1
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Lin Z, Liu B, Lu M, Wang Y, Ren X, Liu Z, Luo C, Shi W, Zou X, Song X, Tang F, Huang H, Huang W. Controlled Reversible N-Terminal Modification of Peptides and Proteins. J Am Chem Soc 2024. [PMID: 39143892 DOI: 10.1021/jacs.4c04894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
A reversible modification strategy enables a switchable cage/decage process of proteins with an array of applications for protein function research. However, general N-terminal selective reversible modification strategies which present site selectivity are specifically limited. Herein, we report a general reversible modification strategy compatible with 20 canonical amino acids at the N-terminal site by the palladium-catalyzed cinnamylation of native peptides and proteins under biologically relevant conditions. This approach broadens the substrate adaptability of N-terminal modification of proteins and shows a potential impact on the more challenging protein substrates such as antibodies. In the presence of 1,3-dimethylbarbituric acid, palladium-catalyzed deconjugation released native peptides and proteins efficiently. Harnessing the reversible nature of this protocol, practical applications were demonstrated by precise function modulation of antibodies and traceless enrichment of the protein-of-interest for proteomics analysis. This novel on/off strategy working on the N-terminus will provide new opportunities in chemical biology and medicinal research.
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Affiliation(s)
- Zeng Lin
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 310024, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zuchongzhi Rd, Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Bo Liu
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 310024, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zuchongzhi Rd, Pudong, Shanghai 201203, China
| | - Mengru Lu
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 310024, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zuchongzhi Rd, Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yongqin Wang
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 310024, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zuchongzhi Rd, Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xuelian Ren
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 310024, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhaoxi Liu
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 310024, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zuchongzhi Rd, Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Caili Luo
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 310024, China
| | - Wei Shi
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zuchongzhi Rd, Pudong, Shanghai 201203, China
| | - Xiangman Zou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zuchongzhi Rd, Pudong, Shanghai 201203, China
| | - Xiaohan Song
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 310024, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Feng Tang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zuchongzhi Rd, Pudong, Shanghai 201203, China
| | - He Huang
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 310024, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wei Huang
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 310024, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zuchongzhi Rd, Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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2
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Ding Y, Pedersen SS, Wang H, Xiang B, Wang Y, Yang Z, Gao Y, Morosan E, Jones MR, Xiao H, Ball ZT. Selective Macrocyclization of Unprotected Peptides with an Ex Situ Gaseous Linchpin Reagent. Angew Chem Int Ed Engl 2024; 63:e202405344. [PMID: 38753429 DOI: 10.1002/anie.202405344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Indexed: 07/16/2024]
Abstract
Peptide cyclization has dramatic effects on a variety of important properties, enhancing metabolic stability, limiting conformational flexibility, and altering cellular entry and intracellular localization. The hydrophilic, polyfunctional nature of peptides creates chemoselectivity challenges in macrocyclization, especially for natural sequences without biorthogonal handles. Herein, we describe a gaseous sulfonyl chloride derived reagent that achieves amine-amine, amine-phenol, and amine-aniline crosslinking through a minimalist linchpin strategy that affords macrocyclic urea or carbamate products. The cyclization reaction is metal-mediated and involves a novel application of sulfine species that remains unexplored in aqueous or biological contexts. The aqueous method delivers unique cyclic or bicyclic topologies directly from a variety of natural bioactive peptides without the need for protecting-group strategies.
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Affiliation(s)
- Yuxuan Ding
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Simon S Pedersen
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
- Carbon Dioxide Activation Center (CADIAC), Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Haofan Wang
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Baorui Xiang
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Yixian Wang
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Zhi Yang
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Yuxiang Gao
- Department of Physics and Astronomy, Rice University, Houston, Texas, 77005, United States
| | - Emilia Morosan
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
- Department of Physics and Astronomy, Rice University, Houston, Texas, 77005, United States
| | - Matthew R Jones
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Han Xiao
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Zachary T Ball
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
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3
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Li B, Parker J, Tong J, Kodadek T. Synthesis of Membrane-Permeable Macrocyclic Peptides via Imidazopyridinium Grafting. J Am Chem Soc 2024; 146:14633-14644. [PMID: 38752889 DOI: 10.1021/jacs.4c01920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Macrocyclic peptides (MPs) are a class of compounds that have been shown to be particularly well suited for engaging difficult protein targets. However, their utility is limited by their generally poor cell permeability and bioavailability. Here, we report an efficient solid-phase synthesis of novel MPs by trapping a reversible intramolecular imine linkage with a 2-formyl- or 2-keto-pyridine to create an imidazopyridinium (IP+)-linked ring. This chemistry is useful for the creation of macrocycles of different sizes and geometries, including head-to-side and side-to-side chain configurations. Many of the IP+-linked MPs exhibit far better passive membrane permeability than expected for "beyond Rule of 5" molecules, in some cases exceeding that of much lower molecular weight, traditional drug molecules. We demonstrate that this chemistry is suitable for the creation of libraries of IP+-linked MPs and show that these libraries can be mined for protein ligands.
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Affiliation(s)
- Bo Li
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
| | - Joshua Parker
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
| | - Joel Tong
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
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4
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Guo P, Chu X, Wu C, Qiao T, Guan W, Zhou C, Wang T, Tian C, He G, Chen G. Peptide Stapling by Crosslinking Two Amines with α-Ketoaldehydes through Diverse Modified Glyoxal-Lysine Dimer Linkers. Angew Chem Int Ed Engl 2024; 63:e202318893. [PMID: 38376389 DOI: 10.1002/anie.202318893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 02/21/2024]
Abstract
α-Ketoaldehydes play versatile roles in the ubiquitous natural processes of protein glycation. However, leveraging the reactivity of α-ketoaldehydes for biomedical applications has been challenging. Previously, the reactivity of α-ketoaldehydes with guanidine has been harnessed to design probes for labeling Arg residues on proteins in an aqueous medium. Herein, a highly effective, broadly applicable, and operationally simple protocol for stapling native peptides by crosslinking two amino groups through diverse imidazolium linkers with various α-ketoaldehyde reagents is described. The use of hexafluoroisopropanol as a solvent facilitates rapid and clean reactions under mild conditions and enables unique selectivity for Lys over Arg. The naturally occurring GOLD/MOLD linkers have been expanded to encompass a wide range of modified glyoxal-lysine dimer (OLD) linkers. In a proof-of-concept trial, these modular stapling reactions enabled a convenient two-round strategy to streamline the structure-activity relationship (SAR) study of the wasp venom peptide anoplin, leading to enhanced biological activities.
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Affiliation(s)
- Pan Guo
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xin Chu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chengjin Wu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Tianjiao Qiao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Wenli Guan
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Tao Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Changlin Tian
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
- Frontiers Science Center for New Organic Matter, Nankai University, Tianjin, 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, China
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5
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Huseynzada A, Aghayev M, Hajiyeva S, Israyilova A, Sayin K, Gasimov E, Rzayev F, Hasanova U, Eyvazova G, Abbasov V, Gakhramanova Z, Huseynova S, Huseynova P, Huseynova L, Salimova N. Synthesis, nanostructuring and in silico studies of a new imine bond containing a macroheterocycle as a promising PBP-2a non-β-lactam inhibitor. J Mater Chem B 2023; 11:8271-8280. [PMID: 37581615 DOI: 10.1039/d3tb00602f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
This study is devoted to the synthesis of a 40-membered macroheterocycle with its further nanostructuring by magnetite nanoparticles. The mentioned macroheterocycle was synthesized by the [2+2] cyclocondensation of the oxygen-containing diamine with an aromatic dialdehyde in a non-catalytic medium and with no work-up procedure. The structure of the obtained macroheterocycle was studied by 1H and 13C nuclear magnetic resonance spectroscopy and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Furthermore, the nanosupramolecular complex of macroheterocycles with magnetite nanoparticles was obtained and investigated by Fourier-transform infrared and ultraviolet-visible spectroscopy methods. Shifts in the infrared spectra of the nanosupramolecular complex indicate the interaction through metal-aromatic ring non-covalent bonding. The shift is also observed for the C-O-C stretching band of ether bonds. The loading rate of macroheterocycles on magnetite nanoparticles was 18.6%. The morphology of the ensemble was studied by transmission electron microscopy, which confirmed the synthesis of nanospherical particles with a diameter range of 10-20 nm. Powder X-ray diffraction analysis showed patterns of cubic Fe3O4 nanoparticles with a crystallite size equal to 9.1 nm. The macroheterocycle and its nanosupramolecular complex were tested against Klebsiella pneumoniae, Pseudomonas aeruginosa and Staphylococcus aureus. The results have shown that the created complex has shown 64 times better activity against Staphylococcus aureus in comparison with the individual macroheterocycle and 32 times better activity in comparison with the pristine antibiotic Ampicillin as a control. In addition, computational analysis of the macroheterocycle was performed at the B3LYP/6-31G level in water. Molecular docking analyses for the macroheterocycle revealed Penicillin-binding protein PBP2a (5M18) from the transpeptidase family as a target protein in Staphylococcus aureus.
