1
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Saidjalolov S, Coelho F, Mercier V, Moreau D, Matile S. Inclusive Pattern Generation Protocols to Decode Thiol-Mediated Uptake. ACS CENTRAL SCIENCE 2024; 10:1033-1043. [PMID: 38799667 PMCID: PMC11117725 DOI: 10.1021/acscentsci.3c01601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 05/29/2024]
Abstract
Thiol-mediated uptake (TMU) is an intriguing enigma in current chemistry and biology. While the appearance of cell-penetrating activity upon attachment of cascade exchangers (CAXs) has been observed by many and is increasingly being used in practice, the molecular basis of TMU is essentially unknown. The objective of this study was to develop a general protocol to decode the dynamic covalent networks that presumably account for TMU. Uptake inhibition patterns obtained from the removal of exchange partners by either protein knockdown or alternative inhibitors are aligned with original patterns generated by CAX transporters and inhibitors and patterns from alternative functions (here cell motility). These inclusive TMU patterns reveal that the four most significant CAXs known today enter cells along three almost orthogonal pathways. Epidithiodiketopiperazines (ETP) exchange preferably with integrins and protein disulfide isomerases (PDIs), benzopolysulfanes (BPS) with different PDIs, presumably PDIA3, and asparagusic acid (AspA), and antisense oligonucleotide phosphorothioates (OPS) exchange with the transferrin receptor and can be activated by the removal of PDIs with their respective inhibitors. These findings provide a solid basis to understand and use TMU to enable and prevent entry into cells.
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Affiliation(s)
| | - Filipe Coelho
- Department
of Organic Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | - Vincent Mercier
- Department
of Biochemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | - Dimitri Moreau
- Department
of Biochemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | - Stefan Matile
- Department
of Organic Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
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2
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Lamouroux A, Tournier M, Iaculli D, Caufriez A, Rusiecka OM, Martin C, Bes V, Carpio LE, Girardin Y, Loris R, Tabernilla A, Molica F, Gozalbes R, Mayán MD, Vinken M, Kwak BR, Ballet S. Structure-Based Design and Synthesis of Stapled 10Panx1 Analogues for Use in Cardiovascular Inflammatory Diseases. J Med Chem 2023; 66:13086-13102. [PMID: 37703077 PMCID: PMC10544015 DOI: 10.1021/acs.jmedchem.3c01116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Indexed: 09/14/2023]
Abstract
Following a rational design, a series of macrocyclic ("stapled") peptidomimetics of 10Panx1, the most established peptide inhibitor of Pannexin1 (Panx1) channels, were developed and synthesized. Two macrocyclic analogues SBL-PX1-42 and SBL-PX1-44 outperformed the linear native peptide. During in vitro adenosine triphosphate (ATP) release and Yo-Pro-1 uptake assays in a Panx1-expressing tumor cell line, both compounds were revealed to be promising bidirectional inhibitors of Panx1 channel function, able to induce a two-fold inhibition, as compared to the native 10Panx1 sequence. The introduction of triazole-based cross-links within the peptide backbones increased helical content and enhanced in vitro proteolytic stability in human plasma (>30-fold longer half-lives, compared to 10Panx1). In adhesion assays, a "double-stapled" peptide, SBL-PX1-206 inhibited ATP release from endothelial cells, thereby efficiently reducing THP-1 monocyte adhesion to a TNF-α-activated endothelial monolayer and making it a promising candidate for future in vivo investigations in animal models of cardiovascular inflammatory disease.
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Affiliation(s)
- Arthur Lamouroux
- Research
Group of Organic Chemistry, Departments of Chemistry and Bioengineering
Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Malaury Tournier
- Department
of Pathology and Immunology and Geneva Center for Inflammation Research,
Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
| | - Debora Iaculli
- Research
Group of Organic Chemistry, Departments of Chemistry and Bioengineering
Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Anne Caufriez
- Research
Group of Organic Chemistry, Departments of Chemistry and Bioengineering
Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Research
Unit of In Vitro Toxicology and Dermato-Cosmetology, Department of
Pharmaceutical Sciences, Vrije Universiteit
Brussel, Laarbeeklaan
103, 1090 Brussels, Belgium
| | - Olga M. Rusiecka
- Department
of Pathology and Immunology and Geneva Center for Inflammation Research,
Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
| | - Charlotte Martin
- Research
Group of Organic Chemistry, Departments of Chemistry and Bioengineering
Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Viviane Bes
- Department
of Pathology and Immunology and Geneva Center for Inflammation Research,
Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
| | - Laureano E. Carpio
- ProtoQSAR
SL, Centro Europeo de Empresas Innovadoras, Parque Tecnológico de Valencia, Avda. Benjamin Franklin 12, 46980 Paterna, Spain
| | - Yana Girardin
- Structural
Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Centre for
Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Remy Loris
- Structural
Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Centre for
Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Andrés Tabernilla
- Research
Unit of In Vitro Toxicology and Dermato-Cosmetology, Department of
Pharmaceutical Sciences, Vrije Universiteit
Brussel, Laarbeeklaan
103, 1090 Brussels, Belgium
| | - Filippo Molica
- Department
of Pathology and Immunology and Geneva Center for Inflammation Research,
Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
| | - Rafael Gozalbes
- ProtoQSAR
SL, Centro Europeo de Empresas Innovadoras, Parque Tecnológico de Valencia, Avda. Benjamin Franklin 12, 46980 Paterna, Spain
- MolDrug
AI Systems SL, c/Olimpia
Arozena 45, 46018 Valencia, Spain
| | - María D. Mayán
- CellCOM
Research Group, Instituto de Investigación Biomédica
de A Coruña, Servizo Galego de Saúde, Universidade da Coruña, 15071 A Coruña, Spain
| | - Mathieu Vinken
- Research
Unit of In Vitro Toxicology and Dermato-Cosmetology, Department of
Pharmaceutical Sciences, Vrije Universiteit
Brussel, Laarbeeklaan
103, 1090 Brussels, Belgium
| | - Brenda R. Kwak
- Department
of Pathology and Immunology and Geneva Center for Inflammation Research,
Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
| | - Steven Ballet
- Research
Group of Organic Chemistry, Departments of Chemistry and Bioengineering
Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
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3
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Bartling CRO, Alexopoulou F, Kuschert S, Chin YKY, Jia X, Sereikaite V, Özcelik D, Jensen TM, Jain P, Nygaard MM, Harpsøe K, Gloriam DE, Mobli M, Strømgaard K. Comprehensive Peptide Cyclization Examination Yields Optimized APP Scaffolds with Improved Affinity toward Mint2. J Med Chem 2023; 66:3045-3057. [PMID: 36749163 DOI: 10.1021/acs.jmedchem.2c02017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Peptides targeting disease-relevant protein-protein interactions are an attractive class of therapeutics covering the otherwise undruggable space between small molecules and therapeutic proteins. However, peptides generally suffer from poor metabolic stability and low membrane permeability. Hence, peptide cyclization has become a valuable approach to develop linear peptide motifs into metabolically stable and potentially cell-permeable cyclic leads. Furthermore, cyclization of side chains, also known as "stapling", can stabilize particular secondary peptide structures. Here, we demonstrate that a comprehensive examination of cyclization strategies in terms of position, chemistry, and length is a prerequisite for the selection of optimal cyclic peptide scaffolds. Our systematic approach identifies cyclic APP dodecamer peptides targeting the phosphotyrosine binding domain of Mint2 with substantially improved affinity. We show that especially all-hydrocarbon stapling provides improved metabolic stability, a significantly stabilized secondary structure and membrane permeability.
