1
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Mi T, Nguyen D, Gao Z, Burgess K. Bioinformatics leading to conveniently accessible, helix enforcing, bicyclic ASX motif mimics (BAMMs). Nat Commun 2024; 15:4217. [PMID: 38760359 PMCID: PMC11101637 DOI: 10.1038/s41467-024-48323-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
Helix mimicry provides probes to perturb protein-protein interactions (PPIs). Helical conformations can be stabilized by joining side chains of non-terminal residues (stapling) or via capping fragments. Nature exclusively uses capping, but synthetic helical mimics are heavily biased towards stapling. This study comprises: (i) creation of a searchable database of unique helical N-caps (ASX motifs, a protein structural motif with two intramolecular hydrogen-bonds between aspartic acid/asparagine and following residues); (ii) testing trends observed in this database using linear peptides comprising only canonical L-amino acids; and, (iii) novel synthetic N-caps for helical interface mimicry. Here we show many natural ASX motifs comprise hydrophobic triangles, validate their effect in linear peptides, and further develop a biomimetic of them, Bicyclic ASX Motif Mimics (BAMMs). BAMMs are powerful helix inducing motifs. They are synthetically accessible, and potentially useful to a broad section of the community studying disruption of PPIs using secondary structure mimics.
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Affiliation(s)
- Tianxiong Mi
- Department of Chemistry, Texas A & M University, College Station, TX, 77842, USA
| | - Duyen Nguyen
- Department of Chemistry, Texas A & M University, College Station, TX, 77842, USA
| | - Zhe Gao
- Department of Chemistry, Texas A & M University, College Station, TX, 77842, USA
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, College Station, TX, 77842, USA.
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2
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He J, Ghosh P, Nitsche C. Biocompatible strategies for peptide macrocyclisation. Chem Sci 2024; 15:2300-2322. [PMID: 38362412 PMCID: PMC10866349 DOI: 10.1039/d3sc05738k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Peptides are increasingly important drug candidates, offering numerous advantages over conventional small molecules. However, they face significant challenges related to stability, cellular uptake and overall bioavailability. While individual modifications may not address all these challenges, macrocyclisation stands out as a single modification capable of enhancing affinity, selectivity, proteolytic stability and membrane permeability. The recent successes of in situ peptide modifications during screening in combination with genetically encoded peptide libraries have increased the demand for peptide macrocyclisation reactions that can occur under biocompatible conditions. In this perspective, we aim to distinguish biocompatible conditions from those well-known examples that are fully bioorthogonal. We introduce key strategies for biocompatible peptide macrocyclisation and contextualise them within contemporary screening methods, providing an overview of available transformations.
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Affiliation(s)
- Junming He
- Research School of Chemistry, Australian National University Canberra ACT Australia
| | - Pritha Ghosh
- Research School of Chemistry, Australian National University Canberra ACT Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University Canberra ACT Australia
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3
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Chen Z, Lim YW, Neo JY, Ting Chan RS, Koh LQ, Yuen TY, Lim YH, Johannes CW, Gates ZP. De Novo Sequencing of Synthetic Bis-cysteine Peptide Macrocycles Enabled by "Chemical Linearization" of Compound Mixtures. Anal Chem 2023; 95:14870-14878. [PMID: 37724843 PMCID: PMC10569172 DOI: 10.1021/acs.analchem.3c01742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/04/2023] [Indexed: 09/21/2023]
Abstract
A "chemical linearization" approach was applied to synthetic peptide macrocycles to enable their de novo sequencing from mixtures using nanoliquid chromatography-tandem mass spectrometry (nLC-MS/MS). This approach─previously applied to individual macrocycles but not to mixtures─involves cleavage of the peptide backbone at a defined position to give a product capable of generating sequence-determining fragment ions. Here, we first established the compatibility of "chemical linearization" by Edman degradation with a prominent macrocycle scaffold based on bis-Cys peptides cross-linked with the m-xylene linker, which are of major significance in therapeutics discovery. Then, using macrocycle libraries of known sequence composition, the ability to recover accurate de novo assignments to linearized products was critically tested using performance metrics unique to mixtures. Significantly, we show that linearized macrocycles can be sequenced with lower recall compared to linear peptides but with similar accuracy, which establishes the potential of using "chemical linearization" with synthetic libraries and selection procedures that yield compound mixtures. Sodiated precursor ions were identified as a significant source of high-scoring but inaccurate assignments, with potential implications for improving automated de novo sequencing more generally.
