1
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Abboud SA, Kodadek T. 2-Pyridone Formation: An Efficient Method for the Solid-Phase Synthesis of Homodimers. Chemistry 2024; 30:e202302937. [PMID: 37939246 PMCID: PMC10843674 DOI: 10.1002/chem.202302937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/09/2023] [Accepted: 11/08/2023] [Indexed: 11/10/2023]
Abstract
This study presents an efficient method for on-resin dimer generation through self-condensation of 3,3-dimethoxypropionic acid-modified molecules, resulting in 2-pyridones. The approach demonstrated remarkable versatility by producing homodimers of peptides, peptoids, and non-peptidic ligands. Its ease of application, broad utility, and mild reaction conditions not only hold significance for peptide and peptoid research but also offer potential for the on-resin development of a wide range of bivalent ligands.
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Affiliation(s)
- Skander A Abboud
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA
| | - Thomas Kodadek
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA
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2
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Zhong W, Wan C, Zhou Z, Dai C, Zhang Y, Lu F, Yin F, Li Z. 4-Iodine N-Methylpyridinium-Mediated Peptide Synthesis. Org Lett 2023; 25:8661-8665. [PMID: 38009639 DOI: 10.1021/acs.orglett.3c03539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Through systematic optimization of halopyridinium compounds, we established a peptide coupling protocol utilizing 4-iodine N-methylpyridinium (4IMP) for solid-phase peptide synthesis (SPPS). The 4IMP coupling reagent is easily prepared, bench stable, and cost-effective. Employing 4IMP in the SPPS process has showcased remarkable chemoselectivity and efficiency, effectively eliminating racemization and epimerization. This achievement has been substantiated through the successful synthesis of a range of peptides via the direct utilization of commercially available amino acid substrates for SPPS.
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Affiliation(s)
- Wanjin Zhong
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Chuan Wan
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118, China
| | - Ziyuan Zhou
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Chuan Dai
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Yichi Zhang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Fei Lu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, China
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3
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Krajcovicova S, Spring DR. Tryptophan in Multicomponent Petasis Reactions for Peptide Stapling and Late-Stage Functionalisation. Angew Chem Int Ed Engl 2023; 62:e202307782. [PMID: 37389988 DOI: 10.1002/anie.202307782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/26/2023] [Accepted: 06/30/2023] [Indexed: 07/02/2023]
Abstract
Peptide stapling is a robust strategy for generating enzymatically stable, macrocyclic peptides. The incorporation of biologically relevant tags (such as cell-penetrating motifs or fluorescent dyes) into peptides, while preserving their binding interactions and enhancing their stability, is highly sought after. Despite the unique opportunities offered by tryptophan's indole scaffold for targeted functionalisation, its utilisation in peptide stapling has been limited as compared to other amino acids. Herein, we present an approach for peptide stapling using the tryptophan-mediated Petasis reaction. This method enables the synthesis of both stapled and labelled peptides and is applicable to both solution and solid-phase synthesis. Importantly, the use of the Petasis reaction in combination with tryptophan facilitates the formation of stapled peptides in a straightforward, multicomponent fashion, while circumventing the formation of undesired by-products. Furthermore, this approach allows for efficient and diverse late-stage peptide modifications, thereby enabling rapid production of numerous conjugates for biological and medicinal applications.
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Affiliation(s)
- Sona Krajcovicova
- Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
- Department of Organic Chemistry, Palacky University Olomouc, Tr. 17. Listopadu 12, 77900, Olomouc, Czech Republic
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
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4
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Bąchor U, Lizak A, Bąchor R, Mączyński M. 5-Amino-3-methyl-Isoxazole-4-carboxylic Acid as a Novel Unnatural Amino Acid in the Solid Phase Synthesis of α/β-Mixed Peptides. Molecules 2022; 27:molecules27175612. [PMID: 36080386 PMCID: PMC9457529 DOI: 10.3390/molecules27175612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
The hybrid peptides consisting of α and β-amino acids show great promise as peptidomimetics that can be used as therapeutic agents. Therefore, the development of new unnatural amino acids and the methods of their incorporation into the peptide chain is an important task. Here, we described our investigation of the possibility of 5-amino-3-methyl-isoxazole-4-carboxylic acid (AMIA) application in the solid phase peptide synthesis. This new unnatural β-amino acid, presenting various biological activities, was successfully coupled to a resin-bound peptide using different reaction conditions, including classical and ultrasonic agitated solid-phase synthesis. All the synthesized compounds were characterized by tandem mass spectrometry. The obtained results present the possibility of the application of this β-amino acid in the synthesis of a new class of bioactive peptides.