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Affiliation(s)
- Alakbar Huseynzada
- ICRL, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
- GPOGC SRI, Azerbaijan State Oil and Industry University, Baku, AZ 1010, Azerbaijan.
- Chemistry Department, Azerbaijan Engineers Union, Bashir Safaroglu 118, Baku, AZ 1009, Azerbaijan
- ICESCO Biomedical Materials Department, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
| | - Mirjavid Aghayev
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, 4209 St, OH-44, Rootstown, OH 44272, USA
| | - Sarvinaz Hajiyeva
- ICRL, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
- Physics Department, Kent State University, 800 E. Summit St., Kent, OH 44242, USA
| | - Aygun Israyilova
- Laboratory of Microbiology and Virology, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
- GPOGC SRI, Azerbaijan State Oil and Industry University, Baku, AZ 1010, Azerbaijan.
- Research Institute of Crop Husbandry, Ministry of Agriculture, Baku, AZ 1098, Azerbaijan
- ICESCO Biomedical Materials Department, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
| | - Koray Sayin
- Chemistry Department, Faculty of Science, Sivas Cumhuriyet University, Sivas, 58140, Turkey
| | - Eldar Gasimov
- Department of Cytology, Embryology and Histology, Azerbaijan Medical University, 163 A Samad Vurgun, Baku AZ1078, Azerbaijan
| | - Fuad Rzayev
- Laboratory of Electron Microscopy of the SRC, Azerbaijan Medical University, 163 A Samad Vurgun, Baku AZ1078, Azerbaijan
| | - Ulviyya Hasanova
- ICRL, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
- GPOGC SRI, Azerbaijan State Oil and Industry University, Baku, AZ 1010, Azerbaijan.
- ICESCO Biomedical Materials Department, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
| | - Goncha Eyvazova
- Nanoresearch Center, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
| | - Vagif Abbasov
- Institute of Petrochemical Processes, K. Avenue 30, Baku, AZ 1005, Azerbaijan
| | - Zarema Gakhramanova
- GPOGC SRI, Azerbaijan State Oil and Industry University, Baku, AZ 1010, Azerbaijan.
| | - Sanam Huseynova
- Department of Molecular Biology and Biotechnology, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
| | - Parvana Huseynova
- Chemistry Department, Ganja State University, H. Aliyev 429, Ganja, AZ 2001, Azerbaijan
| | - Lala Huseynova
- Industrial Safety and Labor Protection Department, Azerbaijan State Oil and Industry University, Baku, AZ 1010, Azerbaijan
| | - Nigar Salimova
- Petrochemical Technology and Industrial Ecology Department, Azerbaijan State Oil and Industry University, Baku, AZ 1010, Azerbaijan
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6
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Mendoza A, Bernardino SJ, Dweck MJ, Valencia I, Evans D, Tian H, Lee W, Li Y, Houk KN, Harran PG. Cascade Synthesis of Fluorinated Spiroheterocyclic Scaffolding for Peptidic Macrobicycles. J Am Chem Soc 2023. [PMID: 37441722 DOI: 10.1021/jacs.3c03071] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Octafluorocyclopentene (OFCP) engages linear, unprotected peptides in polysubstitution cascades that generate complex fluorinated polycycles. The reactions occur in a single flask at 0-25 °C and require no catalysts or heavy metals. OFCP can directly polycyclize linear sequences using native functionality, or fluorospiroheterocyclic intermediates can be intercepted with exogenous nucleophiles. The latter tactic generates molecular hybrids composed of peptides, sugars, lipids, and heterocyclic components. The platform can create stereoisomers of both single- and double-looped macrocycles. Calculations indicate that the latter can mimic diverse protein surface loops. Subsets of the molecules have low energy conformers that shield the polar surface area through intramolecular hydrogen bonding. A significant fraction of OFCP-derived macrocycles tested show moderate to high passive permeability in parallel artificial membrane permeability assays.
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Affiliation(s)
- Angel Mendoza
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Salvador J Bernardino
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Morris J Dweck
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Isabel Valencia
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, Alcalá de Henares 28805, Spain
| | - Declan Evans
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Haowen Tian
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - William Lee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Yu Li
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Patrick G Harran
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
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7
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Yang P, Širvinskas MJ, Li B, Heller NW, Rong H, He G, Yudin AK, Chen G. Teraryl Braces in Macrocycles: Synthesis and Conformational Landscape Remodeling of Peptides. J Am Chem Soc 2023. [PMID: 37326500 DOI: 10.1021/jacs.3c03512] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The three-dimensional structure of medium-sized cyclic peptides accounts for their biological activity and other important physiochemical properties. Despite significant advances in the past few decades, chemists' ability to fine-tune the structure, in particular, the backbone conformation, of short peptides made of canonical amino acids is still quite limited. Nature has shown that cross-linking the aromatic side chains of linear peptide precursors via enzyme catalysis can generate cyclophane-braced products with unusual structures and diverse activities. However, the biosynthetic path to these natural products is challenging to replicate in the synthetic laboratory using practical chemical modifications of peptides. Herein, we report a broadly applicable strategy to remodel the structure of homodetic peptides by cross-linking the aromatic side chains of Trp, His, and Tyr residues with various aryl linkers. The aryl linkers can be easily installed via copper-catalyzed double heteroatom-arylation reactions of peptides with aryl diiodides. These aromatic side chains and aryl linkers can be combined to form a large variety of assemblies of heteroatom-linked multi-aryl units. The assemblies can serve as tension-bearable multijoint braces to modulate the backbone conformation of peptides as an entry to previously inaccessible conformational space.
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Affiliation(s)
- Peng Yang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | | | - Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Nicholas W Heller
- Department of Chemistry, University of Toronto, Toronto M5S 3H4, Canada
| | - Hua Rong
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Andrei K Yudin
- Department of Chemistry, University of Toronto, Toronto M5S 3H4, Canada
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
- Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
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8
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Keyes ED, Mifflin MC, Austin MJ, Alvey BJ, Lovely LH, Smith A, Rose TE, Buck-Koehntop BA, Motwani J, Roberts AG. Chemoselective, Oxidation-Induced Macrocyclization of Tyrosine-Containing Peptides. J Am Chem Soc 2023; 145:10071-10081. [PMID: 37119237 DOI: 10.1021/jacs.3c00210] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Inspired by nature's wide range of oxidation-induced modifications to install cross-links and cycles at tyrosine (Tyr) and other phenol-containing residue side chains, we report a Tyr-selective strategy for the preparation of Tyr-linked cyclic peptides. This approach leverages N4-substituted 1,2,4-triazoline-3,5-diones (TADs) as azo electrophiles that react chemoselectively with the phenolic side chain of Tyr residues to form stable C-N1-linked cyclic peptides. In the developed method, a precursor 1,2,4-triazolidine-3,5-dione moiety, also known as urazole, is readily constructed at any free amine revealed on a solid-supported peptide. Once prepared, the N4-substituted urazole peptide is selectively oxidized using mild, peptide-compatible conditions to generate an electrophilic N4-substituted TAD peptide intermediate that reacts selectively under aqueous conditions with internal and terminal Tyr residues to furnish Tyr-linked cyclic peptides. The approach demonstrates good tolerance of native residue side chains and enables access to cyclic peptides ranging from 3- to 11-residues in size (16- to 38-atom-containing cycles). The identity of the installed Tyr-linkage, a stable covalent C-N1 bond, was characterized using NMR spectroscopy. Finally, we applied the developed method to prepare biologically active Tyr-linked cyclic peptides bearing the integrin-binding RGDf epitope.