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Affiliation(s)
- Christian R O Bartling
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - Flora Alexopoulou
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - Sarah Kuschert
- Center for Advanced Imaging, University of Queensland, St. Lucia, 4072Queensland, Australia
| | - Yanni K-Y Chin
- Center for Advanced Imaging, University of Queensland, St. Lucia, 4072Queensland, Australia
| | - Xinying Jia
- Center for Advanced Imaging, University of Queensland, St. Lucia, 4072Queensland, Australia
| | - Vita Sereikaite
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - Dennis Özcelik
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - Thomas M Jensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - Palash Jain
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - Mads M Nygaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - Kasper Harpsøe
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - Mehdi Mobli
- Center for Advanced Imaging, University of Queensland, St. Lucia, 4072Queensland, Australia
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
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4
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Çetiner E, Sayın K, Ünal Y. Optimization, spectral characterization, QSAR, and molecular docking analyses of newly designed boron compounds. Struct Chem 2022. [DOI: 10.1007/s11224-022-02086-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Negi A, Kesari KK, Voisin-Chiret AS. Estrogen Receptor-α Targeting: PROTACs, SNIPERs, Peptide-PROTACs, Antibody Conjugated PROTACs and SNIPERs. Pharmaceutics 2022; 14:pharmaceutics14112523. [PMID: 36432713 PMCID: PMC9699327 DOI: 10.3390/pharmaceutics14112523] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Targeting selective estrogen subtype receptors through typical medicinal chemistry approaches is based on occupancy-driven pharmacology. In occupancy-driven pharmacology, molecules are developed in order to inhibit the protein of interest (POI), and their popularity is based on their virtue of faster kinetics. However, such approaches have intrinsic flaws, such as pico-to-nanomolar range binding affinity and continuous dosage after a time interval for sustained inhibition of POI. These shortcomings were addressed by event-driven pharmacology-based approaches, which degrade the POI rather than inhibit it. One such example is PROTACs (Proteolysis targeting chimeras), which has become one of the highly successful strategies of event-driven pharmacology (pharmacology that does the degradation of POI and diminishes its functions). The selective targeting of estrogen receptor subtypes is always challenging for chemical biologists and medicinal chemists. Specifically, estrogen receptor α (ER-α) is expressed in nearly 70% of breast cancer and commonly overexpressed in ovarian, prostate, colon, and endometrial cancer. Therefore, conventional hormonal therapies are most prescribed to patients with ER + cancers. However, on prolonged use, resistance commonly developed against these therapies, which led to selective estrogen receptor degrader (SERD) becoming the first-line drug for metastatic ER + breast cancer. The SERD success shows that removing cellular ER-α is a promising approach to overcoming endocrine resistance. Depending on the mechanism of degradation of ER-α, various types of strategies of developed.
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Affiliation(s)
- Arvind Negi
- Department of Bioproduct and Biosystems, Aalto University, 00076 Espoo, Finland
- Correspondence: or (A.N.); or (K.K.K.); (A.S.V.-C.)
| | - Kavindra Kumar Kesari
- Department of Bioproduct and Biosystems, Aalto University, 00076 Espoo, Finland
- Department of Applied Physics, School of Science, Aalto University, 02150 Espoo, Finland
- Correspondence: or (A.N.); or (K.K.K.); (A.S.V.-C.)
| | - Anne Sophie Voisin-Chiret
- CERMN (Centre d’Etudes et de Recherche sur le Médicament de Normandie), Normandie University UNICAEN, 14000 Caen, France
- Correspondence: or (A.N.); or (K.K.K.); (A.S.V.-C.)
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6
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Helical Foldamers and Stapled Peptides as New Modalities in Drug Discovery: Modulators of Protein-Protein Interactions. Processes (Basel) 2022. [DOI: 10.3390/pr10050924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A “foldamer” is an artificial oligomeric molecule with a regular secondary or tertiary structure consisting of various building blocks. A “stapled peptide” is a peptide with stabilized secondary structures, in particular, helical structures by intramolecular covalent side-chain cross-linking. Helical foldamers and stapled peptides are potential drug candidates that can target protein-protein interactions because they enable multipoint molecular recognition, which is difficult to achieve with low-molecular-weight compounds. This mini-review describes a variety of peptide-based foldamers and stapled peptides with a view to their applications in drug discovery, including our recent progress.
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7
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Islam MS, Junod SL, Zhang S, Buuh ZY, Guan Y, Zhao M, Kaneria KH, Kafley P, Cohen C, Maloney R, Lyu Z, Voelz VA, Yang W, Wang RE. Unprotected peptide macrocyclization and stapling via a fluorine-thiol displacement reaction. Nat Commun 2022; 13:350. [PMID: 35039490 PMCID: PMC8763920 DOI: 10.1038/s41467-022-27995-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/19/2021] [Indexed: 12/31/2022] Open
Abstract
We report the discovery of a facile peptide macrocyclization and stapling strategy based on a fluorine thiol displacement reaction (FTDR), which renders a class of peptide analogues with enhanced stability, affinity, cellular uptake, and inhibition of cancer cells. This approach enabled selective modification of the orthogonal fluoroacetamide side chains in unprotected peptides in the presence of intrinsic cysteines. The identified benzenedimethanethiol linker greatly promoted the alpha helicity of a variety of peptide substrates, as corroborated by molecular dynamics simulations. The cellular uptake of benzenedimethanethiol stapled peptides appeared to be universally enhanced compared to the classic ring-closing metathesis (RCM) stapled peptides. Pilot mechanism studies suggested that the uptake of FTDR-stapled peptides may involve multiple endocytosis pathways in a distinct pattern in comparison to peptides stapled by RCM. Consistent with the improved cell permeability, the FTDR-stapled lead Axin and p53 peptide analogues demonstrated enhanced inhibition of cancer cells over the RCM-stapled analogues and the unstapled peptides. Strategies capable of stapling unprotected peptides in a straightforward, chemoselective, and clean manner, as well as promoting cellular uptake are of great interest. Here the authors report a peptide macrocyclization and stapling strategy which satisfies those criteria, based on a fluorine thiol displacement reaction.
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Affiliation(s)
- Md Shafiqul Islam
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Samuel L Junod
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Si Zhang
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Zakey Yusuf Buuh
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Yifu Guan
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Mi Zhao
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Kishan H Kaneria
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Parmila Kafley
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Carson Cohen
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Robert Maloney
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Zhigang Lyu
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Vincent A Voelz
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Weidong Yang
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Rongsheng E Wang
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA.
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8
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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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9
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Yokoo H, Ohoka N, Takyo M, Ito T, Tsuchiya K, Kurohara T, Fukuhara K, Inoue T, Naito M, Demizu Y. Peptide Stapling Improves the Sustainability of a Peptide-Based Chimeric Molecule That Induces Targeted Protein Degradation. Int J Mol Sci 2021; 22:ijms22168772. [PMID: 34445478 PMCID: PMC8396023 DOI: 10.3390/ijms22168772] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 12/31/2022] Open
Abstract
Peptide-based target protein degradation inducers called PROTACs/SNIPERs have low cell penetrability and poor intracellular stability as drawbacks. These shortcomings can be overcome by easily modifying these peptides by conjugation with cell penetrating peptides and side-chain stapling. In this study, we succeeded in developing the stapled peptide stPERML-R7, which is based on the estrogen receptor alpha (ERα)-binding peptide PERML and composed of natural amino acids. stPERML-R7, which includes a hepta-arginine motif and a hydrocarbon stapling moiety, showed increased α-helicity and similar binding affinity toward ERα when compared with those of the parent peptide PERML. Furthermore, we used stPERML-R7 to develop a peptide-based degrader LCL-stPERML-R7 targeting ERα by conjugating stPERML-R7 with a small molecule LCL161 (LCL) that recruits the E3 ligase IAPs to induce proteasomal degradation via ubiquitylation. The chimeric peptide LCL-stPERML-R7 induced sustained degradation of ERα and potently inhibited ERα-mediated transcription more effectively than the unstapled chimera LCL-PERML-R7. These results suggest that a stapled structure is effective in maintaining the intracellular activity of peptide-based degraders.
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Affiliation(s)
- Hidetomo Yokoo
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Kanagawa 210-9501, Japan; (H.Y.); (M.T.); (T.I.); (K.T.); (T.K.)
- Medical Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 606-0823, Japan
| | - Nobumichi Ohoka
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Kanagawa 210-9501, Japan; (N.O.); (T.I.)
| | - Mami Takyo
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Kanagawa 210-9501, Japan; (H.Y.); (M.T.); (T.I.); (K.T.); (T.K.)