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Affiliation(s)
- Urszula Bąchor
- Department of Organic Chemistry and Drug Technology, Faculty of Pharmacy, Wroclaw Medical University, 50-556 Wroclaw, Poland
- Correspondence: (U.B.); (R.B.); Tel.: +48-78-406-34 (U.B.); +48-71-375-7218 (R.B.); Fax: +48-71-328-2348 (R.B.)
| | - Agnieszka Lizak
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Remigiusz Bąchor
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
- Correspondence: (U.B.); (R.B.); Tel.: +48-78-406-34 (U.B.); +48-71-375-7218 (R.B.); Fax: +48-71-328-2348 (R.B.)
| | - Marcin Mączyński
- Department of Organic Chemistry and Drug Technology, Faculty of Pharmacy, Wroclaw Medical University, 50-556 Wroclaw, Poland
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5
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Alfano AI, Lange H, Brindisi M. Amide Bonds Meet Flow Chemistry: A Journey into Methodologies and Sustainable Evolution. ChemSusChem 2022; 15:e202102708. [PMID: 35015338 PMCID: PMC9304223 DOI: 10.1002/cssc.202102708] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/11/2022] [Indexed: 06/03/2023]
Abstract
Formation of amide bonds is of immanent importance in organic and synthetic medicinal chemistry. Its presence in "traditional" small-molecule active pharmaceutical ingredients, in linear or cyclic oligo- and polypeptidic actives, including pseudopeptides, has led to the development of dedicated synthetic approaches for the formation of amide bonds starting from, if necessary, suitably protected amino acids. While the use of solid supported reagents is common in traditional peptide synthesis, similar approaches targeting amide bond formation in continuous-flow mode took off more significantly, after a first publication in 2006, only a couple of years ago. Most efforts rely upon the transition of traditional approaches in flow mode, or the combination of solid-phase peptide synthesis principles with flow chemistry, and advantages are mainly seen in improving space-time yields. This Review summarizes and compares the various approaches in terms of basic amide formation, peptide synthesis, and pseudopeptide generation, describing the technological approaches and the advantages that were generated by the specific flow approaches. A final discussion highlights potential future needs and perspectives in terms of greener and more sustainable syntheses.
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Affiliation(s)
- Antonella Ilenia Alfano
- SPOTS-Lab – Sustainable Pharmaceutical and Organic Technology and Synthesis LaboratoryUniversity of Naples ‘Federico II', Department of PharmacyVia Domenico Montesano 4980131NaplesItaly
| | - Heiko Lange
- University of Milano-Bicocca Department of Earth and Environmental SciencesPiazza della Scienza 120126MilanItaly
| | - Margherita Brindisi
- SPOTS-Lab – Sustainable Pharmaceutical and Organic Technology and Synthesis LaboratoryUniversity of Naples ‘Federico II', Department of PharmacyVia Domenico Montesano 4980131NaplesItaly
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6
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Huang DL, Li Y, Zheng JS. Removable Backbone Modification (RBM) Strategy for the Chemical Synthesis of Hydrophobic Peptides/Proteins. Methods Mol Biol 2022; 2530:241-256. [PMID: 35761053 DOI: 10.1007/978-1-0716-2489-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Chemical synthesis can provide hydrophobic proteins with natural or man-made modifications (e.g. S-palmitoylation, site-specific isotope labeling and mirror-image proteins) that are difficult to obtain through the recombinant expression technology. The difficulty of chemical synthesis of hydrophobic proteins stems from the hydrophobic nature. Removable backbone modificaiton (RBM) strategy has been developed for solubilizing the hydrophobic peptides/proteins. Here we take the chemical synthesis of a S-palmitoylated peptide as an example to describe the detailed procedure of RBM strategy. Three critical steps of this protocol are: (1) installation of Lys6-tagged RBM groups into the peptides by Fmoc (9-fluorenylmethyloxycarbonyl) solid-phase peptide synthesis, (2) chemical ligation of the peptides, and (3) removal of the RBM tags by TFA (trifluoroacetic acid) cocktails to give the target peptide.
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Affiliation(s)
- Dong-Liang Huang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, China
| | - Ying Li
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, China
| | - Ji-Shen Zheng
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, China.