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Affiliation(s)
- Zhi’ang Chen
- Institute
of Molecular and Cell Biology (IMCB), Agency
for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
- Institute
of Sustainability for Chemicals, Energy and Environment (ISCE), Agency for Science, Technology
and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros, Singapore 138665, Republic
of Singapore
| | - Yi Wee Lim
- Institute
of Sustainability for Chemicals, Energy and Environment (ISCE), Agency for Science, Technology
and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros, Singapore 138665, Republic
of Singapore
| | - Jin Yong Neo
- Institute
of Sustainability for Chemicals, Energy and Environment (ISCE), Agency for Science, Technology
and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros, Singapore 138665, Republic
of Singapore
| | - Rachel Shu Ting Chan
- Institute
of Sustainability for Chemicals, Energy and Environment (ISCE), Agency for Science, Technology
and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros, Singapore 138665, Republic
of Singapore
| | - Li Quan Koh
- Institute
of Molecular and Cell Biology (IMCB), Agency
for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
- Institute
of Sustainability for Chemicals, Energy and Environment (ISCE), Agency for Science, Technology
and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros, Singapore 138665, Republic
of Singapore
| | - Tsz Ying Yuen
- Institute
of Sustainability for Chemicals, Energy and Environment (ISCE), Agency for Science, Technology
and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros, Singapore 138665, Republic
of Singapore
| | - Yee Hwee Lim
- Institute
of Sustainability for Chemicals, Energy and Environment (ISCE), Agency for Science, Technology
and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros, Singapore 138665, Republic
of Singapore
| | - Charles W. Johannes
- Institute
of Molecular and Cell Biology (IMCB), Agency
for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
| | - Zachary P. Gates
- Institute
of Molecular and Cell Biology (IMCB), Agency
for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
- Institute
of Sustainability for Chemicals, Energy and Environment (ISCE), Agency for Science, Technology
and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros, Singapore 138665, Republic
of Singapore
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4
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Beeg M, Baroni S, Piotti A, Porta A, De Luigi A, Cagnotto A, Gobbi M, Diomede L, Salmona M. A Comprehensive Technology Platform for the Rapid Discovery of Peptide Inhibitors against SARS-CoV-2 Pseudovirus Infection. Int J Mol Sci 2023; 24:12146. [PMID: 37569522 PMCID: PMC10418426 DOI: 10.3390/ijms241512146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
We developed and validated a technology platform for designing and testing peptides inhibiting the infectivity of SARS-CoV-2 spike protein-based pseudoviruses. This platform integrates target evaluation, in silico inhibitor design, peptide synthesis, and efficacy screening. We generated a cyclic peptide library derived from the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor. The cell-free validation process by ELISA competition assays and Surface Plasmon Resonance (SPR) studies revealed that the cyclic peptide c9_05, but not its linear form, binds well to ACE2. Moreover, it effectively inhibited the transduction in HEK293, stably expressing the human ACE2 receptor of pseudovirus particles displaying the SARS-CoV-2 spike in the Wuhan or UK variants. However, the inhibitory efficacy of c9_05 was negligible against the Omicron variant, and it failed to impede the entry of pseudoviruses carrying the B.1.351 (South African) spike. These variants contain three or more mutations known to increase affinity to ACE2. This suggests further refinement is needed for potential SARS-CoV-2 inhibition. Our study hints at a promising approach to develop inhibitors targeting viral infectivity receptors, including SARS-CoV-2's. This platform also promises swift identification and evaluation of inhibitors for other emergent viruses.
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5
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Brown H, Chung M, Üffing A, Batistatou N, Tsang T, Doskocil S, Mao W, Willbold D, Bast RC, Lu Z, Weiergräber OH, Kritzer JA. Structure-Based Design of Stapled Peptides That Bind GABARAP and Inhibit Autophagy. J Am Chem Soc 2022; 144:14687-14697. [PMID: 35917476 PMCID: PMC9425296 DOI: 10.1021/jacs.2c04699] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The LC3/GABARAP family of proteins is involved in nearly every stage of autophagy. Inhibition of LC3/GABARAP proteins is a promising approach to blocking autophagy, which sensitizes advanced cancers to DNA-damaging chemotherapy. Here, we report the structure-based design of stapled peptides that inhibit GABARAP with nanomolar affinities. Small changes in staple structure produced stapled peptides with very different binding modes and functional differences in LC3/GABARAP paralog selectivity, ranging from highly GABARAP-specific to broad inhibition of both subfamilies. The stapled peptides exhibited considerable cytosolic penetration and resistance to biological degradation. They also reduced autophagic flux in cultured ovarian cancer cells and sensitized ovarian cancer cells to cisplatin. These small, potent stapled peptides represent promising autophagy-modulating compounds that can be developed as novel cancer therapeutics and novel mediators of targeted protein degradation.
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Affiliation(s)
- Hawley Brown
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Mia Chung
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Alina Üffing
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Nefeli Batistatou
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Tiffany Tsang
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Samantha Doskocil
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Weiqun Mao
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Dieter Willbold
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Robert C Bast
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Zhen Lu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Oliver H Weiergräber
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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6
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Tomassi S, Dimmito MP, Cai M, D’Aniello A, Del Bene A, Messere A, Liu Z, Zhu T, Hruby VJ, Stefanucci A, Cosconati S, Mollica A, Di Maro S. CLIPSing Melanotan-II to Discover Multiple Functionally Selective hMCR Agonists. J Med Chem 2022; 65:4007-4017. [DOI: 10.1021/acs.jmedchem.1c01848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Stefano Tomassi
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, Naples 80131, Italy
| | - Marilisa Pia Dimmito
- Dipartimento di Farmacia, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, Chieti 66100, Italy
| | - Minying Cai
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Antonia D’Aniello
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Alessandra Del Bene
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Anna Messere
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Zekun Liu
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Tingyi Zhu
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Victor J. Hruby
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Azzurra Stefanucci
- Dipartimento di Farmacia, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, Chieti 66100, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Adriano Mollica
- Dipartimento di Farmacia, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, Chieti 66100, Italy
| | - Salvatore Di Maro
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
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7
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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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8
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Hu XX, Zhang M, Xu F. Benzylic bromide induced peptide cross-linking for nanofiber assembly. NEW J CHEM 2022. [DOI: 10.1039/d2nj04355f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Herein, we report a cross-linking method for the assembly of coiled-coil peptides into long fibers under mild conditions.
