WO WO2022020652A2 · 2022 [cited by applicant]
WO WO2022261257A1 · 2022 [cited by applicant]
WO WO2024130217A1 · 2024 [cited by applicant]
WO WO2024130218A1 · 2024 [cited by applicant]
Acetamide, N,N′-1,3-phenylenebis[2-bromo- _ C10H10Br2N2O2—PubChem_12499317; retrieved from https://pubchem.ncbi.nlm.nih.gov/compound/12499317; Jun. 2, 2022 (Year: 2007). [cited by examiner]
Sidhu, S.S. et al., [21] Phage Display for Selection of Novel Binding Peptides, Phage Display for Selection of Novel Binding Peptides, Methods in Enzymology, 328: 333-363. (Year: 2000). [cited by examiner]
Grossman, T. N. et al., Inhibition of oncogenic Wnt signaling through direct targeting of 3-catenin, PNAS, 109(44):17942-17947, with Supplemental Information, 9 pages. (Year: 2012). [cited by examiner]
Chen, S. and Heinis, C., Phage Selection of Bicyclic Peptides Based on Two Disulfide Bridges, Chapter 9, Ratmir Derda (ed.), Peptide Libraries: Methods and Protocols, Methods in Molecular Biology, 1248: 119-137, (Year: … [cited by examiner]
NCBI Conserved Domain Search_WP_115971347, generated by examiner on Oc. 14, 2022. (Year: 2018). [cited by examiner]
NCBI Conserved Domain Search_XP_032335171, generated by examiner on Oc. 14, 2022. (Year: 2020). [cited by examiner]
Fairlie, D.P. and Dantas De Araujo, A., Stapling Peptides Using Cysteine Crosslinking, Biopolymers (Peptide Science), 106(6): 843-852 (Year: 2016). [cited by examiner]
Rebollo and Heinis, Phage selection of bicyclic peptides, Methods; 60: 46-54. (Year: 2013). [cited by examiner]
Jafari, M.R. et al., Discovery of Light-Responsive Ligands through Screening of a Light-Responsive Genetically Encoded Library, ACS Chem. Biol., 9: 443-450. (Year: 2014). [cited by examiner]
Chen, S. et al., Peptide Ligands Stabilized by Small Molecules, Angewandte Chemie, 126(6):1628-1632. (Year: 2014). [cited by examiner]
Iyer, A. et al., Stapling monomeric GCN4 peptides allows for DNA binding and enhanced cellular uptake, Organic & Biomolecular Chemistry, 13(13)3856-3862. (Year: 2015). [cited by examiner]
Diderich, P. et al., Phage Selection of Chemically Stabilized a-Helical Peptide Ligands, ACS Chem. Biol., 11(5):1422-1427. (Year: 2016). [cited by examiner]
U.S. Appl. No. 16/298,093, filed Mar. 11, 2019, Verdine et al. [cited by applicant]
U.S. Appl. No. 16/822,722, filed Mar. 18, 2020, Walensky et al. [cited by applicant]
U.S. Appl. No. 16/950,540, filed Nov. 17, 2020, Verdine et al. [cited by applicant]
U.S. Appl. No. 17/091,541, filed Nov. 6, 2020, Walensky et al. [cited by applicant]
Assem, N. et al., Acetone-Linked Peptides: A Convergent Approach for Peptide Macrocyclization and Labeling, Angew. Chem. Int. Ed., 54: 8665-8668 (2015). [cited by applicant]
Chen, S. and Heinis, C., Phage Selection of Bicyclic Peptides Based on Two Disulfide Bridges, Chapter 9, Ratmir Derda (ed.), Peptide Libraries: Methods and Protocols, Methods in Molecular Biology, 1248: 119-137 (2015). [cited by applicant]
Fairlie, D.P. and Dantas De Araujo, A., Stapling Peptides Using Cysteine Crosslinking, Biopolymers (Peptide Science), 106(6): 843-852 (2016). [cited by applicant]
International Search Report for PCT/US2019/47206, 5 pages (Jan. 21, 2020). [cited by applicant]
Jafari, M.R. et al., Discovery of Light-Responsive Ligands through Screening of a Light-Responsive Genetically Encoded Library, ACS Chem. Biol., 9: 443-450 (2014). [cited by applicant]
Jo, H. et al,. Development of a-Helical Calpain Probes by Mimicking a Natural Protein-Protein Interaction, J. Am. Chem. Soc., 134: 17704-17713 (2012). [cited by applicant]