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Takahito Ito
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Kanagawa 210-9501, Japan; (H.Y.); (M.T.); (T.I.); (K.T.); (T.K.)
| | - Keisuke Tsuchiya
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Kanagawa 210-9501, Japan; (H.Y.); (M.T.); (T.I.); (K.T.); (T.K.)
- Graduate School of Pharmacy, Showa University, Tokyo 142-0064, Japan;
| | - Takashi Kurohara
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Kanagawa 210-9501, Japan; (H.Y.); (M.T.); (T.I.); (K.T.); (T.K.)
| | - Kiyoshi Fukuhara
- Graduate School of Pharmacy, Showa University, Tokyo 142-0064, Japan;
| | - Takao Inoue
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Kanagawa 210-9501, Japan; (N.O.); (T.I.)
| | - Mikihiko Naito
- Laboratory of Targeted Protein Degradation, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan;
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Kanagawa 210-9501, Japan; (H.Y.); (M.T.); (T.I.); (K.T.); (T.K.)
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
- Correspondence: ; Tel.: +81-44-270-6578
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10
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Kandler R, Das S, Nag A. Copper-ligand clusters dictate size of cyclized peptide formed during alkyne-azide cycloaddition on solid support. RSC Adv 2021; 11:4842-4852. [PMID: 34377440 PMCID: PMC8351437 DOI: 10.1039/d0ra07491h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Peptide and peptidomimetic cyclization by copper-catalyzed alkyne-azide cycloaddition (CuAAC) reaction have been used to mimic disulfide bonds, alpha helices, amide bonds, and for one-bead-one-compound (OBOC) library development. A limited number of solid-supported CuAAC cyclization methods resulting in monomeric cyclic peptide formation have been reported for specific peptide sequences, but there exists no general study on monocyclic peptide formation using CuAAC cyclization. Since several cyclic peptides identified from an OBOC CuAAC cyclized library has been shown to have important biological applications, we discuss here an efficient method of alkyne-azide 'click' catalyzed monomeric cyclic peptide formation on a solid support. The reason behind the efficiency of the method is explored. CuAAC cyclization of a peptide sequence with azidolysine and propargylglycine is performed under various reaction conditions, with different catalysts, in the presence or absence of an organic base. The results indicate that piperidine plays a critical role in the reaction yield and monomeric cycle formation by coordinating to Cu and forming Cu-ligand clusters. A previously synthesized copper compound containing piperidine, [Cu4I4(pip)4], is found to catalyze the CuAAC cyclization of monomeric peptide effectively. The use of 1.5 equivalents of CuI and the use of DMF as solvent is found to give optimal CuAAC cyclized monomer yields. The effect of the peptide sequence and peptide length on monomer formation are also investigated by varying either parameter systemically. Peptide length is identified as the determining factor for whether the monomeric or dimeric cyclic peptide is the major product. For peptides with six, seven, or eight amino acids, the monomer is the major product from CuAAC cyclization. Longer and shorter peptides on cyclization show less monomer formation. CuAAC peptide cyclization of non-optimal peptide lengths such as pentamers is affected significantly by the amino acid sequence and give lower yields.
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Affiliation(s)
- Rene Kandler
- Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA 01610, USA
| | - Samir Das
- Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA 01610, USA
| | - Arundhati Nag
- Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA 01610, USA
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11
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Ahangarpour M, Kavianinia I, Harris PWR, Brimble MA. Photo-induced radical thiol-ene chemistry: a versatile toolbox for peptide-based drug design. Chem Soc Rev 2021; 50:898-944. [PMID: 33404559 DOI: 10.1039/d0cs00354a] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While the global market for peptide/protein-based therapeutics is witnessing significant growth, the development of peptide drugs remains challenging due to their low oral bioavailability, poor membrane permeability, and reduced metabolic stability. However, a toolbox of chemical approaches has been explored for peptide modification to overcome these obstacles. In recent years, there has been a revival of interest in photoinduced radical thiol-ene chemistry as a powerful tool for the construction of therapeutic peptides.
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Affiliation(s)
- Marzieh Ahangarpour
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand.
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12
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Raynal L, Rose NC, Donald JR, Spicer CD. Photochemical Methods for Peptide Macrocyclisation. Chemistry 2021; 27:69-88. [PMID: 32914455 PMCID: PMC7821122 DOI: 10.1002/chem.202003779] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/10/2020] [Indexed: 12/19/2022]
Abstract
Photochemical reactions have been the subject of renewed interest over the last two decades, leading to the development of many new, diverse and powerful chemical transformations. More recently, these developments have been expanded to enable the photochemical macrocyclisation of peptides and small proteins. These constructs benefit from increased stability, structural rigidity and biological potency over their linear counterparts, providing opportunities for improved therapeutic agents. In this review, an overview of both the established and emerging methods for photochemical peptide macrocyclisation is presented, highlighting both the limitations and opportunities for further innovation in the field.
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Affiliation(s)
- Laetitia Raynal
- Department of ChemistryUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Nicholas C. Rose
- Department of ChemistryUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - James R. Donald
- Department of ChemistryUniversity of YorkHeslingtonYorkYO10 5DDUK
- York Biomedical Research InstituteUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Christopher D. Spicer
- Department of ChemistryUniversity of YorkHeslingtonYorkYO10 5DDUK
- York Biomedical Research InstituteUniversity of YorkHeslingtonYorkYO10 5DDUK
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13
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Liu Y, Hu K, Yin F, Li Z. Facile Chemoselective Modification of Thioethers Generates Chiral Center-Induced Helical Peptides. Methods Mol Biol 2021; 2355:301-322. [PMID: 34386967 DOI: 10.1007/978-1-0716-1617-8_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The modulation of protein-protein interactions (PPIs) is a promising way for interrogating disease. Stapled peptides that stabilize peptides into a fixed α-helical conformation via chemical means are important representative compounds for regulating PPIs. The effect of the secondary conformation of peptides on the biophysical properties has not been explicitly elucidated due to the difficulty of obtaining peptide epimers with the same chemical composition but different conformations. Herein, we systematically designed and demonstrated the concept of "Chiral Center-Induced Helicity" (CIH) to stabilize the secondary structure of peptides. By introducing a precise R-configuration chiral center on the side-ring of a peptide, researchers can decisively regulate the secondary structure of peptides. Through the study of CIH peptides, we found that increasing the helicity can significantly enhance the stability of peptides and improve the cell membrane penetrating capability of the peptides. Moreover, the substitution group in the chiral center could contribute to additional interactions with the binding groove, which shows great significance for fragment-based drug design. This chapter will focus on the method involved in this research, including specific protocols of the synthesis and basic characterization of CIH peptides in Subheading 3.1. In addition, we have also extended the concept of CIH to dual-chiral center systems, including sulfoxide-based and sulfonium-based in-tether chiral center peptides, which we will introduce in Subheadings 3.2 and 3.3.
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Affiliation(s)
- Yinghuan Liu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Kuan Hu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Feng Yin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, China.
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14
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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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15
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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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16
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Jin J, Wu Y, Chen J, Shen Y, Zhang L, Zhang H, Chen L, Yuan H, Chen H, Zhang W, Luan X. The peptide PROTAC modality: a novel strategy for targeted protein ubiquitination. Theranostics 2020; 10:10141-10153. [PMID: 32929339 PMCID: PMC7481416 DOI: 10.7150/thno.46985] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/30/2020] [Indexed: 02/07/2023] Open
Abstract
Despite dramatic advances in drug discovery over the decades, effective therapeutic strategies for cancers treatment are still in urgent demands. PROteolysis TArgeting Chimera (PROTAC), a novel therapeutic modality, has been vigorously promoted in preclinical and clinical applications. Unlike small molecule PROTAC, peptide PROTAC (p-PROTAC) with advantages of high specificity and low toxicity, while avoiding the limitations of shallow binding pockets through large interacting surfaces, provides promising substitutions for E3 ubiquitin ligase complex-mediated ubiquitination of "undruggable proteins". It is worth noting that successful applications of p-PROTAC still have some obstacles, including low stability and poor membrane permeability. Hence, we highlight that p-PROTAC combined with cell-penetrating peptides, constrained conformation technique, and targeted delivery systems could be the future efforts for potential translational research.