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Affiliation(s)
- Xiao-Xiang Hu
- Ministry of Education Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, 214122, Wuxi, China
| | - Meng Zhang
- Ministry of Education Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, 214122, Wuxi, China
| | - Fei Xu
- Ministry of Education Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, 214122, Wuxi, China
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9
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Horsfall AJ, Vandborg BA, Kikhtyak Z, Scanlon DB, Tilley WD, Hickey TE, Bruning JB, Abell AD. A cell permeable bimane-constrained PCNA-interacting peptide. RSC Chem Biol 2021; 2:1499-1508. [PMID: 34704055 PMCID: PMC8496261 DOI: 10.1039/d1cb00113b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/19/2021] [Indexed: 11/21/2022] Open
Abstract
The human sliding clamp protein known as proliferating cell nuclear antigen (PCNA) orchestrates DNA-replication and -repair and as such is an ideal therapeutic target for proliferative diseases, including cancer. Peptides derived from the human p21 protein bind PCNA with high affinity via a 310-helical binding conformation and are known to shut down DNA-replication. Here, we present studies on short analogues of p21 peptides (143-151) conformationally constrained with a covalent linker between i, i + 4 separated cysteine residues at positions 145 and 149 to access peptidomimetics that target PCNA. The resulting macrocycles bind PCNA with K D values ranging from 570 nM to 3.86 μM, with the bimane-constrained peptide 7 proving the most potent. Subsequent X-ray crystallography and computational modelling studies of the macrocyclic peptides bound to PCNA indicated only the high-affinity peptide 7 adopted the classical 310-helical binding conformation. This suggests the 310-helical conformation is critical to high affinity PCNA binding, however NMR secondary shift analysis of peptide 7 revealed this secondary structure was not well-defined in solution. Peptide 7 is cell permeable and localised to the cell cytosol of breast cancer cells (MDA-MB-468), revealed by confocal microscopy showing blue fluorescence of the bimane linker. The inherent fluorescence of the bimane moiety present in peptide 7 allowed it to be directly imaged in the cell uptake assay, without attachment of an auxiliary fluorescent tag. This highlights a significant benefit of using a bimane constraint to access conformationally constrained macrocyclic peptides. This study identifies a small peptidomimetic that binds PCNA with higher affinity than previous reported p21 macrocycles, and is cell permeable, providing a significant advance toward development of a PCNA inhibitor for therapeutic applications.
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Affiliation(s)
- Aimee J Horsfall
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide Adelaide South Australia 5005 Australia .,School of Physical Sciences, The University of Adelaide Adelaide South Australia 5005 Australia.,Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP) Australia
| | - Beth A Vandborg
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide Adelaide South Australia 5005 Australia .,School of Biological Sciences, The University of Adelaide Adelaide South Australia 5005 Australia
| | - Zoya Kikhtyak
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide Adelaide South Australia 5005 Australia
| | - Denis B Scanlon
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide Adelaide South Australia 5005 Australia .,School of Physical Sciences, The University of Adelaide Adelaide South Australia 5005 Australia
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide Adelaide South Australia 5005 Australia
| | - Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide Adelaide South Australia 5005 Australia
| | - John B Bruning
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide Adelaide South Australia 5005 Australia .,School of Biological Sciences, The University of Adelaide Adelaide South Australia 5005 Australia
| | - Andrew D Abell
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide Adelaide South Australia 5005 Australia .,School of Physical Sciences, The University of Adelaide Adelaide South Australia 5005 Australia.,Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP) Australia
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10
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Pace JR, Lampkin BJ, Abakah C, Moyer A, Miao J, Deprey K, Cerulli RA, Lin YS, Baleja JD, Baker D, Kritzer JA. Stapled β-Hairpins Featuring 4-Mercaptoproline. J Am Chem Soc 2021; 143:15039-15044. [PMID: 34516087 DOI: 10.1021/jacs.1c04378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptides constrained by intramolecular cross-links, especially stapled α-helices, have emerged as versatile scaffolds for drug development. However, there are fewer examples of similarly constrained scaffolds for other secondary structures. Here, we used a novel computational strategy to identify an optimal staple for antiparallel β-strands, and then we incorporated that staple within a β-hairpin peptide. The hairpin uses 4-mercaptoproline as a novel staple component, which contributes to a unique, kinked structure. The stapled hairpins show a high degree of structure in aqueous solution, excellent resistance to degradation in cell lysates, and cytosolic penetration at micromolar concentrations. They also overlay with a unique subset of kinked hairpin motifs at protein-protein interaction interfaces. Thus, these scaffolds represent promising starting points for developing inhibitors of cellular protein-protein interactions.
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Affiliation(s)
- Jennifer R Pace
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Bryan J Lampkin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Charles Abakah
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Adam Moyer
- Molecular Engineering and Sciences Institute, University of Washington, Seattle Washington 98195, United States
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Kirsten Deprey
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Robert A Cerulli
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - James D Baleja
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, United States
| | - David Baker
- Molecular Engineering and Sciences Institute, University of Washington, Seattle Washington 98195, United States.,Department of Biochemistry, Institute for Protein Design, and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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11
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Cameron AJ, Harris PWR, Brimble MA. On-Resin Preparation of Allenamidyl Peptides: A Versatile Chemoselective Conjugation and Intramolecular Cyclisation Tool. Angew Chem Int Ed Engl 2020; 59:18054-18061. [PMID: 32700356 DOI: 10.1002/anie.202004656] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Indexed: 12/14/2022]
Abstract
The ability to modify peptides and proteins chemoselectively is of continued interest in medicinal chemistry, with peptide conjugation, lipidation, stapling, and disulfide engineering at the forefront of modern peptide chemistry. Herein we report a robust method for the on-resin preparation of allenamide-modified peptides, an unexplored functionality for peptides that provides a versatile chemical tool for chemoselective inter- or intramolecular bridging reactions with thiols. The bridging reaction is biocompatible, occurring spontaneously at pH 7.4 in catalyst-free aqueous media. By this "click" approach, a model peptide was successfully modified with a diverse range of alkyl and aryl thiols. Furthermore, this technique was demonstrated as a valuable tool to induce spontaneous intramolecular cyclisation by preparation of an oxytocin analogue, in which the native disulfide bridge was replaced with a vinyl sulfide moiety formed by thia-Michael addition of a cysteine thiol to the allenamide handle.