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7
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Kambanis L, Kulkarni SS, Payne RJ. Side-Chain Anchoring Strategies for the Synthesis of Peptide Thioesters and Selenoesters. Methods Mol Biol 2022; 2530:125-140. [PMID: 35761046 DOI: 10.1007/978-1-0716-2489-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Peptides bearing C-terminal thioester and selenoester functionalities are essential precursors for the chemical synthesis of larger proteins using ligation chemistry, including native chemical ligation (NCL) and diselenide-selenoester ligation (DSL). The use of a side-chain anchoring thioesterification or selenoesterification approach offers a robust method to access peptide thioesters or peptide selenoesters in excellent yields and in high purity. Importantly, this methodology overcomes solubility issues and epimerization of the C-terminal amino acid residue that can occur using solution-phase approaches. Detailed methods for the solid-phase synthesis of peptide thioesters and selenoesters using a side-chain anchoring approach are outlined in this article.
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Affiliation(s)
- Lucas Kambanis
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, Australia
| | - Sameer S Kulkarni
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, Australia
| | - Richard J Payne
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, Australia.
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8
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Zhang X, Yang J, Zhao J. Ynamide-Mediated Synthetic Approach to Thioamide-Substituted Peptides. Methods Mol Biol 2022; 2530:69-80. [PMID: 35761043 DOI: 10.1007/978-1-0716-2489-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A novel synthetic approach to thioamide-substituted peptides is reported. It provides a practical tool for the chemical biology study of peptides and proteins by replacing a carbonyl oxygen atom of an amide bond by an sp2-hybridized sulfur atom to precisely introduce a thioamide bond Ψ[CS-NH] into a peptide backbone. The α-thioacyloxyenamide intermediates, originating from ynamide coupling reagent and proteinogenic amino monothioacids, are proved to be novel effective thioacylating reagents in both the solution and solid phase peptide syntheses. Herein, we describe the detailed synthesis protocol for site-specifically incorporating a thioamide bond at 19 of 20 proteinogenic amino acid residues (except for His) of a peptide backbone in a racemization/epimerization-free manner.
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Affiliation(s)
- Xue Zhang
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Jinhua Yang
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Junfeng Zhao
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi, China.
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, China.
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9
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Corvis Y, Guiblin N, Négrier P, Marenco I, Dembélé O, Espeau P. Scalemic mixtures preparation for optimized composition of ibuprofen solid dosage forms. Eur J Pharm Biopharm 2021; 169:91-96. [PMID: 34571192 DOI: 10.1016/j.ejpb.2021.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/18/2021] [Accepted: 09/21/2021] [Indexed: 11/17/2022]
Abstract
The stable and metastable phase diagrams between the sinister and the rectus ibuprofen enantiomers were established by means of thermal analysis and X-ray powder diffraction experiments as a function of temperature. The results obtained allow proving for the first time the existence, for the stable system, of a solid solution by mixing the racemic ibuprofen with one of its enantiomers for low concentration of the enantiomer. Since the rectus ibuprofen is a non-active pharmaceutical agent which can be partially bio-converted into the sinister enantiomer, the present work offers a new approach for scalemic mixtures preparation in order to improve the benefit/risk ratio related to ibuprofen solid dosage form administration.
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Affiliation(s)
- Yohann Corvis
- Université de Paris, Faculté de Santé, CNRS, Inserm, UTCBS, Chemical and Biological Technologies for Health Group (utcbs.cnrs.fr), 4 avenue de l'Observatoire, 75006 Paris, France.
| | - Nicolas Guiblin
- CentraleSupélec, Laboratoire Structures, Propriétés et Modélisation des Solides (SPMS), UMR CNRS 8580, CentraleSupélec, Université Paris Saclay, 3 Rue Joliot Curie, 91190 Gif-sur-Yvette, France
| | - Philippe Négrier
- Laboratoire Ondes et Matière d'Aquitaine (LOMA), UMR 5798, Université de Bordeaux, Talence 33400, France
| | - Ivan Marenco
- Université de Paris, Faculté de Santé, CNRS, Inserm, UTCBS, Chemical and Biological Technologies for Health Group (utcbs.cnrs.fr), 4 avenue de l'Observatoire, 75006 Paris, France
| | - Oumar Dembélé
- Université de Paris, Faculté de Santé, CNRS, Inserm, UTCBS, Chemical and Biological Technologies for Health Group (utcbs.cnrs.fr), 4 avenue de l'Observatoire, 75006 Paris, France
| | - Philippe Espeau
- Université de Paris, Faculté de Santé, CNRS, Inserm, UTCBS, Chemical and Biological Technologies for Health Group (utcbs.cnrs.fr), 4 avenue de l'Observatoire, 75006 Paris, France
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10
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Lin W, Gandhi S, Oviedo Lara AR, Thomas AK, Helbig R, Zhang Y. Controlling Surface Wettability for Automated In Situ Array Synthesis and Direct Bioscreening. Adv Mater 2021; 33:e2102349. [PMID: 34309086 DOI: 10.1002/adma.202102349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/30/2021] [Indexed: 06/13/2023]
Abstract
The in situ synthesis of biomolecules on glass surfaces for direct bioscreening can be a powerful tool in the fields of pharmaceutical sciences, biomaterials, and chemical biology. However, it is still challenging to 1) achieve this conventional multistep combinatorial synthesis on glass surfaces with small feature sizes and high yields and 2) develop a surface which is compatible with solid-phase syntheses, as well as the subsequent bioscreening. This work reports an amphiphilic coating of a glass surface on which small droplets of polar aprotic organic solvents can be deposited with an enhanced contact angle and inhibited motion to permit fully automated multiple rounds of the combinatorial synthesis of small-molecule compounds and peptides. This amphiphilic coating can be switched into a hydrophilic network for protein- and cell-based screening. Employing this in situ synthesis method, chemical space can be probed via array technology with unprecedented speed for various applications, such as lead discovery/optimization in medicinal chemistry and biomaterial development.