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Affiliation(s)
- E Dalles Keyes
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Marcus C Mifflin
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Maxwell J Austin
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Brighton J Alvey
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Lotfa H Lovely
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Andriea Smith
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Tristin E Rose
- 1200 Pharma LLC, 6100 Bristol Parkway, Culver City, California 90230, United States
| | - Bethany A Buck-Koehntop
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Jyoti Motwani
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Andrew G Roberts
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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9
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Li B, Wan Z, Zheng H, Cai S, Tian HW, Tang H, Chu X, He G, Guo DS, Xue XS, Chen G. Construction of Complex Macromulticyclic Peptides via Stitching with Formaldehyde and Guanidine. J Am Chem Soc 2022; 144:10080-10090. [PMID: 35639413 DOI: 10.1021/jacs.2c04620] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is a growing interest in constructing multicyclic peptide structures to expand the chemical space of peptides. Conventional strategies for constructing large peptide structures are limited by the typical reliance on the inflexible coupling between premade templates equipped with fixed reactive handles and peptide substrates via cysteine anchors. Herein, we report the development of a facile three-component condensation reaction of primary alkyl amine, formaldehyde, and guanidine for construction of complex macromulticyclic peptides with novel topologies via lysine anchors. Moreover, the reaction sequences can be orchestrated in different anchor combinations and spatial arrangements to generate various macrocyclic structures crosslinked by distinct fused tetrahydrotriazine linkages. The macrocyclization reactions are selective, efficient, versatile, and workable in both organic and aqueous media. Thus, the condensation reaction provides a smart tool for stitching native peptides in situ using simple methylene threads and guanidine joints in a flexible and programmable manner.
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Affiliation(s)
- Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhao Wan
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hanliang Zheng
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Shaokun Cai
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Han-Wen Tian
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hong Tang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xin Chu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Dong-Sheng Guo
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xiao-Song Xue
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.,Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.,Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
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10
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Taylor CM, Kilah NL. Synthesis of [2+2] Schiff base macrocycles by a solvent templating strategy and halogen bonding directed assembly. J INCL PHENOM MACRO 2022. [DOI: 10.1007/s10847-022-01137-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractSchiff base imine condensations are a useful tool for macrocycle synthesis and applications within supramolecular chemistry. Here we address the mixtures of products that can arise from template free synthesis using dicarbonylheterocycles and diamines, and look to develop metal-free template methods for selective macrocycle formation. A range of alkyl α,ω-diamines were combined with phenanthroline and pyridine heterocyclic dicarbaldehydes under standard literature conditions. The reaction conditions were modified to demonstrate a relationship between choice of solvent and product equilibria. It was observed that benzene and toluene could shift a mixture of products and unreacted starting materials to form predominantly one imine product for a number of systems. Once the macrocyclic products had been characterized in selected solvents, iodinated halogen bonding guest molecules were added to direct macrocycle assemblies using non-covalent interactions. Studies to investigate host – guest suitability and halogen bond interactions were conducted, and it was found that tetraiodoethylene had an influence on the formation of a phenanthroline based macrocycle. Proof of concept experiments were performed to show the influence of the guest molecule, tetraiodoethylene, on the macrocyclic products formed under competitive dynamic combinatorial chemistry conditions.
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11
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Extendable stapling of unprotected peptides by crosslinking two amines with o-phthalaldehyde. Nat Commun 2022; 13:311. [PMID: 35031608 PMCID: PMC8760283 DOI: 10.1038/s41467-022-27985-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/10/2021] [Indexed: 01/01/2023] Open
Abstract
Peptide modification methods that do not rely on the cysteine residue are underdeveloped, and their development could greatly expand the current toolbox for peptide chemistry. During the course of preliminary investigations into the classical ortho-phthalaldehyde (OPA)-amine-thiol condensation reaction, we found that in the absence of thiol, OPA readily condenses with two primary alkyl amines to form a class of underexplored isoindolin-1-imine compounds under mild aqueous conditions. From the intramolecular version of this OPA-2amines reaction, an efficient and selective methodology using mild reaction conditions has been developed for stapling unprotected peptides via crosslinking of two amino groups in both an end-to-side and side-to-side fashion. The stapling method is superfast and broadly applicable for various peptide substrates with the reacting amino groups separated by a wide range of different amino acid units. The macrocyclization reactions of selected substrates are completed within 10 seconds at 5 mM concentration and within 2 minutes at 50 μM concentration. Importantly, the resulting cyclized peptides with an isoindolinimine linkage can be extended in a one-pot sequential addition manner with several different electron-deficient π electrophiles, thereby generating more complex structures. Methods for peptide stapling, or covalently linking amino acid residues to create a non-linear structure, mostly rely on cysteine residues, which imposes a significant practical limitation. Here the authors disclose a method to chemoselectively macrocyclize two free-amine-containing residues in mild, peptide-relevant conditions, using a commercially available reagent.
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12
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Bechtler C, Lamers C. Macrocyclization strategies for cyclic peptides and peptidomimetics. RSC Med Chem 2021; 12:1325-1351. [PMID: 34447937 PMCID: PMC8372203 DOI: 10.1039/d1md00083g] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022] Open
Abstract
Peptides are a growing therapeutic class due to their unique spatial characteristics that can target traditionally "undruggable" protein-protein interactions and surfaces. Despite their advantages, peptides must overcome several key shortcomings to be considered as drug leads, including their high conformational flexibility and susceptibility to proteolytic cleavage. As a general approach for overcoming these challenges, macrocyclization of a linear peptide can usually improve these characteristics. Their synthetic accessibility makes peptide macrocycles very attractive, though traditional synthetic methods for macrocyclization can be challenging for peptides, especially for head-to-tail cyclization. This review provides an updated summary of the available macrocyclization chemistries, such as traditional lactam formation, azide-alkyne cycloadditions, ring-closing metathesis as well as unconventional cyclization reactions, and it is structured according to the obtained functional groups. Keeping peptide chemistry and screening in mind, the focus is given to reactions applicable in solution, on solid supports, and compatible with contemporary screening methods.
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Affiliation(s)
- Clément Bechtler
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
| | - Christina Lamers
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
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13
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Yang P, Wang X, Li B, Yang Y, Yue J, Suo Y, Tong H, He G, Lu X, Chen G. Streamlined construction of peptide macrocycles via palladium-catalyzed intramolecular S-arylation in solution and on DNA. Chem Sci 2021; 12:5804-5810. [PMID: 34168804 PMCID: PMC8179660 DOI: 10.1039/d1sc00789k] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/08/2021] [Indexed: 12/18/2022] Open
Abstract
A highly efficient and versatile method for construction of peptide macrocycles via palladium-catalyzed intramolecular S-arylation of alkyl and aryl thiols with aryl iodides under mild conditions is developed. The method exhibits a broad substrate scope for thiols, aryl iodides and amino acid units. Peptide macrocycles of a wide range of size and composition can be readily assembled in high yield from various easily accessible building blocks. This method has been successfully employed to prepare an 8-million-membered tetrameric cyclic peptide DNA-encoded library (DEL). Preliminary screening of the DEL library against protein p300 identified compounds with single digit micromolar inhibition activity.