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Affiliation(s)
- Alan J Cameron
- School of Chemical Sciences and School of Biological Sciences, The University of Auckland, 23 Symonds St, Auckland, 1142, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, 1142, New Zealand
| | - Paul W R Harris
- School of Chemical Sciences and School of Biological Sciences, The University of Auckland, 23 Symonds St, Auckland, 1142, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, 1142, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences and School of Biological Sciences, The University of Auckland, 23 Symonds St, Auckland, 1142, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, 1142, New Zealand
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12
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Sindhikara D, Wagner M, Gkeka P, Güssregen S, Tiwari G, Hessler G, Yapici E, Li Z, Evers A. Automated Design of Macrocycles for Therapeutic Applications: From Small Molecules to Peptides and Proteins. J Med Chem 2020; 63:12100-12115. [PMID: 33017535 DOI: 10.1021/acs.jmedchem.0c01500] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Macrocycles and cyclic peptides are increasingly attractive therapeutic modalities as they often have improved affinity, are able to bind to extended protein surfaces, and otherwise have favorable properties. Macrocyclization of a known binder may stabilize its bioactive conformation and improve its metabolic stability, cell permeability, and in certain cases oral bioavailability. Herein, we present implementation and application of an approach that automatically generates, evaluates, and proposes cyclizations utilizing a library of well-established chemical reactions and reagents. Using the three-dimensional (3D) conformation of the linear molecule in complex with a target protein as the starting point, this approach identifies attachment points, generates linkers, evaluates their geometric compatibility, and ranks the resulting molecules with respect to their predicted conformational stability and interactions with the target protein. As we show here with prospective and retrospective case studies, this procedure can be applied for the macrocyclization of small molecules and peptides and even PROteolysis TArgeting Chimeras (PROTACs) and proteins.
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Affiliation(s)
- Dan Sindhikara
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Michael Wagner
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Paraskevi Gkeka
- Integrated Drug Discovery, Sanofi R&D, 1 Avenue Pierre Brossolette, 91385 Chilly-Mazarin, France
| | - Stefan Güssregen
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Garima Tiwari
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Gerhard Hessler
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Engin Yapici
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Ziyu Li
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Andreas Evers
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
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13
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Cameron AJ, Harris PWR, Brimble MA. On‐Resin Preparation of Allenamidyl Peptides: A Versatile Chemoselective Conjugation and Intramolecular Cyclisation Tool. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Alan J. Cameron
- School of Chemical Sciences and School of Biological Sciences The University of Auckland 23 Symonds St Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery The University of Auckland Auckland 1142 New Zealand
| | - Paul W. R. Harris
- School of Chemical Sciences and School of Biological Sciences The University of Auckland 23 Symonds St Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery The University of Auckland Auckland 1142 New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences and School of Biological Sciences The University of Auckland 23 Symonds St Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery The University of Auckland Auckland 1142 New Zealand
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14
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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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15
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Horsfall AJ, Dunning KR, Keeling KL, Scanlon DB, Wegener KL, Abell AD. A Bimane‐Based Peptide Staple for Combined Helical Induction and Fluorescent Imaging. Chembiochem 2020; 21:3423-3432. [DOI: 10.1002/cbic.202000485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Aimee J. Horsfall
- The Department of Chemistry, School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
- The ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) The University of Adelaide North Terrace Adelaide SA 5005 Australia
- Institute for Photonics and Advanced Sensing (IPAS) The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Kylie R. Dunning
- The ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) The University of Adelaide North Terrace Adelaide SA 5005 Australia
- Institute for Photonics and Advanced Sensing (IPAS) The University of Adelaide North Terrace Adelaide SA 5005 Australia
- Robinson Research Institute, Adelaide Medical School The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Kelly L. Keeling
- The Department of Chemistry, School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
- Institute for Photonics and Advanced Sensing (IPAS) The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Denis B. Scanlon
- The Department of Chemistry, School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
- Institute for Photonics and Advanced Sensing (IPAS) The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Kate L. Wegener
- Institute for Photonics and Advanced Sensing (IPAS) The University of Adelaide North Terrace Adelaide SA 5005 Australia
- School of Biological Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Andrew D. Abell
- The Department of Chemistry, School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
- The ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) The University of Adelaide North Terrace Adelaide SA 5005 Australia
- Institute for Photonics and Advanced Sensing (IPAS) The University of Adelaide North Terrace Adelaide SA 5005 Australia
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16
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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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17
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Bednar TN, Resnikoff AR, Gavenonis J. Microwave-assisted cleavage of cysteine perfluoroaryl thioethers. Amino Acids 2020; 52:841-845. [PMID: 32350627 DOI: 10.1007/s00726-020-02846-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/23/2020] [Indexed: 11/28/2022]
Abstract
The cysteine- perfluoroarene SNAr reaction allows for the sequence-specific attachment of dyes and affinity tags to peptides and proteins. However, while many methods exist for the desulfuration of native and functionalized cysteine residues, there are no reports of their application to perfluoroarylated cysteines. Herein we report both the hydrogenolysis of a perfluoroarylated cysteine to alanine and elimination to dehydroalanine, reactions that are both accelerated by microwave irradiation.
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Affiliation(s)
- Taylor N Bednar
- Department of Chemistry, Dickinson College, 28 North College Street, Carlisle, PA, 17013, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Alissa R Resnikoff
- Department of Chemistry, Dickinson College, 28 North College Street, Carlisle, PA, 17013, USA.,Chicago Medical School, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL, 60064, USA
| | - Jason Gavenonis
- Department of Chemistry, Dickinson College, 28 North College Street, Carlisle, PA, 17013, USA.
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18
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Mulligan VK. The emerging role of computational design in peptide macrocycle drug discovery. Expert Opin Drug Discov 2020; 15:833-852. [PMID: 32345066 DOI: 10.1080/17460441.2020.1751117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Drug discovery is a laborious process with rising cost per new drug. Peptide macrocycles are promising therapeutics, though conformational flexibility can reduce target affinity and specificity. Recent computational advancements address this problem by enabling rational design of rigidly folded peptide macrocycles. AREAS COVERED This review summarizes currently approved peptide macrocycle therapeutics and discusses advantages of mesoscale drugs over small molecules or protein therapeutics. It describes the history, rationale, and state of the art of computational tools, such as Rosetta, that allow the design of rigidly structured peptide macrocycles. The emerging pipeline for designing peptide macrocycle drugs is described, including current challenges in designing permeable molecules that can emulate the chameleonic behavior of natural macrocycles. Prospects for reducing computational cost and improving accuracy with emerging computational technologies are also discussed. EXPERT OPINION To embrace computational design of peptide macrocycle drugs, we must shift current attitudes regarding the role of computation in drug discovery, and move beyond Lipinski's rules. This technology has the potential to shift failures to earlier in silico stages of the drug discovery process, improving success rates in costly clinical trials. Given the available tools, now is the time for drug developers to incorporate peptide macrocycle design into drug discovery pipelines.