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Affiliation(s)
- Weilin Lin
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Shanil Gandhi
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Alan Rodrigo Oviedo Lara
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Alvin K Thomas
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Ralf Helbig
- Leibniz Institute of Polymer Research Dresden, Max Bergmann Center of Biomaterials Dresden, Hohe Strasse 6, 01069, Dresden, Germany
| | - Yixin Zhang
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
- Cluster of Excellence "Physics of Life", Technische Universität Dresden, 01062, Dresden, Germany
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11
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Abstract
Circular economy and aqueous synthesis are attractive concepts for sustainable chemistry. Here it is reported that the two can be combined in the universal method for peptide chemistry, fluorenylmethoxycarbonyl(Fmoc)/t-Bu solid-phase peptide synthesis (SPPS). It was demonstrated that Fmoc/t-Bu SPPS could be performed under aqueous conditions using standard Fmoc amino acids (AAs) employing TentaGel S as resin and 4 : 1 mixture of water with inexpensive green solvent PolarClean. This resin/solvent combination played a crucial dual role by virtue of improving resin swelling and solubility of starting materials. In a model coupling, TCFH and 2,4,6-collidine afforded a full conversion at only 1.3 equiv. AA, and these conditions were used in SPPS of Leu enkephaline amide affording the model peptide in 85 % yield and 86 % purity. A method to recycle the waste by filtration through a mixed ion exchange resin was developed, allowing reusing the waste without affecting quality of the peptide. The method herein obviates the use of unconventional or processed AAs in aqueous SPPS while using lower amounts of starting materials. By recycling/reusing SPPS waste the hazardous dipolar aprotic solvents used in SPPS were not only replaced with an aqueous medium, solvent use was also significantly reduced. This opens up a new direction in aqueous peptide chemistry in which efficient use of inexpensive starting materials and waste minimization is coupled with the universal Fmoc/t-Bu SPPS.
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Affiliation(s)
- Jan Pawlas
- PolyPeptide Group, Limhamnsvägen 108, PO BOX 30089, 20061, Limhamn, Sweden
| | - Jon H Rasmussen
- PolyPeptide Group, Limhamnsvägen 108, PO BOX 30089, 20061, Limhamn, Sweden
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12
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Roy A, Koesema E, Kodadek T. High-Throughput Quality Control Assay for the Solid-Phase Synthesis of DNA-Encoded Libraries of Macrocycles*. Angew Chem Int Ed Engl 2021; 60:11983-11990. [PMID: 33682283 DOI: 10.1002/anie.202100230] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Indexed: 12/18/2022]
Abstract
There is considerable interest in the development of libraries of scaffold-diverse macrocycles as a source of ligands for difficult targets, such as protein-protein interaction surfaces. A classic problem in the synthesis of high-quality macrocyclic libraries is that some linear precursors will cyclize efficiently while some will not, depending on their conformational preferences. We report here a powerful quality control method that can be employed to readily distinguish between scaffolds that do and do not cyclize efficiently during solid-phase synthesis of thioether macrocycles without the need for tedious liquid chromatography/mass spectrometry analysis. We demonstrate that this assay can be employed to identify linear impurities in a DNA-encoded library of macrocycles. We also use the method to establish a useful quality control protocol for re-synthesis of putative macrocyclic screening hits.