Kale, S. S. et al., Cyclization of peptides with two chemical bridges affords large scaffold diversities, Article and Reporting Summary, Nat. Chem., 12 pages (2018). [cited by applicant]
Kalhor-Monfared, S. et al., Rapid biocompatible macrocyclization of peptides with decafluoro-diphenylsulfone, Chem. Sci., 7: 3785-3790 (2016). [cited by applicant]
Ng, S. and Derda, R., Phage-displayed macrocyclic glycopeptide libraries, Org. Biomol. Chem., 14: 5539-5545 (2016). [cited by applicant]
Peraro, L. et al., Diversity-Oriented Stapling Yields Intrinsically Cell-Penetrant Inducers of Autophagy, J. Am. Chem. Soc., 139:7792-7802 (2017). [cited by applicant]
Pub Chem CID 23678, N,N′-Ethylenebis(iodoacetamide) (2005), <https://pubchem.ncbi.nlm.nih.gov/compound/23678>. Retrieved on Nov. 7, 2019. [cited by applicant]
Pub Chem CID 621238, 4,4′-Bis (bromomethyl)biphenyl (2005), <https://pubchem.ncbi.nlm.nih.gov/compound/621238>. Retrieved on Nov. 7, 2019. [cited by applicant]
PubChem CID 12499317, Create: Feb. 8, 2008. Modify: Nov. 2, 2019. URL: https://pubchem.ncbi.nlm.nih.gov/compound/12499317 [Retrieved Nov. 6, 2019). [cited by applicant]
Sidhu, S.S. et al., [21] Phage Display for Selection of Novel Binding Peptides, Phage Display for Selection of Novel Binding Peptides, Methods in Enzymology, 328: 333-363 (2000). [cited by applicant]
Wang, Y. and Chou, D. H-C., AThiol-Ene Coupling Approach to Native Peptide Stapling and Macrocyclization, Angew. Chem. Int. Ed., 54: 10931-10934 (2015). [cited by applicant]
Written Opinion for PCT/US2019/47206, 8 pages (Jan. 21, 2020). [cited by applicant]
Bellotto, S. et al., Phage Selection of Photoswitchable Peptide Ligands, J. Am. Chem. Soc., 136:5880-5883, (2014). [cited by applicant]
Chen, S. et al., Peptide Ligands Stabilized by Small Molecules, Angewandte Chemie, 126(6):1628-1632, (2014). [cited by applicant]
Grossman, T. N. et al., Inhibition of oncogenic Wnt signaling through direct targeting of β-catenin, PNAS, 109(44):17942-17947, (2012), with Supplemental Information, 9 pages. [cited by applicant]
Iyer, A. et al., Stapling monomeric GCN4 peptides allows for DNA binding and enhanced cellular uptake, Organic & Biomolecular Chemistry, 13(13)3856-3862, (2015). [cited by applicant]
Schafmeister et al., An All-Hydrocarbon Cross-Linking System for Enhancing the Helicity and Metabolic Stability of Peptides, J. Am. Chem. Soc., 122: 5891-5892 (2000). [cited by applicant]
Bernal, F. et al., A stapled p53 helix overcomes HDMX-mediated suppression of p53, Cancer Cell, 18(5):411-422 (2010). [cited by applicant]
Bernal, F. et al., A Stapled p53 Helix Targets HDMX to Overcome Nutlin-3 Resistance and Reactivate the p53 Tumor Suppressor Pathway in Cancer, Blood, 112(11):2645 (2008). [cited by applicant]
Chen, S. and Heinis, C., Phage selection of bicyclic peptides based on two disulfide bridges, Methods Mol. Biol., 1248:119-137 (2015). [cited by applicant]
De Paola, I. et al., Cullin3-BTB interface: a novel target for stapled peptides, PLoS One, 10(4):e012114 (2015). [cited by applicant]
Diderich, P. et al., Phage Selection of Chemically Stabilized a-Helical Peptide Ligands, ACS Chem. Biol., 11(5):1422-1427 (2016). [cited by applicant]
Dietrich, L. et al., Cell Permeable Stapled Peptide Inhibitor of Wnt Signaling that Targets β-Catenin Protein-Protein Interactions, Cell Chem. Bio., 24:958-968 (2017). [cited by applicant]
Distefano, M.D. and Miranda, L., APS 2022 27th American Peptide Symposium, 122 pages, (2022). [cited by applicant]