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Affiliation(s)
- Vikram K Mulligan
- Systems Biology, Center for Computational Biology, Flatiron Institute , New York, NY, USA
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19
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Frost JR, Essman JZ, Huang C, Pierson NA, Pissarnitski N, Meng T. Proline‐to‐cysteine
cyclization for generating conformationally constrained cyclic peptides. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- John R. Frost
- Discovery Chemistry, Chemistry Capabilities for Accelerating TherapeuticsMerck & Co., Inc. Kenilworth New Jersey USA
| | - Jake Z. Essman
- Discovery Chemistry, Chemistry Capabilities for Accelerating TherapeuticsMerck & Co., Inc. Kenilworth New Jersey USA
| | - Chunhui Huang
- Discovery ChemistryMerck & Co., Inc Boston Massachusetts USA
| | | | - Natalya Pissarnitski
- Discovery Chemistry, Chemistry Capabilities for Accelerating TherapeuticsMerck & Co., Inc. Kenilworth New Jersey USA
| | - Tao Meng
- Discovery Chemistry, Chemistry Capabilities for Accelerating TherapeuticsMerck & Co., Inc. Kenilworth New Jersey USA
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20
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Ricardo MG, Ali AM, Plewka J, Surmiak E, Labuzek B, Neochoritis CG, Atmaj J, Skalniak L, Zhang R, Holak TA, Groves M, Rivera DG, Dömling A. Multicomponent Peptide Stapling as a Diversity‐Driven Tool for the Development of Inhibitors of Protein–Protein Interactions. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Manuel G. Ricardo
- Faculty of Chemistry, Center for Natural Product ResearchUniversity of Havana Cuba
| | - Ameena M. Ali
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
| | - Jacek Plewka
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Ewa Surmiak
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Beata Labuzek
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Constantinos G. Neochoritis
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
- Department of ChemistryUniversity of Crete Greece
| | - Jack Atmaj
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
- Faculty of ChemistryJagiellonian University Krakow Poland
| | | | - Ran Zhang
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
| | - Tad A. Holak
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Matthew Groves
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
| | - Daniel G. Rivera
- Faculty of Chemistry, Center for Natural Product ResearchUniversity of Havana Cuba
| | - Alexander Dömling
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
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21
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Ricardo MG, Ali AM, Plewka J, Surmiak E, Labuzek B, Neochoritis CG, Atmaj J, Skalniak L, Zhang R, Holak TA, Groves M, Rivera DG, Dömling A. Multicomponent Peptide Stapling as a Diversity-Driven Tool for the Development of Inhibitors of Protein-Protein Interactions. Angew Chem Int Ed Engl 2020; 59:5235-5241. [PMID: 31944488 DOI: 10.1002/anie.201916257] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Indexed: 12/12/2022]
Abstract
Stapled peptides are chemical entities in-between biologics and small molecules, which have proven to be the solution to high affinity protein-protein interaction antagonism, while keeping control over pharmacological performance such as stability and membrane penetration. We demonstrate that the multicomponent reaction-based stapling is an effective strategy for the development of α-helical peptides with highly potent dual antagonistic action of MDM2 and MDMX binding p53. Such a potent inhibitory activity of p53-MDM2/X interactions was assessed by fluorescence polarization, microscale thermophoresis, and 2D NMR, while several cocrystal structures with MDM2 were obtained. This MCR stapling protocol proved efficient and versatile in terms of diversity generation at the staple, as evidenced by the incorporation of both exo- and endo-cyclic hydrophobic moieties at the side chain cross-linkers. The interaction of the Ugi-staple fragments with the target protein was demonstrated by crystallography.
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Affiliation(s)
- Manuel G Ricardo
- Faculty of Chemistry, Center for Natural Product Research, University of Havana, Cuba
| | - Ameena M Ali
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
| | - Jacek Plewka
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Ewa Surmiak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Beata Labuzek
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Constantinos G Neochoritis
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands.,Department of Chemistry, University of, Crete, Greece
| | - Jack Atmaj
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands.,Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Lukasz Skalniak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Ran Zhang
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Matthew Groves
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
| | - Daniel G Rivera
- Faculty of Chemistry, Center for Natural Product Research, University of Havana, Cuba
| | - Alexander Dömling
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
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22
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Navaratna T, Atangcho L, Mahajan M, Subramanian V, Case M, Min A, Tresnak D, Thurber GM. Directed Evolution Using Stabilized Bacterial Peptide Display. J Am Chem Soc 2020; 142:1882-1894. [PMID: 31880439 DOI: 10.1021/jacs.9b10716] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chemically stabilized peptides have attracted intense interest by academics and pharmaceutical companies due to their potential to hit currently "undruggable" targets. However, engineering an optimal sequence, stabilizing linker location, and physicochemical properties is a slow and arduous process. By pairing non-natural amino acid incorporation and cell surface click chemistry in bacteria with high-throughput sorting, we developed a method to quantitatively select high affinity ligands and applied the Stabilized Peptide Evolution by E. coli Display technique to develop disrupters of the therapeutically relevant MDM2-p53 interface. Through in situ stabilization on the bacterial surface, we demonstrate rapid isolation of stabilized peptides with improved affinity and novel structures. Several peptides evolved a second loop including one sequence (Kd = 1.8 nM) containing an i, i+4 disulfide bond. NMR structural determination indicated a bent helix in solution and bound to MDM2. The bicyclic peptide had improved protease stability, and we demonstrated that protease resistance could be measured both on the bacterial surface and in solution, enabling the method to test and/or screen for additional drug-like properties critical for biologically active compounds.