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Affiliation(s)
- Animesh Roy
- Deluge Biotechnologies, 6671 W. Indiantown Rd., Suite 50-325, Jupiter, FL, 33458, USA
| | - Eric Koesema
- Deluge Biotechnologies, 6671 W. Indiantown Rd., Suite 50-325, Jupiter, FL, 33458, USA
| | - Thomas Kodadek
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
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13
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Meschaninova MI, Entelis NS, Chernolovskaya EL, Venyaminova AG. A Versatile Solid-Phase Approach to the Synthesis of Oligonucleotide Conjugates with Biodegradable Hydrazone Linker. Molecules 2021; 26:molecules26082119. [PMID: 33917095 PMCID: PMC8067880 DOI: 10.3390/molecules26082119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/03/2021] [Accepted: 04/04/2021] [Indexed: 12/02/2022] Open
Abstract
One of the ways to efficiently deliver various drugs, including therapeutic nucleic acids, into the cells is conjugating them with different transport ligands via labile or stable bonds. A convenient solid-phase approach for the synthesis of 5′-conjugates of oligonucleotides with biodegradable pH-sensitive hydrazone covalent bonds is proposed in this article. The approach relies on introducing a hydrazide of the ligand under aqueous/organic media to a fully protected support-bound oligonucleotide containing aldehyde function at the 5′-end. We demonstrated the proof-of-principle of this approach by synthesizing 5′-lipophilic (e.g., cholesterol and α-tocopherol) conjugates of modified siRNA and non-coding RNAs imported into mitochondria (antireplicative RNAs and guide RNAs for Mito-CRISPR/system). The developed method has the potential to be extended for the synthesis of pH-sensitive conjugates of oligonucleotides of different types (ribo-, deoxyribo-, 2′-O-methylribo-, and others) with ligands of different nature.
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Affiliation(s)
- Mariya I. Meschaninova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.L.C.); (A.G.V.)
- Correspondence: ; Tel.: +7-383-363-5129
| | - Nina S. Entelis
- UMR Genetique Moleculaire, Genomique, Microbiologie (GMGM), Strasbourg University—CNRS, 67084 Strasbourg, France;
| | - Elena L. Chernolovskaya
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.L.C.); (A.G.V.)
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.L.C.); (A.G.V.)
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14
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Yang H, Peng T, Wen X, Chen T, Sun Y, Liu S, Wang G, Zhang S, Wang L. A Photolabile Carboxyl Protecting Group for Solid Phase Peptide Synthesis. ChemistryOpen 2021; 10:497-502. [PMID: 33908701 PMCID: PMC8080293 DOI: 10.1002/open.202000324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/18/2021] [Indexed: 11/08/2022] Open
Abstract
A new kind of photolabile protecting group (PLPG) for carboxyl moieties was designed and synthesized as the linker between resin and peptide. This group can be used for the protection of amino acid carboxyl groups. The peptide was synthesized on Nph (2-hydroxy-3-(2-nitrophenyl)-heptanoic acid)-derivatized resins and could be cleaved under UV exposure, thus avoiding the necessity for harsh acid-mediated resin cleavage. The PLPG has been successfully used for solid-phase synthesis of peptides.
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Affiliation(s)
- Hongpeng Yang
- Faculty of Environment & Life, Beijing University of Technology, Beijing, 100124, China
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Tao Peng
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Xiaoxue Wen
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Tingting Chen
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Yunbo Sun
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Shuchen Liu
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Gang Wang
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Shouguo Zhang
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Lin Wang
- Faculty of Environment & Life, Beijing University of Technology, Beijing, 100124, China
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Haidian District, Beijing, 100850, China
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15
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Abstract
Proteins have attracted increasing attention as biopharmaceutics and diagnostics due to their high specificity, biocompatibility, and biodegradability. The biopharmaceutical sector in particular is experiencing rapid growth, which has led to an increase in the production and sale of protein drugs and diagnostics over the last two decades. Since the first-generation biopharmaceutics dominated by native proteins, both recombinant and chemical technologies have evolved and transformed the outlook of this rapidly developing field. This review article presents updates on the fabrication of covalent and supramolecular fusion hybrids, as well as protein-polymer hybrids using solid-phase approaches that hold great promise for preparing protein hybrids with precise control at the macromolecular level to incorporate additional features. In addition, the applications of the resultant protein hybrids in medicine and diagnostics are highlighted where possible.