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Affiliation(s)
- Peng Yang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Xuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong Shanghai 201203 China
| | - Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Yixuan Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong Shanghai 201203 China
| | - Jinfeng Yue
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong Shanghai 201203 China
| | - Yanrui Suo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong Shanghai 201203 China
| | - Huarong Tong
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong Shanghai 201203 China
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
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14
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Li B, Tang H, Turlik A, Wan Z, Xue X, Li L, Yang X, Li J, He G, Houk KN, Chen G. Cooperative Stapling of Native Peptides at Lysine and Tyrosine or Arginine with Formaldehyde. Angew Chem Int Ed Engl 2021; 60:6646-6652. [DOI: 10.1002/anie.202016267] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Hong Tang
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Aneta Turlik
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095 USA
| | - Zhao Wan
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Xiao‐Song Xue
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095 USA
| | - Li Li
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation Institute of Materia Medica Chinese Academy of Medical Sciences Peking Union Medical College Beijing 100050 China
| | - Xiaoxiao Yang
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation Institute of Materia Medica Chinese Academy of Medical Sciences Peking Union Medical College Beijing 100050 China
| | - Jiuyuan Li
- Asymchem Life Science Co., Ltd. TEDA Tianjin 300457 China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095 USA
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
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15
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Li B, Tang H, Turlik A, Wan Z, Xue X, Li L, Yang X, Li J, He G, Houk KN, Chen G. Cooperative Stapling of Native Peptides at Lysine and Tyrosine or Arginine with Formaldehyde. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Hong Tang
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Aneta Turlik
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095 USA
| | - Zhao Wan
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Xiao‐Song Xue
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095 USA
| | - Li Li
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation Institute of Materia Medica Chinese Academy of Medical Sciences Peking Union Medical College Beijing 100050 China
| | - Xiaoxiao Yang
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation Institute of Materia Medica Chinese Academy of Medical Sciences Peking Union Medical College Beijing 100050 China
| | - Jiuyuan Li
- Asymchem Life Science Co., Ltd. TEDA Tianjin 300457 China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095 USA
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
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16
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Rivera DG, Ojeda-Carralero GM, Reguera L, Van der Eycken EV. Peptide macrocyclization by transition metal catalysis. Chem Soc Rev 2020; 49:2039-2059. [PMID: 32142086 DOI: 10.1039/c9cs00366e] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peptide macrocyclization has traditionally relied on lactam, lactone and disulfide bond-forming reactions that aim at introducing conformational constraints into small peptide sequences. With the advent of ruthenium-catalyzed ring-closing metathesis and copper-catalyzed alkyne-azide cycloaddition, peptide chemists embraced transition metal catalysis as a powerful macrocyclization tool with relevant applications in chemical biological and peptide drug discovery. This article provides a comprehensive overview of the reactivity and methodological diversification of metal-catalyzed peptide macrocyclization as a special class of late-stage peptide derivatization method. We report the evolution from classic palladium-catalyzed cross-coupling approaches to more modern oxidative versions based on C-H activation, heteroatom alkylation/arylation and annulation processes, in which aspects such as chemoselectivity and diversity generation at the ring-closing moiety became dominant over the last years. The transit from early cycloadditions and alkyne couplings as ring-closing steps to very recent 3d metal-catalyzed macrocyclization methods is highlighted. Similarly, the new trends in decarboxylative radical macrocyclizations and the interplay between photoredox and transition metal catalysis are included. This review charts future perspectives in the field hoping to encourage further progress and applications, while bringing attention to the countless possibilities available by diversifying not only the metal, but also the reactivity modes and tactics to bring peptide functional groups together and produce structurally diverse macrocycles.
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Affiliation(s)
- Daniel G Rivera
- Laboratory for Organic & Microwave-Assisted Chemistry (LOMAC), Department of Chemistry, University of Leuven (KU Leuven), Celestijnenlaan 200F, B-3001 Leuven, Belgium. and Center for Natural Product Research, Faculty of Chemistry, University of Havana, Zapata y G, Havana 10400, Cuba.
| | - Gerardo M Ojeda-Carralero
- Laboratory for Organic & Microwave-Assisted Chemistry (LOMAC), Department of Chemistry, University of Leuven (KU Leuven), Celestijnenlaan 200F, B-3001 Leuven, Belgium. and Center for Natural Product Research, Faculty of Chemistry, University of Havana, Zapata y G, Havana 10400, Cuba.
| | - Leslie Reguera
- Center for Natural Product Research, Faculty of Chemistry, University of Havana, Zapata y G, Havana 10400, Cuba.
| | - Erik V Van der Eycken
- Laboratory for Organic & Microwave-Assisted Chemistry (LOMAC), Department of Chemistry, University of Leuven (KU Leuven), Celestijnenlaan 200F, B-3001 Leuven, Belgium. and Peoples' Friendship University of Russia (RUDN University), Miklukho-Maklaya Street 6, 117198 Moscow, Russia
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17
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Saha I, Dang EK, Svatunek D, Houk KN, Harran PG. Computational generation of an annotated gigalibrary of synthesizable, composite peptidic macrocycles. Proc Natl Acad Sci U S A 2020; 117:24679-24690. [PMID: 32948694 PMCID: PMC7547232 DOI: 10.1073/pnas.2007304117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Peptidomimetic macrocycles have the potential to regulate challenging therapeutic targets. Structures of this type having precise shapes and drug-like character are particularly coveted, but are relatively difficult to synthesize. Our laboratory has developed robust methods that integrate small-peptide units into designed scaffolds. These methods create macrocycles and embed condensed heterocycles to diversify outcomes and improve pharmacological properties. The hypothetical scope of the methodology is vast and far outpaces the capacity of our experimental format. We now describe a computational rendering of our methodology that creates an in silico three-dimensional library of composite peptidic macrocycles. Our open-source platform, CPMG (Composite Peptide Macrocycle Generator), has algorithmically generated a library of 2,020,794,198 macrocycles that can result from the multistep reaction sequences we have developed. Structures are generated based on predicted site reactivity and filtered on the basis of physical and three-dimensional properties to identify maximally diverse compounds for prioritization. For conformational analyses, we also introduce ConfBuster++, an RDKit port of the open-source software ConfBuster, which allows facile integration with CPMG and ready parallelization for better scalability. Our approach deeply probes ligand space accessible via our synthetic methodology and provides a resource for large-scale virtual screening.
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Affiliation(s)
- Ishika Saha
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Eric K Dang
- Department of Computer Science, University of California, Los Angeles, CA 90095
| | - Dennis Svatunek
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095;
| | - Patrick G Harran
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095;
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18
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Fullenkamp CR, Hsu YP, Quardokus EM, Zhao G, Bewley CA, VanNieuwenhze M, Sulikowski GA. Synthesis of 9-Dechlorochrysophaentin A Enables Studies Revealing Bacterial Cell Wall Biosynthesis Inhibition Phenotype in B. subtilis. J Am Chem Soc 2020; 142:16161-16166. [PMID: 32866011 DOI: 10.1021/jacs.0c04917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chrysophaentin A is an antimicrobial natural product isolated from the marine alga C. taylori in milligram quantity. Structurally, chrysophaentin A features a macrocyclic biaryl ether core incorporating two trisubstituted chloroalkenes at its periphery. A concise synthesis of iso- and 9-dechlorochrysophaentin A enabled by a Z-selective ring-closing metathesis (RCM) cyclization followed by an oxygen to carbon ring contraction is described. Fluorescent microscopy studies revealed 9-dechlorochrysophaentins leads to inhibition of bacterial cell wall biosynthesis by disassembly of key divisome proteins, the cornerstone to bacterial cell wall biosynthesis and division.
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Affiliation(s)
| | - Yen-Pang Hsu
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Ellen M Quardokus
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Gengxiang Zhao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Carole A Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Michael VanNieuwenhze
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Gary A Sulikowski
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, United States.,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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19
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Syntheses of hybrid cyclopeptidyl [n]sulfanes by internal alkyl group exchange. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Sulfane transalkylations and metal catalyzed allylic substitutions for the synthesis of composite macrobicyclic peptides. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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21
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Wallraven K, Holmelin FL, Glas A, Hennig S, Frolov AI, Grossmann TN. Adapting free energy perturbation simulations for large macrocyclic ligands: how to dissect contributions from direct binding and free ligand flexibility. Chem Sci 2020; 11:2269-2276. [PMID: 32180932 PMCID: PMC7057854 DOI: 10.1039/c9sc04705k] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/20/2020] [Indexed: 11/25/2022] Open
Abstract
Large and flexible ligands gain increasing interest in the development of bioactive agents. They challenge the applicability of computational ligand optimization strategies originally developed for small molecules. Free energy perturbation (FEP) is often used for predicting binding affinities of small molecule ligands, however, its use for more complex ligands remains limited. Herein, we report the structure-based design of peptide macrocycles targeting the protein binding site of human adaptor protein 14-3-3. We observe a surprisingly strong dependency of binding affinities on relatively small variations in substituent size. FEP was performed to rationalize observed trends. To account for insufficient convergence of FEP, restrained calculations were performed and complemented with extensive REST MD simulations of the free ligands. These calculations revealed that changes in affinity originate both from altered direct interactions and conformational changes of the free ligand. In addition, MD simulations provided the basis to rationalize unexpected trends in ligand lipophilicity. We also verified the anticipated interaction site and binding mode for one of the high affinity ligands by X-ray crystallography. The introduced fully-atomistic simulation protocol can be used to rationalize the development of structurally complex ligands which will support future ligand maturation efforts.