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Affiliation(s)
- Tejas Navaratna
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Lydia Atangcho
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Mukesh Mahajan
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | | | - Marshall Case
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Andrew Min
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Daniel Tresnak
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Greg M Thurber
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Biomedical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
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23
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Merritt HI, Sawyer N, Arora PS. Bent Into Shape: Folded Peptides to Mimic Protein Structure and Modulate Protein Function. Pept Sci (Hoboken) 2020; 112:e24145. [PMID: 33575525 PMCID: PMC7875438 DOI: 10.1002/pep2.24145] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 12/11/2019] [Indexed: 12/16/2022]
Abstract
Protein secondary and tertiary structure mimics have served as model systems to probe biophysical parameters that guide protein folding and as attractive reagents to modulate protein interactions. Here we review contemporary methods to reproduce loop, helix, sheet and coiled-coil conformations in short peptides.
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Affiliation(s)
| | | | - Paramjit S. Arora
- Department of Chemistry New York University, New York, New York 10003, United States
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24
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Meng G, Pu J, Li Y, Han A, Tian Y, Xu W, Zhang T, Li X, Lu L, Wang C, Jiang S, Liu K. Design and Biological Evaluation of m-Xylene Thioether-Stapled Short Helical Peptides Targeting the HIV-1 gp41 Hexameric Coiled-Coil Fusion Complex. J Med Chem 2019; 62:8773-8783. [PMID: 31513410 DOI: 10.1021/acs.jmedchem.9b00882] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Short peptide-based inhibition of fusion remains an attractive goal in antihuman immunodeficiency virus (HIV) research based on its potential for the development of technically and economically desirable antiviral agents. Herein, we report the use of the dithiol bisalkylation reaction to generate a series of m-xylene thioether-stapled 22-residue α-helical peptides that have been identified as fusion inhibitors targeting HIV-1 glycoprotein 41 (gp41). The peptide sequence is based on the helix-zone binding domain of the gp41 C-terminal heptad repeat region. We found that one of these stapled peptides, named hCS6ERE, showed promising inhibitory potency against HIV-1 Env-mediated cell-cell fusion and viral replication at a level comparable to the clinically used 36-mer peptide T20. Furthermore, combining hCS6ERE with a fusion inhibitor having a different target site, such as HP23, produced synergistic anti-HIV-1 activity. Collectively, our study offers new insight into the design of anti-HIV peptides with short sequences.
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Affiliation(s)
- Guangpeng Meng
- Key Laboratory of Structure-Based Drug Design & Discovery of the Ministry of Education , Shenyang Pharmaceutical University , Shenyang 110016 , China
| | - Jing Pu
- Key Laboratory of Medical Molecular Virology of (MOE/NHC/CAMS), School of Basic Medical Sciences & Shanghai Public Health Clinical Center , Fudan University , 131 Dong An Road , Shanghai 200032 , China
| | - Yue Li
- Key Laboratory of Structure-Based Drug Design & Discovery of the Ministry of Education , Shenyang Pharmaceutical University , Shenyang 110016 , China
| | - Aixin Han
- State Key Laboratory of Toxicology and Medical Countermeasures , Beijing Institute of Pharmacology and Toxicology , 27 Tai-Ping Road , Beijing 100850 , China
| | - Yangli Tian
- State Key Laboratory of Toxicology and Medical Countermeasures , Beijing Institute of Pharmacology and Toxicology , 27 Tai-Ping Road , Beijing 100850 , China
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology of (MOE/NHC/CAMS), School of Basic Medical Sciences & Shanghai Public Health Clinical Center , Fudan University , 131 Dong An Road , Shanghai 200032 , China
| | - Tianhong Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures , Beijing Institute of Pharmacology and Toxicology , 27 Tai-Ping Road , Beijing 100850 , China
| | - Xue Li
- State Key Laboratory of Toxicology and Medical Countermeasures , Beijing Institute of Pharmacology and Toxicology , 27 Tai-Ping Road , Beijing 100850 , China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology of (MOE/NHC/CAMS), School of Basic Medical Sciences & Shanghai Public Health Clinical Center , Fudan University , 131 Dong An Road , Shanghai 200032 , China
| | - Chao Wang
- State Key Laboratory of Toxicology and Medical Countermeasures , Beijing Institute of Pharmacology and Toxicology , 27 Tai-Ping Road , Beijing 100850 , China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology of (MOE/NHC/CAMS), School of Basic Medical Sciences & Shanghai Public Health Clinical Center , Fudan University , 131 Dong An Road , Shanghai 200032 , China.,Lindsley F. Kimball Research Institute , New York Blood Center , 310 East 67th Street , New York , New York 10065 , United States
| | - Keliang Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of the Ministry of Education , Shenyang Pharmaceutical University , Shenyang 110016 , China.,State Key Laboratory of Toxicology and Medical Countermeasures , Beijing Institute of Pharmacology and Toxicology , 27 Tai-Ping Road , Beijing 100850 , China
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25
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Guarracino DA, Riordan JA, Barreto GM, Oldfield AL, Kouba CM, Agrinsoni D. Macrocyclic Control in Helix Mimetics. Chem Rev 2019; 119:9915-9949. [DOI: 10.1021/acs.chemrev.8b00623] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Danielle A. Guarracino
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Jacob A. Riordan
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Gianna M. Barreto
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Alexis L. Oldfield
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Christopher M. Kouba
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Desiree Agrinsoni
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
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26
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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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27
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Zhang G, Barragan F, Wilson K, Levy N, Herskovits A, Sapozhnikov M, Rodríguez Y, Kelmendi L, Alkasimi H, Korsmo H, Chowdhury M, Gerona‐Navarro G. A Solid‐Phase Approach to Accessing Bisthioether‐Stapled Peptides Resulting in a Potent Inhibitor of PRC2 Catalytic Activity. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Gan Zhang
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
- Ph.D. Program in Chemistry The Graduate Center of The City University of New York New York NY USA
| | - Flavia Barragan
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Khadija Wilson
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Nissim Levy
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Adam Herskovits
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Milana Sapozhnikov
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Yoel Rodríguez
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
- Department of Natural Sciences Hostos Community College of The City University of New York 475 Grand Concourse Bronx NY 10451 USA
| | - Leutrim Kelmendi
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Haleem Alkasimi
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Hunter Korsmo
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Maisha Chowdhury
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Guillermo Gerona‐Navarro
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
- Ph.D. Program in Chemistry The Graduate Center of The City University of New York New York NY USA
- Ph.D. Program in Biochemistry The Graduate Center of The City University of New York New York NY USA
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28
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Roy S, Ghosh P, Ahmed I, Chakraborty M, Naiya G, Ghosh B. Constrained α-Helical Peptides as Inhibitors of Protein-Protein and Protein-DNA Interactions. Biomedicines 2018; 6:E118. [PMID: 30567318 PMCID: PMC6315407 DOI: 10.3390/biomedicines6040118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 02/06/2023] Open
Abstract
Intracellular regulatory pathways are replete with protein-protein and protein-DNA interactions, offering attractive targets for therapeutic interventions. So far, most drugs are targeted toward enzymes and extracellular receptors. Protein-protein and protein-DNA interactions have long been considered as "undruggable". Protein-DNA interactions, in particular, present a difficult challenge due to the repetitive nature of the B-DNA. Recent studies have provided several breakthroughs; however, a design methodology for these classes of inhibitors is still at its infancy. A dominant motif of these macromolecular interactions is an α-helix, raising possibilities that an appropriate conformationally-constrained α-helical peptide may specifically disrupt these interactions. Several methods for conformationally constraining peptides to the α-helical conformation have been developed, including stapling, covalent surrogates of hydrogen bonds and incorporation of unnatural amino acids that restrict the conformational space of the peptide. We will discuss these methods and several case studies where constrained α-helices have been used as building blocks for appropriate molecules. Unlike small molecules, the delivery of these short peptides to their targets is not straightforward as they may possess unfavorable cell penetration and ADME properties. Several methods have been developed in recent times to overcome some of these problems. We will discuss these issues and the prospects of this class of molecules as drugs.