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Affiliation(s)
- Seah Ling Kuan
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert-Einstein-Allee 1189081UlmGermany
| | - Marco Raabe
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert-Einstein-Allee 1189081UlmGermany
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16
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Kossmann C, Ma S, Clemmensen LS, Strømgaard K. Chemical Synthesis of PDZ Domains. Methods Mol Biol 2021; 2256:193-216. [PMID: 34014524 DOI: 10.1007/978-1-0716-1166-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Developments in chemical protein synthesis have enabled the generation of tailor-made proteins including incorporation of many types of modifications into proteins, enhancing our ability to control site-specificity of protein posttranslational modifications (PTMs), modify protein backbones and introduce photocrosslinking probes. For PDZ (postsynaptic density protein, disks large, zonula occludens) protein domains, expressed protein ligation (EPL) has been employed to introduce analogs of cognate amino acids, amide-to-ester bond mutations, and phosphorylations in the study of PDZ domain-mediated protein-protein interactions (PPIs). Here, we present protocols for EPL of PDZ domains focusing on phosphorylation and amide-to-ester modifications in the PDZ domain proteins.
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Affiliation(s)
- Christin Kossmann
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
| | - Sana Ma
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
| | - Louise S Clemmensen
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark.
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17
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Cankařová N, Krchňák V. Isocyanide Multicomponent Reactions on Solid Phase: State of the Art and Future Application. Int J Mol Sci 2020; 21:E9160. [PMID: 33271974 PMCID: PMC7729642 DOI: 10.3390/ijms21239160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 01/17/2023] Open
Abstract
Drug discovery efforts largely depend on access to structural diversity. Multicomponent reactions allow for time-efficient chemical transformations and provide advanced intermediates with three or four points of diversification for further expansion to a structural variety of organic molecules. This review is aimed at solid-phase syntheses of small molecules involving isocyanide-based multicomponent reactions. The majority of all reported syntheses employ the Ugi four-component reaction. The review also covers the Passerini and Groebke-Blackburn-Bienaymé reactions. To date, the main advantages of the solid-phase approach are the ability to prepare chemical libraries intended for biological screening and elimination of the isocyanide odor. However, the potential of multicomponent reactions has not been fully exploited. The unexplored avenues of these reactions, including chiral frameworks, DNA-encoded libraries, eco-friendly synthesis, and chiral auxiliary reactions, are briefly outlined.
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Affiliation(s)
- Naděžda Cankařová
- Department of Organic Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 779 00 Olomouc, Czech Republic;
| | - Viktor Krchňák
- Department of Organic Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 779 00 Olomouc, Czech Republic;
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Center, University of Notre Dame, Notre Dame, IN 46556, USA
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18
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Kumar A, Alhassan M, Lopez J, Albericio F, de la Torre BG. N-Butylpyrrolidinone for Solid-Phase Peptide Synthesis is Environmentally Friendlier and Synthetically Better than DMF. ChemSusChem 2020; 13:5288-5294. [PMID: 32720474 DOI: 10.1002/cssc.202001647] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/26/2020] [Indexed: 06/11/2023]
Abstract
Solid-phase peptide synthesis (SPPS) is the method of choice for the preparation of peptides in both laboratory scale and large production. Although the methodology has been improved during the last decades allowing the achievement of long peptides and challenging sequences in good yields and purities, the process was not revised from an environmental point of view. One of the main problems in this regard is the large amount of solvents used, and therefore the tons of generated waste. Moreover, the solvent of choice for the SPPS is N,N-dimethylformamide (DMF), which is considered as reprotoxic; thus, there is an urgent necessity to replace it with safer solvents. The DMF substitution by a green solvent is not a trivial task, because it should solubilize all the reagents and byproducts involved in the process, and, in addition to facilitating the coupling of the different amino acids, it should not favor the formation of side-reactions compared with DMF. Herein, it was demonstrated that the use of the green solvent N-butylpyrrolidinone (NBP) as a replacement of DMF was beneficial in two well-documented side reactions in peptide synthesis, racemization and aspartimide formation. The use of NBP rendered a lower or equal level of racemization in the amino acids more prone to this side reaction than DMF, whilst the aspartimide formation was clearly lower when NBP was used as solvent. Our findings demonstrate that the use of a green solvent does not hamper the synthetic process and could even improve it, making it environmentally friendlier and synthetically better.