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Affiliation(s)
- Kerstin Wallraven
- Department of Chemistry & Pharmaceutical Sciences , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands .
| | - Fredrik L Holmelin
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism , BioPharmaceuticals R&D , AstraZeneca , Pepparedsleden 1, Mölndal , 431 83 , Sweden .
| | - Adrian Glas
- Department of Chemistry & Pharmaceutical Sciences , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands .
| | - Sven Hennig
- Department of Chemistry & Pharmaceutical Sciences , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands .
| | - Andrey I Frolov
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism , BioPharmaceuticals R&D , AstraZeneca , Pepparedsleden 1, Mölndal , 431 83 , Sweden .
| | - Tom N Grossmann
- Department of Chemistry & Pharmaceutical Sciences , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands .
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22
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Adebomi V, Cohen RD, Wills R, Chavers HAH, Martin GE, Raj M. CyClick Chemistry for the Synthesis of Cyclic Peptides. Angew Chem Int Ed Engl 2019; 58:19073-19080. [DOI: 10.1002/anie.201911900] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Victor Adebomi
- Department of Chemistry and Biochemistry Auburn University Auburn AL 36830 USA
| | - Ryan D. Cohen
- Analytical Research and Development Merck & Co. Inc. Rahway NJ 07065 USA
- Department of Chemistry & Biochemistry Seton Hall University South Orange NJ 07079 USA
| | - Rachel Wills
- Department of Chemistry and Biochemistry Auburn University Auburn AL 36830 USA
| | | | - Gary E. Martin
- Analytical Research and Development Merck & Co. Inc. Rahway NJ 07065 USA
- Department of Chemistry & Biochemistry Seton Hall University South Orange NJ 07079 USA
| | - Monika Raj
- Department of Chemistry and Biochemistry Auburn University Auburn AL 36830 USA
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23
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Adebomi V, Cohen RD, Wills R, Chavers HAH, Martin GE, Raj M. CyClick Chemistry for the Synthesis of Cyclic Peptides. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911900] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Victor Adebomi
- Department of Chemistry and Biochemistry Auburn University Auburn AL 36830 USA
| | - Ryan D. Cohen
- Analytical Research and Development Merck & Co. Inc. Rahway NJ 07065 USA
- Department of Chemistry & Biochemistry Seton Hall University South Orange NJ 07079 USA
| | - Rachel Wills
- Department of Chemistry and Biochemistry Auburn University Auburn AL 36830 USA
| | | | - Gary E. Martin
- Analytical Research and Development Merck & Co. Inc. Rahway NJ 07065 USA
- Department of Chemistry & Biochemistry Seton Hall University South Orange NJ 07079 USA
| | - Monika Raj
- Department of Chemistry and Biochemistry Auburn University Auburn AL 36830 USA
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24
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Mortensen KT, Osberger TJ, King TA, Sore HF, Spring DR. Strategies for the Diversity-Oriented Synthesis of Macrocycles. Chem Rev 2019; 119:10288-10317. [DOI: 10.1021/acs.chemrev.9b00084] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Kim T. Mortensen
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Thomas J. Osberger
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Thomas A. King
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Hannah F. Sore
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - David R. Spring
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
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25
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Abstract
This Review is devoted to the chemistry of macrocyclic peptides having heterocyclic fragments in their structure. These motifs are present in many natural products and synthetic macrocycles designed against a particular biochemical target. Thiazole and oxazole are particularly common constituents of naturally occurring macrocyclic peptide molecules. This frequency of occurrence is because the thiazole and oxazole rings originate from cysteine, serine, and threonine residues. Whereas other heteroaryl groups are found less frequently, they offer many insightful lessons that range from conformational control to receptor/ligand interactions. Many options to develop new and improved technologies to prepare natural products have appeared in recent years, and the synthetic community has been pursuing synthetic macrocycles that have no precedent in nature. This Review attempts to summarize progress in this area.
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Affiliation(s)
- Ivan V Smolyar
- Department of Chemistry , Moscow State University , Leninskije Gory , 199991 Moscow , Russia
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
| | - Valentine G Nenajdenko
- Department of Chemistry , Moscow State University , Leninskije Gory , 199991 Moscow , Russia
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26
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Li B, Li X, Han B, Chen Z, Zhang X, He G, Chen G. Construction of Natural-Product-Like Cyclophane-Braced Peptide Macrocycles via sp3 C–H Arylation. J Am Chem Soc 2019; 141:9401-9407. [DOI: 10.1021/jacs.9b04221] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xinghua Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Boyang Han
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhijie Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xuekai Zhang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
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27
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Lee H, Boyer NC, Deng Q, Kim HY, Sawyer TK, Sciammetta N. Photoredox Ni-catalyzed peptide C(sp 2)-O cross-coupling: from intermolecular reactions to side chain-to-tail macrocyclization. Chem Sci 2019; 10:5073-5078. [PMID: 31183058 PMCID: PMC6524625 DOI: 10.1039/c9sc00694j] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/08/2019] [Indexed: 12/13/2022] Open
Abstract
Ni/photoredox (4DPAIPN) dual catalysis enabled challenging peptide C(sp2)-O coupling reactions. Successful cross-coupling reactions were demonstrated with highly functionalized alcohols including side chains of amino acids (i.e., serine, threonine, tyrosine), trans-4-hydroxy-l-proline, alkyl alcohols, alkynylated alcohols, and carbohydrates. Coupling reactions between bromobenzoyl-capped peptides containing various side chains and either a protected serine building block or a serine-containing dipeptide also proceeded efficiently. Chemoselective C-O coupling (over C-N) was achieved in intermolecular reactions in the presence of a C-terminal primary amide. Furthermore, by judicious structural design in combination with computational modeling, we demonstrated side chain-to-tail macrocyclization of peptides containing a β-turn motif via C-O coupling. The methodology developed in this work brings new opportunities for late-stage diversification of complex linear and macrocyclic peptides.
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Affiliation(s)
- Hyelee Lee
- Department of Discovery Chemistry , MRL , Merck & Co., Inc. , Boston , Massachusetts 02115 , USA . ;
| | - Nicolas C Boyer
- Department of Discovery Chemistry , MRL , Merck & Co., Inc. , Boston , Massachusetts 02115 , USA . ;
| | - Qiaolin Deng
- Computational and Structural Chemistry , MRL , Merck & Co., Inc. , Kenilworth , New Jersey 07033 , USA
| | - Hai-Young Kim
- Process and Analytical Research and Development , MRL , Merck & Co., Inc. , Boston , Massachusetts 02115 , USA
| | - Tomi K Sawyer
- Chemistry Capabilities for Accelerating Therapeutics , MRL , Merck & Co., Inc. , Boston , Massachusetts 02115 , USA
| | - Nunzio Sciammetta
- Department of Discovery Chemistry , MRL , Merck & Co., Inc. , Boston , Massachusetts 02115 , USA . ;
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28
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Mull RW, Harrington A, Sanchez LA, Tal-Gan Y. Cyclic Peptides that Govern Signal Transduction Pathways: From Prokaryotes to Multi-Cellular Organisms. Curr Top Med Chem 2018; 18:625-644. [PMID: 29773060 DOI: 10.2174/1568026618666180518090705] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/30/2016] [Accepted: 12/17/2017] [Indexed: 12/16/2022]
Abstract
Cyclic peptide scaffolds are key components of signal transduction pathways in both prokaryotic and eukaryotic organisms since they act as chemical messengers that activate or inhibit specific cognate receptors. In prokaryotic organisms these peptides are utilized in non-essential pathways, such as quorum sensing, that are responsible for virulence and pathogenicity. In the more evolved eukaryotic systems, cyclic peptide hormones play a key role in the regulation of the overall function of multicellular organisms, mainly through the endocrine system. This review will highlight several prokaryote and eukaryote systems that use cyclic peptides as their primary signals and the potential associated with utilizing these scaffolds for the discovery of novel therapeutics for a wide range of diseases and illnesses.