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Affiliation(s)
- Siddhartha Roy
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Piya Ghosh
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Israr Ahmed
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Madhumita Chakraborty
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Gitashri Naiya
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Basusree Ghosh
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
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29
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Zhang G, Barragan F, Wilson K, Levy N, Herskovits A, Sapozhnikov M, Rodríguez Y, Kelmendi L, Alkasimi H, Korsmo H, Chowdhury M, Gerona-Navarro G. A Solid-Phase Approach to Accessing Bisthioether-Stapled Peptides Resulting in a Potent Inhibitor of PRC2 Catalytic Activity. Angew Chem Int Ed Engl 2018; 57:17073-17078. [PMID: 30339297 DOI: 10.1002/anie.201810007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/05/2018] [Indexed: 12/11/2022]
Abstract
Stapled peptides have emerged as a new class of therapeutics to effectively target intractable protein-protein interactions. Thus, efficient and versatile methods granting easy access to this class of compounds and expanding the scope(s) of the currently available ones are of great interest. Now, a solid phase approach is described for the synthesis of bisthioether stapled peptides with multiple architectures, including single-turn, double-turn, and double-stapled macrocycles. This method allows for ligation with all-hydrocarbon linkers of various lengths, avoiding the use of unnatural amino acids and expensive catalysts, and affords cyclopeptides with remarkable resistance to proteolytic degradation. The potential of this procedure is demonstrated by applying it to generate a stapled peptide that shows potent in vitro inhibition of methyltransferase activity of the polycomb repressive complex 2 (PRC2) of proteins.
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Affiliation(s)
- Gan Zhang
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA.,Ph.D. Program in Chemistry, The Graduate Center of The City University of New York, New York, NY, USA
| | - Flavia Barragan
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Khadija Wilson
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Nissim Levy
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Adam Herskovits
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Milana Sapozhnikov
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Yoel Rodríguez
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA.,Department of Natural Sciences, Hostos Community College of The City University of New York, 475 Grand Concourse, Bronx, NY, 10451, USA
| | - Leutrim Kelmendi
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Haleem Alkasimi
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Hunter Korsmo
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Maisha Chowdhury
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Guillermo Gerona-Navarro
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA.,Ph.D. Program in Chemistry, The Graduate Center of The City University of New York, New York, NY, USA.,Ph.D. Program in Biochemistry, The Graduate Center of The City University of New York, New York, NY, USA
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30
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Peraro L, Deprey KL, Moser MK, Zou Z, Ball HL, Levine B, Kritzer JA. Cell Penetration Profiling Using the Chloroalkane Penetration Assay. J Am Chem Soc 2018; 140:11360-11369. [PMID: 30118219 PMCID: PMC6205923 DOI: 10.1021/jacs.8b06144] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biotherapeutics are a promising class of molecules in drug discovery, but they are often limited to extracellular targets due to their poor cell penetration. High-throughput cell penetration assays are required for the optimization of biotherapeutics for enhanced cell penetration. We developed a HaloTag-based assay called the chloroalkane penetration assay (CAPA), which is quantitative, high-throughput, and compartment-specific. We demonstrate the ability of CAPA to profile extent of cytosolic penetration with respect to concentration, presence of serum, temperature, and time. We also used CAPA to investigate structure-penetration relationships for bioactive stapled peptides and peptides fused to cell-penetrating sequences. CAPA is not only limited to measuring cytosolic penetration. Using a cell line where HaloTag is localized to the nucleus, we show quantitative measurement of nuclear penetration. Going forward, CAPA will be a valuable method for measuring and optimizing the cell penetration of biotherapeutics.
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Affiliation(s)
- Leila Peraro
- Department of Chemistry, Tufts University, Medford, MA 02155
| | | | | | - Zhongju Zou
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75230
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75230
| | - Haydn L. Ball
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75230
| | - Beth Levine
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75230
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75230
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75230
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31
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Ballantine RD, Li YX, Qian PY, Cochrane SA. Rational design of new cyclic analogues of the antimicrobial lipopeptide tridecaptin A 1. Chem Commun (Camb) 2018; 54:10634-10637. [PMID: 30179243 PMCID: PMC6146376 DOI: 10.1039/c8cc05790g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyclization of tridecaptin A1 imparts stability to the d-peptidase TriF.