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Affiliation(s)
- Jinmei Jin
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ye Wu
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jinjiao Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yiwen Shen
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lijun Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hong Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lili Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hebao Yuan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109 US
| | - Hongzhuan Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Department of Pharmacology and Chemical Biology, Shanghai Universities Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Weidong Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xin Luan
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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17
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Yokoo H, Ohoka N, Naito M, Demizu Y. Design and synthesis of peptide-based chimeric molecules to induce degradation of the estrogen and androgen receptors. Bioorg Med Chem 2020; 28:115595. [PMID: 32631565 DOI: 10.1016/j.bmc.2020.115595] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 01/12/2023]
Abstract
Peptide-based inducers of estrogen receptor (ER) α and androgen receptor (AR) degradations via the ubiquitin-proteasome system (UPS) were developed. The designated inducers were composed of two biologically active scaffolds: the helical peptide PERM3, which is an LXXLL-like mimic of the coactivator SRC-1, and various small molecules (MV1, LCL161, VH032, and POM) that bind to E3 ligases (IAPs, VHL, and cereblon, respectively), to induce ubiquitylation of nuclear receptors that bind to SRC-1. All of the synthesized chimeric E3 ligand-containing molecules induced the UPS-mediated degradation of ERα and AR. The PERM3 peptide was applicable for the development of the ERα and AR degraders using these E3 ligands.
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Affiliation(s)
- Hidetomo Yokoo
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan; Graduate School of Medical Health Sciences, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Nobumichi Ohoka
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Mikihiko Naito
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Yosuke Demizu
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan; Graduate School of Medical Health Sciences, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan.
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18
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Hetherington K, Hegedus Z, Edwards TA, Sessions RB, Nelson A, Wilson AJ. Stapled Peptides as HIF-1α/p300 Inhibitors: Helicity Enhancement in the Bound State Increases Inhibitory Potency. Chemistry 2020; 26:7638-7646. [PMID: 32307728 PMCID: PMC7318359 DOI: 10.1002/chem.202000417] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/13/2020] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions (PPIs) control virtually all cellular processes and have thus emerged as potential targets for development of molecular therapeutics. Peptide-based inhibitors of PPIs are attractive given that they offer recognition potency and selectivity features that are ideal for function, yet, they do not predominantly populate the bioactive conformation, frequently suffer from poor cellular uptake and are easily degraded, for example, by proteases. The constraint of peptides in a bioactive conformation has emerged as a promising strategy to mitigate against these liabilities. In this work, using peptides derived from hypoxia-inducible factor 1 (HIF-1α) together with dibromomaleimide stapling, we identify constrained peptide inhibitors of the HIF-1α/p300 interaction that are more potent than their unconstrained sequences. Contrary to expectation, the increased potency does not correlate with an increased population of an α-helical conformation in the unbound state as demonstrated by experimental circular dichroism analysis. Rather, the ability of the peptide to adopt a bioactive α-helical conformation in the p300 bound state is better supported in the constrained variant as demonstrated by molecular dynamics simulations and circular dichroism difference spectra.
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Affiliation(s)
- Kristina Hetherington
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Zsofia Hegedus
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Thomas A. Edwards
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Richard B. Sessions
- School of BiochemistryUniversity of BristolMedical Sciences Building, University WalkBristolBS8 1TDUK
- BrisSynBioUniversity of Bristol, Life Sciences BuildingTyndall AvenueBristolBS8 1TQUK
| | - Adam Nelson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Andrew J. Wilson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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19
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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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20
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Jeganathan S, Wendt M, Kiehstaller S, Brancaccio D, Kuepper A, Pospiech N, Carotenuto A, Novellino E, Hennig S, Grossmann TN. Constrained Peptides with Fine‐Tuned Flexibility Inhibit NF‐Y Transcription Factor Assembly. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sadasivam Jeganathan
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
| | - Mathias Wendt
- Department of Chemistry and Pharmaceutical SciencesVU University Amsterdam De Boelelaan 1083 1081 HZ Amsterdam The Netherlands
| | - Sebastian Kiehstaller
- Department of Chemistry and Pharmaceutical SciencesVU University Amsterdam De Boelelaan 1083 1081 HZ Amsterdam The Netherlands
| | - Diego Brancaccio
- Department of PharmacyUniversity of Naples “Federico II” Via D. Montesano 49, 80131 Naples Italy
| | - Arne Kuepper
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
| | - Nicole Pospiech
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
| | - Alfonso Carotenuto
- Department of PharmacyUniversity of Naples “Federico II” Via D. Montesano 49, 80131 Naples Italy
| | - Ettore Novellino
- Department of PharmacyUniversity of Naples “Federico II” Via D. Montesano 49, 80131 Naples Italy
| | - Sven Hennig
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
- Department of Chemistry and Pharmaceutical SciencesVU University Amsterdam De Boelelaan 1083 1081 HZ Amsterdam The Netherlands
| | - Tom N. Grossmann
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
- Department of Chemistry and Pharmaceutical SciencesVU University Amsterdam De Boelelaan 1083 1081 HZ Amsterdam The Netherlands
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21
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Jeganathan S, Wendt M, Kiehstaller S, Brancaccio D, Kuepper A, Pospiech N, Carotenuto A, Novellino E, Hennig S, Grossmann TN. Constrained Peptides with Fine-Tuned Flexibility Inhibit NF-Y Transcription Factor Assembly. Angew Chem Int Ed Engl 2019; 58:17351-17358. [PMID: 31539186 PMCID: PMC6900064 DOI: 10.1002/anie.201907901] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/19/2019] [Indexed: 12/17/2022]
Abstract
Protein complex formation depends on the interplay between preorganization and flexibility of the binding epitopes involved. The design of epitope mimetics typically focuses on stabilizing a particular bioactive conformation, often without considering conformational dynamics, which limits the potential of peptidomimetics against challenging targets such as transcription factors. We developed a peptide-derived inhibitor of the NF-Y transcription factor by first constraining the conformation of an epitope through hydrocarbon stapling and then fine-tuning its flexibility. In the initial set of constrained peptides, a single non-interacting α-methyl group was observed to have a detrimental effect on complex stability. Biophysical characterization revealed how this methyl group affects the conformation of the peptide in its bound state. Adaption of the methylation pattern resulted in a peptide that inhibits transcription factor assembly and subsequent recruitment to the target DNA.
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Affiliation(s)
- Sadasivam Jeganathan
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany
| | - Mathias Wendt
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1083, 1081, HZ, Amsterdam, The Netherlands
| | - Sebastian Kiehstaller
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1083, 1081, HZ, Amsterdam, The Netherlands
| | - Diego Brancaccio
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, 80131, Naples, Italy
| | - Arne Kuepper
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany
| | - Nicole Pospiech
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany
| | - Alfonso Carotenuto
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, 80131, Naples, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, 80131, Naples, Italy
| | - Sven Hennig
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany.,Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1083, 1081, HZ, Amsterdam, The Netherlands
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany.,Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1083, 1081, HZ, Amsterdam, The Netherlands
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22
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Cholesterol-conjugated stapled peptides inhibit Ebola and Marburg viruses in vitro and in vivo. Antiviral Res 2019; 171:104592. [PMID: 31473342 DOI: 10.1016/j.antiviral.2019.104592] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 08/22/2019] [Accepted: 08/25/2019] [Indexed: 02/07/2023]
Abstract
Filoviridae currently includes five official and one proposed genera. Genus Ebolavirus includes five established and one proposed ebolavirus species for Bombali virus (BOMV), Bundibugyo virus (BDBV), Ebola virus (EBOV), Reston virus (RESTV), Sudan virus (SUDV) and Taï Forest virus (TAFV), and genus Marburgvirus includes a single species for Marburg virus (MARV) and Ravn virus (RAVV). Ebola virus (EBOV) has emerged as a significant public health concern since the 2013-2016 Ebola Virus Disease outbreak in Western Africa. Currently, there are no therapeutics approved and the need for Ebola-specific therapeutics remains a gap. In search for anti-Ebola therapies we tested the idea of using inhibitory properties of peptides corresponding to the C-terminal heptad-repeat (HR2) domains of class I fusion proteins against EBOV infection. The fusion protein GP2 of EBOV belongs to class I, suggesting that a similar strategy to HIV may be applied to inhibit EBOV infection. The serum half-life of peptides was expanded by cholesterol conjugation to allow daily dosing. The peptides were further constrained to stabilize a helical structure to increase the potency of inhibition. The EC50s of lead peptides were in low micromolar range, as determined by a high-content imaging test of EBOV-infected cells. Lead peptides were tested in an EBOV lethal mouse model and efficacy of the peptides were determined following twice-daily administration of peptides for 9 days. The most potent peptide was able to protect mice from lethal challenge of mouse-adapted Ebola virus. These data show that engineered peptides coupled with cholesterol can inhibit viral production, protect mice against lethal EBOV infection, and may be used to build novel therapeutics against EBOV.