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Affiliation(s)
- Ryan W Mull
- Department of Chemistry, University of Nevada, Reno, NV 89557, United States
| | - Anthony Harrington
- Department of Chemistry, University of Nevada, Reno, NV 89557, United States
| | - Lucia A Sanchez
- Department of Chemistry, University of Nevada, Reno, NV 89557, United States
| | - Yftah Tal-Gan
- Department of Chemistry, University of Nevada, Reno, NV 89557, United States
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29
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A general strategy for synthesis of cyclophane-braced peptide macrocycles via palladium-catalysed intramolecular sp3 C−H arylation. Nat Chem 2018; 10:540-548. [DOI: 10.1038/s41557-018-0006-y] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 12/06/2017] [Indexed: 11/08/2022]
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30
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Kaldas SJ, Yudin AK. Achieving Skeletal Diversity in Peptide Macrocycles through The Use of Heterocyclic Grafts. Chemistry 2018; 24:7074-7082. [DOI: 10.1002/chem.201705418] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Sherif J. Kaldas
- Davenport Research Laboratories, Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Andrei K. Yudin
- Davenport Research Laboratories, Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
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31
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Curtin BH, Manoni F, Park J, Sisto LJ, Lam YH, Gravel M, Roulston A, Harran PG. Assembly of Complex Macrocycles by Incrementally Amalgamating Unprotected Peptides with a Designed Four-Armed Insert. J Org Chem 2018; 83:3090-3108. [DOI: 10.1021/acs.joc.7b02958] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Brice H. Curtin
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Francesco Manoni
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Jiyong Park
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Luke J. Sisto
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Yu-hong Lam
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Michel Gravel
- Laboratory for Therapeutic Development, Rosalind and Morris Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Anne Roulston
- Laboratory for Therapeutic Development, Rosalind and Morris Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Patrick G. Harran
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
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32
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Hubert JG, Stepek IA, Noda H, Bode JW. Synthetic fermentation of β-peptide macrocycles by thiadiazole-forming ring-closing reactions. Chem Sci 2018; 9:2159-2167. [PMID: 29719689 PMCID: PMC5896468 DOI: 10.1039/c7sc05057g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 01/05/2018] [Indexed: 01/12/2023] Open
Abstract
A new thiadiazole-forming macrocyclization reaction enables the one-pot synthesis of cyclic β-peptide libraries from readily accessible building blocks without additional reagents.
Macrocyclic β-peptides were efficiently prepared using a thiadiazole-forming cyclization reaction between an α-ketoacid and a thiohydrazide. The linear β-peptide precursors were assembled from isoxazolidine monomers by α-ketoacid-hydroxylamine (KAHA) ligations with a bifunctional initiator – a process we have termed ‘synthetic fermentation’ due to the analogy of producing natural product-like molecules from simpler building blocks. The linear synthetic fermentation products underwent Boc-deprotection/thiadiazole-forming macrocyclization under aqueous, acidic conditions to provide the cyclic products in a one-pot process. This reaction sequence proceeds from easily accessed initiator and monomer building blocks without the need for additional catalysts or reagents, enabling facile production of macrocyclic β-peptides, a relatively underexplored structural class.
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Affiliation(s)
- Jonathan G Hubert
- Laboratorium für Organische Chemie , Department of Chemistry and Applied Biosciences , ETH Zürich , Zürich , Switzerland 8093 . ; http://www.bode.ethz.ch
| | - Iain A Stepek
- Laboratorium für Organische Chemie , Department of Chemistry and Applied Biosciences , ETH Zürich , Zürich , Switzerland 8093 . ; http://www.bode.ethz.ch
| | - Hidetoshi Noda
- Institute of Microbial Chemistry (Bikaken) , 3-14-23 Kamiosaki, Shinagawa-ku , Tokyo 141-0021 , Japan
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie , Department of Chemistry and Applied Biosciences , ETH Zürich , Zürich , Switzerland 8093 . ; http://www.bode.ethz.ch
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Verma H, Khatri B, Chakraborti S, Chatterjee J. Increasing the bioactive space of peptide macrocycles by thioamide substitution. Chem Sci 2018; 9:2443-2451. [PMID: 29732120 PMCID: PMC5909342 DOI: 10.1039/c7sc04671e] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 01/19/2018] [Indexed: 12/23/2022] Open
Abstract
We show that substituting a single atom, O to S (amide to thioamide), in a peptide bond results in global restriction of the conformational flexibility in peptide macrocycles with minimal perturbation of the parent conformation. The van der Waals interactions between the C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 S group and the surrounding atoms are the major driving force in inducing the conformational restriction, resulting in well-defined structures of these cyclic peptides with static 3-D presentation of the pharmacophores. Utilizing this property of thioamides, we report the development of a superactive antagonist of pro-angiogenic αvβ3, αvβ5 and α5β1 integrins, which are responsible for cancer cell proliferation and survival. Using simple thio-scanning and spatial screening of a non-efficacious and conformationally flexible cyclic peptide, we could achieve a more than 105 fold enhancement in its efficacy in cellulo via a single O to S substitution. The developed peptide shows better efficacy in inhibiting the pro-angiogenic integrins than the drug candidate cilengitide, with a significantly enhanced serum half-life of 36 h compared to that of cilengitide (12 h). The long shelf-life, absence of non-specific toxicity and resistance to degradation of the thioamidated macrocyclic peptides in human serum suggest the promise of thioamides in markedly improving the affinity, efficacy and pharmacology of peptide macrocycles.
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Affiliation(s)
- Hitesh Verma
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Bhavesh Khatri
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Sohini Chakraborti
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Jayanta Chatterjee
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India . .,NMR Research Centre , Indian Institute of Science , Bangalore 560012 , India
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34
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Hui EYL, Rout B, Tan YS, Verma CS, Chan KP, Johannes CW. An intramolecular tryptophan-condensation approach for peptide stapling. Org Biomol Chem 2018; 16:389-392. [DOI: 10.1039/c7ob02667f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Stapled peptides are gaining tremendous interest as next-generation therapeutic agents to target protein–protein interactions. Herein, we report an intramolecular peptide stapling method which links two tryptophan residues at C2 position of the indole moieties via acid-mediated condensation with an aldehyde.