Non-ribosomal peptides (NRPs) are a rich source of antibiotic candidates. However, it was recently discovered that resistance to NRPs can be mediated by d-stereoselective peptidases. The tridecaptins, a class of NRPs that selectively target Gram-negative bacteria, are degraded by the d-peptidase TriF. Through analysis of a solution NMR structure of tridecaptin A1, we have rationally synthesized new cyclic tridecaptin analogues that retain strong antimicrobial activity and are resistant to TriF.
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Affiliation(s)
- Ross D Ballantine
- School of Chemistry and Chemical Engineering, David Keir Building, Stranmillis Road, Queen's University Belfast, Belfast BT9 5AG, UK.
| | - Yong-Xin Li
- Department of Ocean Science and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Pei-Yuan Qian
- Department of Ocean Science and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Stephen A Cochrane
- School of Chemistry and Chemical Engineering, David Keir Building, Stranmillis Road, Queen's University Belfast, Belfast BT9 5AG, UK.
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32
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Richardson SL, Dods KK, Abrigo NA, Iqbal ES, Hartman MC. In vitro genetic code reprogramming and expansion to study protein function and discover macrocyclic peptide ligands. Curr Opin Chem Biol 2018; 46:172-179. [PMID: 30077877 DOI: 10.1016/j.cbpa.2018.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 05/02/2018] [Accepted: 07/13/2018] [Indexed: 01/26/2023]
Abstract
The ability to introduce non-canonical amino acids into peptides and proteins is facilitated by working within in vitro translation systems. Non-canonical amino acids can be introduced into these systems using sense codon reprogramming, stop codon suppression, and by breaking codon degeneracy. Here, we review how these techniques have been used to create proteins with novel properties and how they facilitate sophisticated studies of protein function. We also discuss how researchers are using in vitro translation experiments with non-canonical amino acids to explore the tolerance of the translation apparatus to artificial building blocks. Finally, we give several examples of how non-canonical amino acids can be combined with mRNA-displayed peptide libraries for the creation of protease-stable, macrocyclic peptide libraries for ligand discovery.
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Affiliation(s)
- Stacie L Richardson
- Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, USA; Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, USA
| | - Kara K Dods
- Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, USA; Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, USA
| | - Nicolas A Abrigo
- Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, USA; Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, USA
| | - Emil S Iqbal
- Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, USA; Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, USA
| | - Matthew Ct Hartman
- Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, USA; Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, USA.
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33
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St. Louis LE, Rodriguez TM, Waters ML. A study of 2-component i, i + 3 peptide stapling using thioethers. Bioorg Med Chem 2018; 26:1203-1205. [DOI: 10.1016/j.bmc.2017.10.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/20/2017] [Accepted: 10/28/2017] [Indexed: 10/18/2022]
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34
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Thioether-stapled macrocyclic inhibitors of the EH domain of EHD1. Bioorg Med Chem 2017; 26:1206-1211. [PMID: 28951093 DOI: 10.1016/j.bmc.2017.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/31/2017] [Accepted: 09/06/2017] [Indexed: 11/24/2022]
Abstract
Recycling of receptors from the endosomal recycling compartment to the plasma membrane is a critical cellular process, and recycling is particularly important for maintaining invasiveness in solid tumors. In this work, we continue our efforts to inhibit EHD1, a critical adaptor protein involved in receptor recycling. We applied a diversity-oriented macrocyclization approach to produce cyclic peptides with varied conformations, but that each contain a motif that binds to the EH domain of EHD1. Screening these uncovered several new inhibitors for EHD1's EH domain, the most potent of which bound with a Kd of 3.1μM. Several of the most potent inhibitors were tested in a cellular assay that measures extent of vesicle recycling. Inhibiting EHD1 could potentially slow cancer invasiveness and metastasis, and these cyclic peptides represent the most potent inhibitors of EHD1 to date.
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35
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Peraro L, Zou Z, Makwana KM, Cummings AE, Ball HL, Yu H, Lin YS, Levine B, Kritzer JA. Diversity-Oriented Stapling Yields Intrinsically Cell-Penetrant Inducers of Autophagy. J Am Chem Soc 2017; 139:7792-7802. [PMID: 28414223 PMCID: PMC5473019 DOI: 10.1021/jacs.7b01698] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Autophagy
is an essential pathway by which cellular and foreign
material are degraded and recycled in eukaryotic cells. Induction
of autophagy is a promising approach for treating diverse human diseases,
including neurodegenerative disorders and infectious diseases. Here,
we report the use of a diversity-oriented stapling approach to produce
autophagy-inducing peptides that are intrinsically cell-penetrant.
These peptides induce autophagy at micromolar concentrations in vitro,
have aggregate-clearing activity in a cellular model of Huntington’s
disease, and induce autophagy in vivo. Unexpectedly, the solution
structure of the most potent stapled peptide, DD5-o, revealed an α-helical
conformation in methanol, stabilized by an unusual (i,i+3) staple which cross-links two d-amino
acids. We also developed a novel assay for cell penetration that reports
exclusively on cytosolic access and used it to quantitatively compare
the cell penetration of DD5-o and other autophagy-inducing peptides.
These new, cell-penetrant autophagy inducers and their molecular details
are critical advances in the effort to understand and control autophagy.
More broadly, diversity-oriented stapling may provide a promising
alternative to polycationic sequences as a means for rendering peptides
more cell-penetrant.
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Affiliation(s)
- Leila Peraro
- Department of Chemistry, Tufts University , Medford, Massachusetts 02155, United States
| | | | - Kamlesh M Makwana
- Department of Chemistry, Tufts University , Medford, Massachusetts 02155, United States
| | - Ashleigh E Cummings
- Department of Chemistry, Tufts University , Medford, Massachusetts 02155, United States
| | | | - Hongtao Yu
- Department of Chemistry, Tufts University , Medford, Massachusetts 02155, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University , Medford, Massachusetts 02155, United States
| | | | - Joshua A Kritzer
- Department of Chemistry, Tufts University , Medford, Massachusetts 02155, United States
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