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23
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Skowron KJ, Booker K, Cheng C, Creed S, David BP, Lazzara PR, Lian A, Siddiqui Z, Speltz TE, Moore TW. Steroid receptor/coactivator binding inhibitors: An update. Mol Cell Endocrinol 2019; 493:110471. [PMID: 31163202 PMCID: PMC6645384 DOI: 10.1016/j.mce.2019.110471] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/30/2019] [Accepted: 05/30/2019] [Indexed: 12/14/2022]
Abstract
The purpose of this review is to highlight recent developments in small molecules and peptides that block the binding of coactivators to steroid receptors. These coactivator binding inhibitors bind at the coregulator binding groove, also known as Activation Function-2, rather than at the ligand-binding site of steroid receptors. Steroid receptors that have been targeted with coactivator binding inhibitors include the androgen receptor, estrogen receptor and progesterone receptor. Coactivator binding inhibitors may be useful in some cases of resistance to currently prescribed therapeutics. The scope of the review includes small-molecule and peptide coactivator binding inhibitors for steroid receptors, with a particular focus on recent compounds that have been assayed in cell-based models.
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Affiliation(s)
- Kornelia J Skowron
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Kenneth Booker
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Changfeng Cheng
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Simone Creed
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Brian P David
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Phillip R Lazzara
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Amy Lian
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Zamia Siddiqui
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Thomas E Speltz
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA; Department of Chemistry, University of Chicago, 929 E. 57th Street, E547, Chicago, IL, 60637, USA
| | - Terry W Moore
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA; University of Illinois Cancer Center, University of Illinois at Chicago, 1801 W. Taylor Street, Chicago, IL, 60612, USA.
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24
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Ganeshpurkar A, Swetha R, Kumar D, Gangaram GP, Singh R, Gutti G, Jana S, Kumar D, Kumar A, Singh SK. Protein-Protein Interactions and Aggregation Inhibitors in Alzheimer's Disease. Curr Top Med Chem 2019; 19:501-533. [PMID: 30836921 DOI: 10.2174/1568026619666190304153353] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/31/2018] [Accepted: 11/20/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Alzheimer's Disease (AD), a multifaceted disorder, involves complex pathophysiology and plethora of protein-protein interactions. Thus such interactions can be exploited to develop anti-AD drugs. OBJECTIVE The interaction of dynamin-related protein 1, cellular prion protein, phosphoprotein phosphatase 2A and Mint 2 with amyloid β, etc., studied recently, may have critical role in progression of the disease. Our objective has been to review such studies and their implications in design and development of drugs against the Alzheimer's disease. METHODS Such studies have been reviewed and critically assessed. RESULTS Review has led to show how such studies are useful to develop anti-AD drugs. CONCLUSION There are several PPIs which are current topics of research including Drp1, Aβ interactions with various targets including PrPC, Fyn kinase, NMDAR and mGluR5 and interaction of Mint2 with PDZ domain, etc., and thus have potential role in neurodegeneration and AD. Finally, the multi-targeted approach in AD may be fruitful and opens a new vista for identification and targeting of PPIs in various cellular pathways to find a cure for the disease.
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Affiliation(s)
- Ankit Ganeshpurkar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Rayala Swetha
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Devendra Kumar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Gore P Gangaram
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Ravi Singh
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Gopichand Gutti
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Srabanti Jana
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Dileep Kumar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Ashok Kumar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Sushil K Singh
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
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25
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Malde AK, Hill TA, Iyer A, Fairlie DP. Crystal Structures of Protein-Bound Cyclic Peptides. Chem Rev 2019; 119:9861-9914. [DOI: 10.1021/acs.chemrev.8b00807] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alpeshkumar K. Malde
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Abishek Iyer
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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26
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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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27
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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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28
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Rentier C, Takayama K, Saitoh M, Nakamura A, Ikeyama H, Taguchi A, Taniguchi A, Hayashi Y. Design and synthesis of potent myostatin inhibitory cyclic peptides. Bioorg Med Chem 2019; 27:1437-1443. [PMID: 30777663 DOI: 10.1016/j.bmc.2019.02.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/06/2019] [Accepted: 02/08/2019] [Indexed: 12/29/2022]
Abstract
Myostatin is a negative regulator of skeletal muscle growth and myostatin inhibitors are promising lead compounds against muscle atrophic disorders such as muscular dystrophy. Previously, we published the first report of synthetic myostatin inhibitory 23-mer peptide 1, which was identified from a myostatin precursor-derived prodomain protein. Our structure-activity relationship study afforded the potent inhibitory peptide 3. In this paper, we report an investigation of the synthesis of conformationally-constrained cyclic peptide based on the linear peptide 3. To examine the potency of side chain-to-side chain cyclized peptides, a series of disulfide-, lactam- and diester-bridged derivatives were designed and synthesized, and their myostatin inhibitory activities were evaluated. The diester-bridged peptide (11) displayed potent inhibitory activity with an in vitro IC50 value of 0.26 µM, suggesting that it could serve as a new platform for development of cyclic peptide inhibitors.
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Affiliation(s)
- Cédric Rentier
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Kentaro Takayama
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Mariko Saitoh
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Akari Nakamura
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Hiroaki Ikeyama
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Akihiro Taguchi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Atsuhiko Taniguchi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.
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29
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Skowron KJ, Speltz TE, Moore TW. Recent structural advances in constrained helical peptides. Med Res Rev 2018; 39:749-770. [PMID: 30307621 DOI: 10.1002/med.21540] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 12/20/2022]
Abstract
Given the ubiquity of the ⍺-helix in the proteome, there has been much research in developing mimics of ⍺-helices, and most of this study has been toward developing protein-protein interaction inhibitors. A common strategy for mimicking ⍺-helices has been through the use of constrained, helical peptides. The addition of a constraint typically provides for conformational and proteolytic stability and, in some cases, cell permeability. Some of the most well-known strategies included are lactam formation and hydrocarbon "stapling." Beyond those strategies, there have been many recent advances in developing constrained peptides. The purpose of this review is to highlight recent advances in the development of new helix-stabilizing technologies, constraint diversification strategies, tether diversification strategies, and combination strategies that create new bicyclic helical peptides.