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Affiliation(s)
- Ashish Kumar
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Mahama Alhassan
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - John Lopez
- Novartis Pharma AG, Lichtstrasse 35, 4056, Basel, Switzerland
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine & Department of Organic Chemistry, University of Barcelona, 08028, Barcelona, Spain
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Beatriz G de la Torre
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
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19
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Wu Y, Zheng YY, Lin Q, Sheng J. Detection and Quantification of RNA Phosphorothioate Modifications Using Mass Spectrometry. Curr Protoc Nucleic Acid Chem 2020; 82:e113. [PMID: 32822120 PMCID: PMC7700719 DOI: 10.1002/cpnc.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This article describes a protocol for detecting and quantifying RNA phosphorothioate modifications in cellular RNA samples. Starting from solid-phase synthesis of phosphorothioate RNA dinucleotides, followed by purification with reversed-phase HPLC, phosphorothioate RNA dinucleotide standards are prepared for UPLC-MS and LC-MS/MS methods. RNA samples are extracted from cells using TRIzol reagent, then digested with a nuclease mixture and analyzed by mass spectrometry. UPLC-MS is employed first to identify RNA phosphorothioate modifications. An optimized LC-MS/MS method is then employed to quantify the frequency of RNA phosphorothioate modifications in a series of model cells. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Synthesis, purification, and characterization of RNA phosphorothioate dinucleotides Basic Protocol 2: Digestion of RNA samples extracted from cells Basic Protocol 3: Detection and quantification of RNA phosphorothioate modifications by mass spectrometry.
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Affiliation(s)
- Ying Wu
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, New York
| | - Ya Ying Zheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, New York
| | - Qishan Lin
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, New York
| | - Jia Sheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, New York
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20
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Kar A, Mannuthodikayil J, Singh S, Biswas A, Dubey P, Das A, Mandal K. Efficient Chemical Protein Synthesis using Fmoc-Masked N-Terminal Cysteine in Peptide Thioester Segments. Angew Chem Int Ed Engl 2020; 59:14796-14801. [PMID: 32333711 PMCID: PMC7891605 DOI: 10.1002/anie.202000491] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/27/2020] [Indexed: 01/23/2023]
Abstract
We report an operationally simple method to facilitate chemical protein synthesis by fully convergent and one-pot native chemical ligations utilizing the fluorenylmethyloxycarbonyl (Fmoc) moiety as an N-masking group of the N-terminal cysteine of the middle peptide thioester segment(s). The Fmoc group is stable to the harsh oxidative conditions frequently used to generate peptide thioesters from peptide hydrazide or o-aminoanilide. The ready availability of Fmoc-Cys(Trt)-OH, which is routinely used in Fmoc solid-phase peptide synthesis, where the Fmoc group is pre-installed on cysteine residue, minimizes additional steps required for the temporary protection of the N-terminal cysteinyl peptides. The Fmoc group is readily removed after ligation by short exposure (<7 min) to 20 % piperidine at pH 11 in aqueous conditions at room temperature. Subsequent native chemical ligation reactions can be performed in presence of piperidine in the same solution at pH 7.
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Affiliation(s)
- Abhisek Kar
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
| | - Jamsad Mannuthodikayil
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
| | - Sameer Singh
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
| | - Anamika Biswas
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
| | - Puneet Dubey
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
| | - Amit Das
- Protein Crystallography Section, Radiation Biology and Health Sciences DivisionBhabha Atomic Research CentreTrombayMumbai400085India
- Homi Bhabha National InstituteAnushaktinagarMumbai400094India
| | - Kalyaneswar Mandal
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
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21
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Krasheninina OA, Fishman VS, Lomzov AA, Ustinov AV, Venyaminova AG. Postsynthetic On-Column 2' Functionalization of RNA by Convenient Versatile Method. Int J Mol Sci 2020; 21:E5127. [PMID: 32698484 PMCID: PMC7404181 DOI: 10.3390/ijms21145127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 12/26/2022] Open
Abstract
We report a universal straightforward strategy for the chemical synthesis of modified oligoribonucleotides containing functional groups of different structures at the 2' position of ribose. The on-column synthetic concept is based on the incorporation of two types of commercial nucleotide phosphoramidites containing orthogonal 2'-O-protecting groups, namely 2'-O-thiomorpholine-carbothioate (TC, as "permanent") and 2'-O-tert-butyl(dimethyl)silyl (tBDMS, as "temporary"), to RNA during solid-phase synthesis. Subsequently, the support-bound RNA undergoes selective deprotection and follows postsynthetic 2' functionalization of the naked hydroxyl group. This convenient method to tailor RNA, utilizing the advantages of solid phase approaches, gives an opportunity to introduce site-specifically a wide range of linkers and functional groups. By this strategy, a series of RNAs containing diverse 2' functionalities were synthesized and studied with respect to their physicochemical properties.