Grossmann, T. N. et al., Inhibition of oncogenic Wnt signaling through direct targeting of β-catenin, PNAS, 109(44):17942-17947 (2012). [cited by applicant]
Heinis, C. et al., Phage-encoded combinatorial chemical libraries based on bicyclic peptides, Nat. Chem. Biol., 5(7):502-507 (2009). [cited by applicant]
Misawa, T. et al., Structural development of stapled short helical peptides as vitamin D receptor (VDR)-coactivator interaction inhibitors, Bioorg. Med. Chem., 23(5):1055-1061 (2015). [cited by applicant]
Neri, D. and Brandli, A.W., Encoding chemistry, Nat. Chem. Biol., 5(7):452-453 (2009). [cited by applicant]
Nevola, L. et al., Light-regulated stapled peptides to inhibit protein-protein interactions involved in clathrin-mediated endocytosis, Angew. Chem. Int. Ed. Engl., 52(30):7704-7708 (2013). [cited by applicant]
Ortet, P. et al., Exploring the scope of i,i+4 thioether staples on a b-catenin peptide inhibitor, Fog Pharmaceuticals, Inc., 1 page, (2022). [cited by applicant]
Phillips, C. et al., Design and structure of stapled peptides binding to estrogen receptors, J. Am. Chem. Soc., 133(25):9696-9699 (2011). [cited by applicant]
Rebollo, I.R., et al., Identification of target-binding peptide motifs by high-throughput sequencing of phage-selected peptides, Nucleic Acids Research, 42(22):e169 (2014). [cited by applicant]
Spiegel, J. et al., Direct targeting of Rab-GTPase-effector interactions, Angew. Chem. Int. Ed. Engl., 53(9):2498-2503 (2014). [cited by applicant]
Takeda, K. et al., Targeted disruption of the BCL9/β-catenin complex inhibits oncogenic Wnt signaling, Sci. Transl. Med., 4(148):148ra117 (2012). [cited by applicant]
Walensky, L.D. et al., Activation of apoptosis in vivo by a hydrocarbon-stapled BH3 helix, Science, 305(5689):1466-70 (2004). [cited by applicant]
U.S. Appl. No. 17/751,451, filed May 23, 2023, Verdine et al. [cited by applicant]
U.S. Appl. No. 17/912,029, filed Sep. 15, 2022, Tremblay et al. [cited by applicant]
U.S. Appl. No. 18/017,024, filed Jan. 19, 2023, White et al. [cited by applicant]
U.S. Appl. No. 18/017,033, filed Jan. 19, 2023, Tremblay et al. [cited by applicant]
Chen, Q. et al., Optimization of PROTAC Ternary Complex Using DNA Encoded Library Approach, ACS Chem. Biol., 18:25-33 (2023). [cited by applicant]
Li, K. et al., De novo mapping of α-helix recognition sites on protein surfaces using unbiased libraries, Proc. National Acad. Sci., 119(e2210435119):1-11 (2022). [cited by applicant]
Mason, J. W. et al., DNA-encoded library (DEL)-enabled discovery of proximity-inducing small molecules, Biorxiv, 1-29 (2022). [cited by applicant]
Mcgee, J.H. et al., Exceptionally high-affinity Ras binders that remodel its effector domain, J. Biol. Chem., 293(9):3265-3280 (2018). [cited by applicant]
Mund, T. et al., Peptide and small molecule inhibitors of HECT-type ubiquitin ligases, Proc. National Acad. Sci., 111(47):16736-16741 (2014). [cited by applicant]
U.S. Appl. No. 18/345,550, filed Jun. 30, 2023, Verdine et al. [cited by applicant]
U.S. Appl. No. 18/453,118, filed Aug. 21, 2023, Verdine et al. [cited by applicant]
U.S. Appl. No. 18/497,597, filed Oct. 30, 2023, Tokareva et al. [cited by applicant]
U.S. Appl. No. 18/568,212, filed Dec. 7, 2023, White et al. [cited by applicant]
Armstrong, A., Introducing Fierce Biotech's 2023 Fierce 15, Fierce Biotech, 25 pages, posted Aug. 28, 2023, <https://www.fiercebiotech.com/special-reports/introducing-fierce-15-2023>. [cited by applicant]
U.S. Appl. No. 18/427,677, filed Jan. 30, 2024, Tokareva et al. [cited by applicant]