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Affiliation(s)
- Kornelia J Skowron
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Thomas E Speltz
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Terry W Moore
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois.,Translational Oncology Program, University of Illinois Cancer Center, Chicago, Illinois
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30
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Massonnet P, Haler JRN, Upert G, Smargiasso N, Mourier G, Gilles N, Quinton L, De Pauw E. Disulfide Connectivity Analysis of Peptides Bearing Two Intramolecular Disulfide Bonds Using MALDI In-Source Decay. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1995-2002. [PMID: 29987664 DOI: 10.1007/s13361-018-2022-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/07/2018] [Accepted: 06/21/2018] [Indexed: 06/08/2023]
Abstract
Disulfide connectivity in peptides bearing at least two intramolecular disulfide bonds is highly important for the structure and the biological activity of the peptides. In that context, analytical strategies allowing a characterization of the cysteine pairing are of prime interest for chemists, biochemists, and biologists. For that purpose, this study evaluates the potential of MALDI in-source decay (ISD) for characterizing cysteine pairs through the systematic analysis of identical peptides bearing two disulfide bonds, but not the same cysteine connectivity. Three different matrices have been tested in positive and/or in negative mode (1,5-DAN, 2-AB and 2-AA). As MALDI-ISD is known to partially reduce disulfide bonds, the data analysis of this study rests firstly on the deconvolution of the isotope pattern of the parent ions. Moreover, data analysis is also based on the formed fragment ions and their signal intensities. Results from MS/MS-experiments (MALDI-ISD-MS/MS) constitute the last reference for data interpretation. Owing to the combined use of different ISD-promoting matrices, cysteine connectivity identification could be performed on the considered peptides. Graphical Abstract ᅟ.
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Affiliation(s)
- Philippe Massonnet
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium.
| | - Jean R N Haler
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
| | - Gregory Upert
- Commissariat à l'Energie Atomique, DRF/SIMOPRO, 91191, Gif sur Yvette, France
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
| | - Gilles Mourier
- Commissariat à l'Energie Atomique, DRF/SIMOPRO, 91191, Gif sur Yvette, France
| | - Nicolas Gilles
- Commissariat à l'Energie Atomique, DRF/SIMOPRO, 91191, Gif sur Yvette, France
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
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31
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Qin W, Xie M, Qin X, Fang Q, Yin F, Li Z. Recent advances in peptidomimetics antagonists targeting estrogen receptor α-coactivator interaction in cancer therapy. Bioorg Med Chem Lett 2018; 28:2827-2836. [DOI: 10.1016/j.bmcl.2018.05.062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/25/2018] [Accepted: 05/30/2018] [Indexed: 02/07/2023]
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32
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Abstract
Peptide secondary and tertiary structure motifs frequently serve as inspiration for the development of protein-protein interaction (PPI) inhibitors. While a wide variety of strategies have been used to stabilize or imitate α-helices, similar strategies for β-sheet stabilization are more limited. Synthetic scaffolds that stabilize reverse turns and cross-strand interactions have provided important insights into β-sheet stability and folding. However, these templates occupy regions of the β-sheet that might impact the β-sheet's ability to bind at a PPI interface. Here, we present the hydrogen bond surrogate (HBS) approach for stabilization of β-hairpin peptides. The HBS linkage replaces a cross-strand hydrogen bond with a covalent linkage, conferring significant conformational and proteolytic resistance. Importantly, this approach introduces the stabilizing linkage in the buried β-sheet interior, retains all side chains for further functionalization, and allows efficient solid-phase macrocyclization. We anticipate that HBS stabilization of PPI β-sheets will enhance the development of β-sheet PPI inhibitors and expand the repertoire of druggable PPIs.
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Affiliation(s)
- Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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33
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Iegre J, Gaynord JS, Robertson NS, Sore HF, Hyvönen M, Spring DR. Two-Component Stapling of Biologically Active and Conformationally Constrained Peptides: Past, Present, and Future. ADVANCED THERAPEUTICS 2018. [DOI: 10.1002/adtp.201800052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jessica Iegre
- Department of Chemistry; University of Cambridge; Cambridge CB2 1EW UK
| | | | | | - Hannah F. Sore
- Department of Chemistry; University of Cambridge; Cambridge CB2 1EW UK
| | - Marko Hyvönen
- Department of Biochemistry; University of Cambridge; Cambridge CB2 1GA UK
| | - David R. Spring
- Department of Chemistry; University of Cambridge; Cambridge CB2 1EW UK
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34
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Qin X, Zhao H, Jiang Y, Yin F, Tian Y, Xie M, Ye X, Xu N, Li Z. Development of a potent peptide inhibitor of estrogen receptor α. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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35
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Synthesis, biophysical and functional studies of two BP100 analogues modified by a hydrophobic chain and a cyclic peptide. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1502-1516. [PMID: 29750913 DOI: 10.1016/j.bbamem.2018.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/02/2018] [Accepted: 05/07/2018] [Indexed: 12/22/2022]
Abstract
Antimicrobial peptides (AMPs) work as a primary defense against pathogenic microorganisms. BP100, (KKLFKKILKYL-NH2), a rationally designed short, highly cationic AMP, acts against many bacteria, displaying low toxicity to eukaryotic cells. Previously we found that its mechanism of action depends on membrane surface charge and on peptide-to-lipid ratio. Here we present the synthesis of two BP100 analogs: BP100‑alanyl‑hexadecyl‑1‑amine (BP100-Ala-NH-C16H33) and cyclo(1‑4)‑d‑Cys1, Ile2, Leu3, Cys4-BP100 (Cyclo(1‑4)‑cILC-BP100). We examined their binding to large unilamellar vesicles (LUV), conformational and functional properties, and compared with those of BP100. The analogs bound to membranes with higher affinity and a lesser dependence on electrostatic forces than BP100. In the presence of LUV, BP100 and BP100-Ala-NH-C16H33 acquired α-helical conformation, while Cyclo(1‑4)‑cILC-BP100) was partly α-helical and partly β-turn. Taking in conjunction: 1. particle sizes and zeta potential, 2. effects on lipid flip-flop, 3. leakage of LUVs internal contents, and 4. optical microscopy of giant unilamellar vesicles, we concluded that at high concentrations, all three peptides acted by a carpet mechanism, while at low concentrations the peptides acted by disorganizing the lipid bilayer, probably causing membrane thinning. The higher activity and lesser membrane surface charge dependence of the analogs was probably due to their greater hydrophobicity. The MIC values of both analogs towards Gram-positive and Gram-negative bacteria were similar to those of BP100 but both analogues were more hemolytic. Confocal microscopy showed Gram-positive B. subtilis killing with concomitant extensive membrane damage suggestive of lipid clustering, or peptide-lipid aggregation. These results were in agreement with those found in model membranes.
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36
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Jiang Y, Hu K, Shi X, Tang Q, Wang Z, Ye X, Li Z. Switching substitution groups on the in-tether chiral centre influences backbone peptides' permeability and target binding affinity. Org Biomol Chem 2018; 15:541-544. [PMID: 27929189 DOI: 10.1039/c6ob02289h] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Different substitution groups on the in-tether chiral centre of chirality-induced helical peptides (CIH peptides) showed distinguishable effects on the peptides' cellular uptakes and binding affinities with the estrogen receptor α(ER-α). This study proves that in-tether chiral centres are a valuable modification site for constructing peptide ligands with preferable biophysical properties.
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Affiliation(s)
- Yixiang Jiang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Kuan Hu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Xiaodong Shi
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Qingzhuang Tang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - ZiChen Wang
- Shenzhen Middle School, Shenzhen 518001, China
| | - Xiyang Ye
- Department of Gynecology, Shenzhen People's Hospital, Shenzhen 518055, China
| | - Zigang Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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37
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Jiang Y, Deng Q, Zhao H, Xie M, Chen L, Yin F, Qin X, Zheng W, Zhao Y, Li Z. Development of Stabilized Peptide-Based PROTACs against Estrogen Receptor α. ACS Chem Biol 2018; 13:628-635. [PMID: 29271628 DOI: 10.1021/acschembio.7b00985] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Peptide modulators targeting protein-protein interactions (PPIs) exhibit greater potential than small-molecule drugs in several important aspects including facile modification and relative large contact surface area. Stabilized peptides constructed by variable chemistry methods exhibit improved peptide stability and cell permeability compared to that of the linears. Herein, we designed a stabilized peptide-based proteolysis-targeting chimera (PROTAC) targeting estrogen receptor α (ERα) by tethering an N-terminal aspartic acid cross-linked stabilized peptide ERα modulator (TD-PERM) with a pentapeptide that binds the Von Hippel-Lindau (VHL) E3 ubiquitin ligase complex. The resulting heterobifunctional peptide (TD-PROTAC) selectively recruits ERα to the VHL E3 ligase complex, leading to the degradation of ERα in a proteasome-dependent manner. Compared with the control peptides, TD-PROTAC shows significantly enhanced activities in reducing the transcription of the ERα-downstream genes and inhibiting the proliferation of ERα-positive breast cancer cells. In addition, in vivo experiments indicate that TD-PROTAC leads to tumor regression in the MCF-7 mouse xenograft model. This work is a successful attempt to construct PROTACs based on cell-permeable stabilized peptides, which significantly broadens the chemical space of PROTACs and stabilized peptides.