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Affiliation(s)
- Eunice Y.-L. Hui
- Division of Organic Chemistry
- Institute of Chemical and Engineering Sciences
- Agency for Science Technology and Research (A*STAR)
- Singapore 138665
| | - Bhimsen Rout
- Experimental Dermatology Division
- Institute of Medical Biology
- A*STAR
- Singapore 138648
| | - Yaw Sing Tan
- Bioinformatics Institute
- Agency for Science Technology and Research (A*STAR)
- Singapore 138671
| | - Chandra S. Verma
- Bioinformatics Institute
- Agency for Science Technology and Research (A*STAR)
- Singapore 138671
- Department of Biological Sciences
- National University of Singapore
| | - Kok-Ping Chan
- Division of Organic Chemistry
- Institute of Chemical and Engineering Sciences
- Agency for Science Technology and Research (A*STAR)
- Singapore 138665
| | - Charles W. Johannes
- Division of Organic Chemistry
- Institute of Chemical and Engineering Sciences
- Agency for Science Technology and Research (A*STAR)
- Singapore 138665
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35
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Wu J, Tang J, Chen H, He Y, Wang H, Yao H. Recent developments in peptide macrocyclization. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2017.12.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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36
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Sindhikara D, Spronk SA, Day T, Borrelli K, Cheney DL, Posy SL. Improving Accuracy, Diversity, and Speed with Prime Macrocycle Conformational Sampling. J Chem Inf Model 2017; 57:1881-1894. [DOI: 10.1021/acs.jcim.7b00052] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Dan Sindhikara
- Schrödinger, Inc., 120 West 45th Street,
17th Floor, New York, New
York 10036, United States
| | - Steven A. Spronk
- Bristol-Myers
Squibb Research and Development, Computer-Assisted Drug Design, Molecular Discovery Technologies, P.O. Box 5400, Princeton, New Jersey 08543, United States
| | - Tyler Day
- Schrödinger, Inc., 120 West 45th Street,
17th Floor, New York, New
York 10036, United States
| | - Ken Borrelli
- Schrödinger, Inc., 120 West 45th Street,
17th Floor, New York, New
York 10036, United States
| | - Daniel L. Cheney
- Bristol-Myers
Squibb Research and Development, Computer-Assisted Drug Design, Molecular Discovery Technologies, P.O. Box 5400, Princeton, New Jersey 08543, United States
| | - Shana L. Posy
- Bristol-Myers
Squibb Research and Development, Computer-Assisted Drug Design, Molecular Discovery Technologies, P.O. Box 5400, Princeton, New Jersey 08543, United States
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37
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Dual-targeting peptide probe for sequence- and structure-sensitive sensing of serum albumin. Biosens Bioelectron 2017; 94:657-662. [DOI: 10.1016/j.bios.2017.03.067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/24/2017] [Accepted: 03/31/2017] [Indexed: 01/06/2023]
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38
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Malins LR, deGruyter JN, Robbins KJ, Scola PM, Eastgate MD, Ghadiri MR, Baran PS. Peptide Macrocyclization Inspired by Non-Ribosomal Imine Natural Products. J Am Chem Soc 2017; 139:5233-5241. [PMID: 28326777 PMCID: PMC5391502 DOI: 10.1021/jacs.7b01624] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A thermodynamic approach to peptide macrocyclization inspired by the cyclization of non-ribosomal peptide aldehydes is presented. The method provides access to structurally diverse macrocycles by exploiting the reactivity of transient macrocyclic peptide imines toward inter- and intramolecular nucleophiles. Reactions are performed in aqueous media, in the absence of side chain protecting groups, and are tolerant of all proteinogenic functional groups. Macrocyclic products bearing non-native and rigidifying structural motifs, isotopic labels, and a variety of bioorthogonal handles are prepared, along with analogues of four distinct natural products. Structural interrogation of the linear and macrocyclic peptides using variable-temperature NMR and circular dichroism suggests that preorganization of linear substrates is not a prerequisite for macrocyclization.
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Affiliation(s)
- Lara R Malins
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Justine N deGruyter
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Kevin J Robbins
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Paul M Scola
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Martin D Eastgate
- Chemical Development, Bristol-Myers Squibb , One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - M Reza Ghadiri
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Phil S Baran
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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39
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Zhang J, Mulumba M, Ong H, Lubell WD. Diversity-Oriented Synthesis of Cyclic Azapeptides by A3-Macrocyclization Provides High-Affinity CD36-Modulating Peptidomimetics. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611685] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Jinqiang Zhang
- Département de Chimie; Université de Montréal; C.P. 6128, Succursale Centre-Ville Montréal Québec H3C 3J7 Canada
- Present address: School of Pharmaceutical Science; Chongqing University; Chongqing 401331 China
| | - Mukandila Mulumba
- Faculté de Pharmacie; Université de Montréal; C.P. 6128, Succursale Centre-Ville Montréal Québec H3C 3J7 Canada
| | - Huy Ong
- Faculté de Pharmacie; Université de Montréal; C.P. 6128, Succursale Centre-Ville Montréal Québec H3C 3J7 Canada
| | - William D. Lubell
- Département de Chimie; Université de Montréal; C.P. 6128, Succursale Centre-Ville Montréal Québec H3C 3J7 Canada
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40
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Zhang J, Mulumba M, Ong H, Lubell WD. Diversity-Oriented Synthesis of Cyclic Azapeptides by A 3 -Macrocyclization Provides High-Affinity CD36-Modulating Peptidomimetics. Angew Chem Int Ed Engl 2017; 56:6284-6288. [PMID: 28090719 DOI: 10.1002/anie.201611685] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 12/14/2016] [Indexed: 11/11/2022]
Abstract
Macrocyclization has enabled the use of peptides in drug discovery creating a need for methods to synthesize diverse peptide macrocycles. Azapeptides have advanced to clinically used drugs, however, few cyclic azapeptides have been studied. A multiple component "A3 -macrocyclization" strategy is described for the preparation of diverse cyclic azapeptides and is demonstrated by the synthesis of 15 growth hormone releasing hormone-6 (GHRP-6) analogs. Certain cyclic aza-GHRP-6 analogs exhibited unprecedented affinity for the CD36 receptor, and capacity to modulate Toll-like receptor agonist-induced overproduction of nitric oxide, and reduce pro-inflammatory cytokine and chemokine production in macrophages.
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Affiliation(s)
- Jinqiang Zhang
- Département de Chimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, Québec, H3C 3J7, Canada.,Present address: School of Pharmaceutical Science, Chongqing University, Chongqing, 401331, China
| | - Mukandila Mulumba
- Faculté de Pharmacie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Huy Ong
- Faculté de Pharmacie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - William D Lubell
- Département de Chimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, Québec, H3C 3J7, Canada
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41
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Metrano A, Abascal NC, Mercado BQ, Paulson EK, Hurtley AE, Miller SJ. Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences. J Am Chem Soc 2017; 139:492-516. [PMID: 28029251 PMCID: PMC5312972 DOI: 10.1021/jacs.6b11348] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Indexed: 11/30/2022]
Abstract
X-ray crystallography has been applied to the structural analysis of a series of tetrapeptides that were previously assessed for catalytic activity in an atroposelective bromination reaction. Common to the series is a central Pro-Xaa sequence, where Pro is either l- or d-proline, which was chosen to favor nucleation of canonical β-turn secondary structures. Crystallographic analysis of 35 different peptide sequences revealed a range of conformational states. The observed differences appear not only in cases where the Pro-Xaa loop-region is altered, but also when seemingly subtle alterations to the flanking residues are introduced. In many instances, distinct conformers of the same sequence were observed, either as symmetry-independent molecules within the same unit cell or as polymorphs. Computational studies using DFT provided additional insight into the analysis of solid-state structural features. Select X-ray crystal structures were compared to the corresponding solution structures derived from measured proton chemical shifts, 3J-values, and 1H-1H-NOESY contacts. These findings imply that the conformational space available to simple peptide-based catalysts is more diverse than precedent might suggest. The direct observation of multiple ground state conformations for peptides of this family, as well as the dynamic processes associated with conformational equilibria, underscore not only the challenge of designing peptide-based catalysts, but also the difficulty in predicting their accessible transition states. These findings implicate the advantages of low-barrier interconversions between conformations of peptide-based catalysts for multistep, enantioselective reactions.