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Affiliation(s)
- Yanhong Jiang
- Key Lab of Chemical Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Qiwen Deng
- Key Lab of Chemical Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Hui Zhao
- Division of Life Sciences, Clarivate Analytics, Beijing, 100190, China
| | - Mingsheng Xie
- Key Lab of Chemical Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Longjian Chen
- Key Lab of Chemical Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Feng Yin
- Key Lab of Chemical Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Xuan Qin
- Key Lab of Chemical Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Weihao Zheng
- Key Lab of Chemical Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Yongjuan Zhao
- Key Lab of Chemical Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Zigang Li
- Key Lab of Chemical Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
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38
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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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39
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Xie M, Zhao H, Liu Q, Zhu Y, Yin F, Liang Y, Jiang Y, Wang D, Hu K, Qin X, Wang Z, Wu Y, Xu N, Ye X, Wang T, Li Z. Structural Basis of Inhibition of ERα-Coactivator Interaction by High-Affinity N-Terminus Isoaspartic Acid Tethered Helical Peptides. J Med Chem 2017; 60:8731-8740. [PMID: 29045135 DOI: 10.1021/acs.jmedchem.7b00732] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Direct inhibition of the protein-protein interaction of ERα and its endogenous coactivators with a cell permeable stabilized peptide may offer a novel, promising strategy for combating ERα positive breast cancers. Here, we report the co-crystal structure of a helical peptide stabilized by a N-terminal unnatural cross-linked aspartic acid (TD) in complex with the ERα ligand binding domain (LBD). We designed a series of peptides and peptide 6 that showed direct and high-affinity binding to ERα with selective antiproliferative activity in ERα positive breast cancer cells. The co-crystal structure of the TD-stabilized peptide 6 in complex with ERα LBD further demonstrates that it forms an α helical conformation and directly binds at the coactivator binding site of ERα. Further studies showed that peptide 6W could potently inhibit cellular ERα's transcriptional activity. This approach demonstrates the potential of TD stabilized peptides to modulate various intracellular protein-protein interactions involved in a range of disorders.
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Affiliation(s)
- Mingsheng Xie
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China
| | - Hui Zhao
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China
| | - Qisong Liu
- Shenzhen Key Lab of Tissue Engineering, The Second People's Hospital of Shenzhen , Shenzhen 518035, China
| | - Yujia Zhu
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center , Guangzhou 510060, Guangdong, China
| | - Feng Yin
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China
| | - Yujie Liang
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China
| | - Yanhong Jiang
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China
| | - Dongyuan Wang
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China
| | - Kuan Hu
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China
| | - Xuan Qin
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China
| | - Zichen Wang
- Shenzhen Middle School , Shenzhen 518001, China
| | - Yujie Wu
- Department of Biology, Southern University of Science and Technology , Shenzhen 518055, China
| | - Naihan Xu
- Key Lab in Healthy Science and Technology, Division of Life Science, Shenzhen Graduate School of Tsinghua University , Shenzhen 518055, China
| | - Xiyang Ye
- Department of Gynecology, Shenzhen People's Hospital , Shenzhen 518020, China
| | - Tao Wang
- Department of Biology, Southern University of Science and Technology , Shenzhen 518055, China
| | - Zigang Li
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China
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40
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Vultos F, Fernandes C, Mendes F, Marques F, Correia JDG, Santos I, Gano L. A Multifunctional Radiotheranostic Agent for Dual Targeting of Breast Cancer Cells. ChemMedChem 2017. [PMID: 28628723 DOI: 10.1002/cmdc.201700287] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A straightforward synthetic route for a new multifunctional 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) derivative is described. To demonstrate the versatility of this pro-chelator for the preparation of radiolabeled hybrid compounds containing two different biological targeting moieties, an antitumor agent (e.g., a DNA-intercalating agent) and an estrogen receptor (ER) ligand (e.g., LXXLL-based peptide) were regiospecifically conjugated to the DOTA derivative. The bifunctional probe was radiolabeled with the auger electron emitter indium-111, and the resulting radioconjugate was demonstrated to induce DNA damage in vitro, which, along with the nuclear internalization exhibited in breast cancer cells, might enhance its therapeutic activity. This favorable in vitro performance suggests that these hybrid compounds could be attractive probes for theranostic applications.
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Affiliation(s)
- Filipe Vultos
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, km 139.7, 2695-066, Bobadela, LRS, Portugal
| | - Célia Fernandes
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, km 139.7, 2695-066, Bobadela, LRS, Portugal
| | - Filipa Mendes
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, km 139.7, 2695-066, Bobadela, LRS, Portugal
| | - Fernanda Marques
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, km 139.7, 2695-066, Bobadela, LRS, Portugal
| | - João D G Correia
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, km 139.7, 2695-066, Bobadela, LRS, Portugal
| | - Isabel Santos
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, km 139.7, 2695-066, Bobadela, LRS, Portugal
| | - Lurdes Gano
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, km 139.7, 2695-066, Bobadela, LRS, Portugal
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41
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42
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Zhao H, Jiang Y, Tian Y, Yang D, Qin X, Li Z. Improving cell penetration of helical peptides stabilized by N-terminal crosslinked aspartic acids. Org Biomol Chem 2017; 15:459-464. [DOI: 10.1039/c6ob02501c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Physicochemical properties including hydrophobicity and isoelectric point are the driving forces for cellular uptake and nucleus translocation of stabilized helices.
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Affiliation(s)
- Hui Zhao
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Yanhong Jiang
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Yuan Tian
- School of Life Science and Engineering
- Southwest Jiaotong University
- Chengdu
- China
| | - Dan Yang
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Xuan Qin
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Zigang Li
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
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43
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Goyal B, Srivastava KR, Durani S. Examination of the Effect of N-terminal Diproline and Charged Side Chains on the Stabilization of Helical Conformation in Alanine-based Short Peptides: A Molecular Dynamics Study. ChemistrySelect 2016. [DOI: 10.1002/slct.201601381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai-400076 India
- Department of Chemistry; School of Basic and Applied Sciences; Sri Guru Granth Sahib World University, Fatehgarh; Sahib-140406, Punjab India
| | - Kinshuk Raj Srivastava
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai-400076 India
- Life Sciences Institute; University of Michigan; Ann Arbor, MI USA 48105
| | - Susheel Durani
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai-400076 India
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44
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Zhao H, Liu QS, Geng H, Tian Y, Cheng M, Jiang YH, Xie MS, Niu XG, Jiang F, Zhang YO, Lao YZ, Wu YD, Xu NH, Li ZG. Crosslinked Aspartic Acids as Helix-Nucleating Templates. Angew Chem Int Ed Engl 2016; 55:12088-93. [DOI: 10.1002/anie.201606833] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Hui Zhao
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
| | - Qi-Song Liu
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
- Shenzhen Key Lab of Tissue Engineering; The Second People's Hospital of Shenzhen; Shenzhen 518035 China
| | - Hao Geng
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
| | - Yuan Tian
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
| | - Min Cheng
- Key Lab in Healthy Science and Technology; Division of Life Science; Shenzhen Graduate School of Tsinghua University; Shenzhen 518055 China
| | - Yan-Hong Jiang
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
| | - Ming-Sheng Xie
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
| | - Xiao-Gang Niu
- College of Chemistry and Molecular Engineering; Beijing Nuclear Magnetic Resonance Center; Peking University; Beijing 100871 China
| | - Fan Jiang
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
| | - Ya-Ou Zhang
- Key Lab in Healthy Science and Technology; Division of Life Science; Shenzhen Graduate School of Tsinghua University; Shenzhen 518055 China
| | - Yuan-Zhi Lao
- School of Pharmacy; Shanghai University of Traditional Chinese Medicine; Shanghai 201203 China
| | - Yun-Dong Wu
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
| | - Nai-Han Xu
- Key Lab in Healthy Science and Technology; Division of Life Science; Shenzhen Graduate School of Tsinghua University; Shenzhen 518055 China
| | - Zi-Gang Li
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
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45
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Zhao H, Liu QS, Geng H, Tian Y, Cheng M, Jiang YH, Xie MS, Niu XG, Jiang F, Zhang YO, Lao YZ, Wu YD, Xu NH, Li ZG. Crosslinked Aspartic Acids as Helix-Nucleating Templates. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606833] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hui Zhao
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
| | - Qi-Song Liu
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
- Shenzhen Key Lab of Tissue Engineering; The Second People's Hospital of Shenzhen; Shenzhen 518035 China
| | - Hao Geng
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
| | - Yuan Tian
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
| | - Min Cheng
- Key Lab in Healthy Science and Technology; Division of Life Science; Shenzhen Graduate School of Tsinghua University; Shenzhen 518055 China
| | - Yan-Hong Jiang
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
| | - Ming-Sheng Xie
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
| | - Xiao-Gang Niu
- College of Chemistry and Molecular Engineering; Beijing Nuclear Magnetic Resonance Center; Peking University; Beijing 100871 China
| | - Fan Jiang
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
| | - Ya-Ou Zhang
- Key Lab in Healthy Science and Technology; Division of Life Science; Shenzhen Graduate School of Tsinghua University; Shenzhen 518055 China
| | - Yuan-Zhi Lao
- School of Pharmacy; Shanghai University of Traditional Chinese Medicine; Shanghai 201203 China
| | - Yun-Dong Wu
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
| | - Nai-Han Xu
- Key Lab in Healthy Science and Technology; Division of Life Science; Shenzhen Graduate School of Tsinghua University; Shenzhen 518055 China
| | - Zi-Gang Li
- School of Chemical Biology and Biotechnology; Shenzhen Graduate School of Peking University; Shenzhen 518055 China
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46
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Tice CM, Zheng YJ. Non-canonical modulators of nuclear receptors. Bioorg Med Chem Lett 2016; 26:4157-64. [PMID: 27503683 DOI: 10.1016/j.bmcl.2016.07.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/19/2016] [Accepted: 07/27/2016] [Indexed: 12/13/2022]
Abstract
Like G protein-coupled receptors (GPCRs) and protein kinases, nuclear receptors (NRs) are a rich source of pharmaceutical targets. Over 80 NR-targeting drugs have been approved for 18 NRs. The focus of drug discovery in NRs has hitherto been on identifying ligands that bind to the canonical ligand binding pockets of the C-terminal ligand binding domains (LBDs). Due to the development of drug resistance and selectivity concerns, there has been considerable interest in exploring other, non-canonical ligand binding sites. Unfortunately, the potencies of compounds binding at other sites have generally not been sufficient for clinical development. However, the situation has changed dramatically over the last 3years, as compounds with sufficient potency have been reported for several NR targets. Here we review recent developments in this area from a medicinal chemistry point of view in the hope of stimulating further interest in this area of research.
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Affiliation(s)
- Colin M Tice
- Vitae Pharmaceuticals, Inc., 502 West Office Center Drive, Fort Washington, PA 19034, United States
| | - Ya-Jun Zheng
- Vitae Pharmaceuticals, Inc., 502 West Office Center Drive, Fort Washington, PA 19034, United States
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47
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Demizu Y, Ohoka N, Nagakubo T, Yamashita H, Misawa T, Okuhira K, Naito M, Kurihara M. Development of a peptide-based inducer of nuclear receptors degradation. Bioorg Med Chem Lett 2016; 26:2655-8. [DOI: 10.1016/j.bmcl.2016.04.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/01/2016] [Accepted: 04/06/2016] [Indexed: 02/07/2023]
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48
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Diderich P, Bertoldo D, Dessen P, Khan MM, Pizzitola I, Held W, Huelsken J, Heinis C. Phage Selection of Chemically Stabilized α-Helical Peptide Ligands. ACS Chem Biol 2016; 11:1422-7. [PMID: 26929989 DOI: 10.1021/acschembio.5b00963] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Short α-helical peptides stabilized by linkages between constituent amino acids offer an attractive format for ligand development. In recent years, a range of excellent ligands based on stabilized α-helices were generated by rational design using α-helical peptides of natural proteins as templates. Herein, we developed a method to engineer chemically stabilized α-helical ligands in a combinatorial fashion. In brief, peptides containing cysteines in position i and i + 4 are genetically encoded by phage display, the cysteines are modified with chemical bridges to impose α-helical conformations, and binders are isolated by affinity selection. We applied the strategy to affinity mature an α-helical peptide binding β-catenin. We succeeded in developing ligands with Kd's as low as 5.2 nM, having >200-fold improved affinity. The strategy is generally applicable for affinity maturation of any α-helical peptide. Compared to hydrocarbon stapled peptides, the herein evolved thioether-bridged peptide ligands can be synthesized more easily, as no unnatural amino acids are required and the cyclization reaction is more efficient and yields no stereoisomers. A further advantage of the thioether-bridged peptide ligands is that they can be expressed recombinantly as fusion proteins.
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Affiliation(s)
- Philippe Diderich
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Davide Bertoldo
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Pierre Dessen
- Swiss
Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Maola M. Khan
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Irene Pizzitola
- Ludwig
Center for Cancer Research, Department of Oncology, University of Lausanne, CH-1066 Epalinges, Switzerland
| | - Werner Held
- Ludwig
Center for Cancer Research, Department of Oncology, University of Lausanne, CH-1066 Epalinges, Switzerland
| | - Joerg Huelsken
- Swiss
Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Christian Heinis
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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49
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Hu K, Geng H, Zhang Q, Liu Q, Xie M, Sun C, Li W, Lin H, Jiang F, Wang T, Wu YD, Li Z. An In-tether Chiral Center Modulates the Helicity, Cell Permeability, and Target Binding Affinity of a Peptide. Angew Chem Int Ed Engl 2016; 55:8013-7. [PMID: 27167181 DOI: 10.1002/anie.201602806] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Indexed: 11/11/2022]
Abstract
The addition of a precisely positioned chiral center in the tether of a constrained peptide is reported, yielding two separable peptide diastereomers with significantly different helicity, as supported by circular dichroism (CD) and NMR spectroscopy. Single crystal X-ray diffraction analysis suggests that the absolute configuration of the in-tether chiral center in helical form is R, which is in agreement with theoretical simulations. The relationship between the secondary structure of the short peptides and their biochemical/biophysical properties remains elusive, largely because of the lack of proper controls. The present strategy provides the only method for investigating the influence of solely conformational differences upon the biochemical/biophysical properties of peptides. The significant differences in permeability and target binding affinity between the peptide diastereomers demonstrate the importance of helical conformation.
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Affiliation(s)
- Kuan Hu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Hao Geng
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Qingzhou Zhang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Qisong Liu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Mingsheng Xie
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Chengjie Sun
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Wenjun Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Huacan Lin
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Fan Jiang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Tao Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Yun-Dong Wu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Zigang Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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50
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Hu K, Geng H, Zhang Q, Liu Q, Xie M, Sun C, Li W, Lin H, Jiang F, Wang T, Wu YD, Li Z. An In-tether Chiral Center Modulates the Helicity, Cell Permeability, and Target Binding Affinity of a Peptide. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602806] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kuan Hu
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Hao Geng
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Qingzhou Zhang
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Qisong Liu
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Mingsheng Xie
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Chengjie Sun
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Wenjun Li
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Huacan Lin
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Fan Jiang
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Tao Wang
- Department of Biology; Southern University of Science and Technology; Shenzhen 518055 China
| | - Yun-Dong Wu
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Zigang Li
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
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