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Affiliation(s)
- Anthony
J. Metrano
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Nadia C. Abascal
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Brandon Q. Mercado
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Eric K. Paulson
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Anna E. Hurtley
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Scott J. Miller
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
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42
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Hopkins BA, Smith GF, Sciammetta N. Synthesis of Cyclic Peptidomimetics via a Pd-Catalyzed Macroamination Reaction. Org Lett 2016; 18:4072-5. [DOI: 10.1021/acs.orglett.6b01961] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Brett A. Hopkins
- Discovery Chemistry, Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Graham F. Smith
- Discovery Chemistry, Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Nunzio Sciammetta
- Discovery Chemistry, Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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43
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Forbes CR, Pandey AK, Ganguly HK, Yap GPA, Zondlo NJ. 4R- and 4S-iodophenyl hydroxyproline, 4R-pentynoyl hydroxyproline, and S-propargyl-4-thiolphenylalanine: conformationally biased and tunable amino acids for bioorthogonal reactions. Org Biomol Chem 2016; 14:2327-46. [PMID: 26806113 PMCID: PMC5824642 DOI: 10.1039/c5ob02473k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bioorthogonal reactions allow the introduction of new functionalities into peptides, proteins, and other biological molecules. The most readily accessible amino acids for bioorthogonal reactions have modest conformational preferences or bases for molecular interactions. Herein we describe the synthesis of 4 novel amino acids containing functional groups for bioorthogonal reactions. (2S,4R)- and (2S,4S)-iodophenyl ethers of hydroxyproline are capable of modification via rapid, specific Suzuki and Sonogashira reactions in water. The synthesis of these amino acids, as Boc-, Fmoc- and free amino acids, was achieved through succinct sequences. These amino acids exhibit well-defined conformational preferences, with the 4S-iodophenyl hydroxyproline crystallographically exhibiting β-turn (ϕ, ψ∼-80°, 0°) or relatively extended (ϕ, ψ∼-80°, +170°) conformations, while the 4R-diastereomer prefers a more compact conformation (ϕ∼-60°). The aryloxyproline diastereomers present the aryl groups in a highly divergent manner, suggesting their stereospecific use in molecular design, medicinal chemistry, and catalysis. Thus, the 4R- and 4S-iodophenyl hydroxyprolines can be differentially applied in distinct structural contexts. The pentynoate ester of 4R-hydroxyproline introduces an alkyne functional group within an amino acid that prefers compact conformations. The propargyl thioether of 4-thiolphenylalanine was synthesized via copper-mediated cross-coupling reaction of thioacetic acid with protected 4-iodophenylalanine, followed by thiolysis and alkylation. This amino acid combines an alkyne functional group with an aromatic amino acid and the ability to tune aromatic and side chain properties via sulfur oxidation. These amino acids provide novel loci for peptide functionalization, with greater control of conformation possible than with other amino acids containing these functional groups.
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Affiliation(s)
- Christina R. Forbes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Anil K. Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Himal K. Ganguly
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Glenn P. A. Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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Bartoloni M, Jin X, Marcaida MJ, Banha J, Dibonaventura I, Bongoni S, Bartho K, Gräbner O, Sefkow M, Darbre T, Reymond JL. Bridged bicyclic peptides as potential drug scaffolds: synthesis, structure, protein binding and stability. Chem Sci 2015; 6:5473-5490. [PMID: 29861888 PMCID: PMC5949603 DOI: 10.1039/c5sc01699a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/12/2015] [Indexed: 12/28/2022] Open
Abstract
Double cyclization of short linear peptides obtained by solid phase peptide synthesis was used to prepare bridged bicyclic peptides (BBPs) corresponding to the topology of bridged bicyclic alkanes such as norbornane. Diastereomeric norbornapeptides were investigated by 1H-NMR, X-ray crystallography and CD spectroscopy and found to represent rigid globular scaffolds stabilized by intramolecular backbone hydrogen bonds with scaffold geometries determined by the chirality of amino acid residues and sharing structural features of β-turns and α-helices. Proteome profiling by capture compound mass spectrometry (CCMS) led to the discovery of the norbornapeptide 27c binding selectively to calmodulin as an example of a BBP protein binder. This and other BBPs showed high stability towards proteolytic degradation in serum.
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Affiliation(s)
- Marco Bartoloni
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
| | - Xian Jin
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
| | - Maria José Marcaida
- School of Life Sciences , Ecole Polytechnique de Lausanne , 1015 Lausanne , Switzerland
| | - João Banha
- caprotec bioanalytics GmbH , Berlin , Germany
| | - Ivan Dibonaventura
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
| | - Swathi Bongoni
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
| | | | | | | | - Tamis Darbre
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
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Martí-Centelles V, Pandey MD, Burguete MI, Luis SV. Macrocyclization Reactions: The Importance of Conformational, Configurational, and Template-Induced Preorganization. Chem Rev 2015; 115:8736-834. [DOI: 10.1021/acs.chemrev.5b00056] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Mrituanjay D. Pandey
- Departament de Química
Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain
| | - M. Isabel Burguete
- Departament de Química
Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain
| | - Santiago V. Luis
- Departament de Química
Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain
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Mendive-Tapia L, Preciado S, García J, Ramón R, Kielland N, Albericio F, Lavilla R. New peptide architectures through C-H activation stapling between tryptophan-phenylalanine/tyrosine residues. Nat Commun 2015; 6:7160. [PMID: 25994485 PMCID: PMC4455059 DOI: 10.1038/ncomms8160] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 04/10/2015] [Indexed: 12/22/2022] Open
Abstract
Natural peptides show high degrees of specificity in their biological action. However, their therapeutical profile is severely limited by their conformational freedom and metabolic instability. Stapled peptides constitute a solution to these problems and access to these structures lies on a limited number of reactions involving the use of non-natural amino acids. Here, we describe a synthetic strategy for the preparation of unique constrained peptides featuring a covalent bond between tryptophan and phenylalanine or tyrosine residues. The preparation of such peptides is achieved in solution and on solid phase directly from the corresponding sequences having an iodo-aryl amino acid through an intramolecular palladium-catalysed C–H activation process. Moreover, complex topologies arise from the internal stapling of cyclopeptides and double intramolecular arylations within a linear peptide. Finally, as a proof of principle, we report the application to this new stapling method to relevant biologically active compounds. Macrocyclic, constrained peptides show promise in therapeutic applications due to the stable and defined conformations that can be produced. Here, the authors report a method to form macrocyclic peptides through C–H activation on tryptophan and coupling with iodo-substituted aryl amino acids
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Affiliation(s)
- Lorena Mendive-Tapia
- 1] Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain [2] Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1-11, 08028 Barcelona, Spain [3] CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine
| | - Sara Preciado
- Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1-11, 08028 Barcelona, Spain
| | - Jesús García
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Rosario Ramón
- Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Nicola Kielland
- Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Fernando Albericio
- 1] Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain [2] Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1-11, 08028 Barcelona, Spain [3] CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine [4] School of Chemistry, Yachay Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador
| | - Rodolfo Lavilla
- 1] Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain [2] Laboratory of Organic Chemistry, Faculty of Pharmacy, University of Barcelona, Avda. Joan XXII s.n., 08028 Barcelona, Spain
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Rose TE, Lawson KV, Harran PG. Large ring-forming alkylations provide facile access to composite macrocycles. Chem Sci 2015; 6:2219-2223. [PMID: 28694951 PMCID: PMC5485560 DOI: 10.1039/c4sc03848g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/05/2015] [Indexed: 11/21/2022] Open
Abstract
Macrocyclic compounds have potential to enable drug discovery for protein targets with extended, solvent-exposed binding sites. Crystallographic structures of peptides bound at such sites show strong surface complementarity and frequent aromatic side-chain contacts. In an effort to capture these features in stabilized small molecules, we describe a method to convert linear peptides into constrained macrocycles based upon their aromatic content. Designed templates initiate the venerable Friedel-Crafts alkylation to form large rings efficiently at room temperature - routinely within minutes - and unimpeded by polar functional groups. No protecting groups, metals, or air-free techniques are required. Regiochemistry can be tuned electronically to explore diverse macrocycle connectivities. Templates with additional reaction capabilities can further manipulate macrocycle structure. The chemistry lays a foundation to extend studies of how the size, shape and constitution of peptidyl macrocycles correlate with their pharmacological properties.
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Affiliation(s)
- Tristan E Rose
- Department of Chemistry and Biochemistry , University of California Los Angeles , 607 Charles E. Young Drive East , Los Angeles , USA .
| | - Kenneth V Lawson
- Department of Chemistry and Biochemistry , University of California Los Angeles , 607 Charles E. Young Drive East , Los Angeles , USA .
| | - Patrick G Harran
- Department of Chemistry and Biochemistry , University of California Los Angeles , 607 Charles E. Young Drive East , Los Angeles , USA .
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Tsomaia N. Peptide therapeutics: Targeting the undruggable space. Eur J Med Chem 2015; 94:459-70. [DOI: 10.1016/j.ejmech.2015.01.014] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 01/04/2023]
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Rao VA. Perspectives on Engineering Biobetter Therapeutic Proteins with Greater Stability in Inflammatory Environments. BIOBETTERS 2015. [DOI: 10.1007/978-1-4939-2543-8_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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