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Affiliation(s)
- Olga A. Krasheninina
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, Innsbruck 6020, Austria
| | - Veniamin S. Fishman
- Institute of Cytology and Genetics SB RAS Lavrentiev Ave. 10, 630090 Novosibirsk, Russia;
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (A.A.L.); (A.G.V.)
| | - Alexey V. Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia;
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (A.A.L.); (A.G.V.)
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22
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Sidorova M, Studneva I, Bushuev V, Pal'keeva M, Molokoedov A, Veselova O, Ovchinnikov M, Pisarenko O. [MeArg 1, NLe 10]-apelin-12: Optimization of solid-phase synthesis and evaluation of biological properties in vitro and in vivo. Peptides 2020; 129:170320. [PMID: 32380198 DOI: 10.1016/j.peptides.2020.170320] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022]
Abstract
Chemically modified peptide apelin-12 ([MeArg1, NLe10]-apelin12, peptide M) is able to reduce reactive oxygen species (ROS) formation, cell death, and metabolic and ionic homeostasis disorders in experimental myocardial ischemia-reperfusion injury. These beneficial effects indicate the therapeutic potential of this compound in cardiovascular diseases. The goals of this work were to optimize the synthesis of peptide M, and to study its proteolytic stability and effect on the heart function of rabbits with doxorubicin (Dox) cardiomyopathy. We have developed a rational method of solid-phase synthesis of peptide M using the Fmoc methodology in combination with the temporary protection of the guanidine function of arginine residues by protonation (salt formation) during the formation of the amide bond. It avoids the formation of by-products, and simplifies the post-synthetic procedures, providing an increase in the yield of the final product of higher purity. Comparative evaluation of the proteolytic stability of peptide M and apelin-12 in human blood plasma was carried out using 1H NMR spectroscopy. It was shown that the half-life of peptide M in plasma is approximately three times longer than that of apelin-12. Intravenous infusion of increasing doses of peptide M caused a gradual increase in left ventricular (LV) fractional shortening and ejection fraction in rabbits after 8 weeks of Dox administration (2 mg/kg weekly). The effect of the modified peptide on LV systolic dysfunction was significantly more pronounced than the effect of apelin-12, which suggests the promise of using this pharmacological agonist of the APJ receptor in patients with heart failure.
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Affiliation(s)
- Maria Sidorova
- National Medical Research Center for Cardiology, 3rd Cherepkovskaya Str., 15A, 121552 Moscow, Russian Federation.
| | - Irina Studneva
- National Medical Research Center for Cardiology, 3rd Cherepkovskaya Str., 15A, 121552 Moscow, Russian Federation.
| | - Valery Bushuev
- National Medical Research Center for Cardiology, 3rd Cherepkovskaya Str., 15A, 121552 Moscow, Russian Federation.
| | - Marina Pal'keeva
- National Medical Research Center for Cardiology, 3rd Cherepkovskaya Str., 15A, 121552 Moscow, Russian Federation.
| | - Alexander Molokoedov
- National Medical Research Center for Cardiology, 3rd Cherepkovskaya Str., 15A, 121552 Moscow, Russian Federation.
| | - Oksana Veselova
- National Medical Research Center for Cardiology, 3rd Cherepkovskaya Str., 15A, 121552 Moscow, Russian Federation.
| | - Michael Ovchinnikov
- National Medical Research Center for Cardiology, 3rd Cherepkovskaya Str., 15A, 121552 Moscow, Russian Federation.
| | - Oleg Pisarenko
- National Medical Research Center for Cardiology, 3rd Cherepkovskaya Str., 15A, 121552 Moscow, Russian Federation.
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23
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Neumann K, Farnung J, Baldauf S, Bode JW. Prevention of aspartimide formation during peptide synthesis using cyanosulfurylides as carboxylic acid-protecting groups. Nat Commun 2020; 11:982. [PMID: 32080186 PMCID: PMC7033154 DOI: 10.1038/s41467-020-14755-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 01/23/2020] [Indexed: 12/13/2022] Open
Abstract
Although peptide chemistry has made great progress, the frequent occurrence of aspartimide formation during peptide synthesis remains a formidable challenge. Aspartimide formation leads to low yields in addition to costly purification or even inaccessible peptide sequences. Here, we report an alternative approach to address this longstanding challenge of peptide synthesis by utilizing cyanosulfurylides to mask carboxylic acids by a stable C-C bond. These functional groups-formally zwitterionic species-are exceptionally stable to all common manipulations and impart improved solubility during synthesis. Deprotection is readily and rapidly achieved under aqueous conditions with electrophilic halogenating agents via a highly selective C-C bond cleavage reaction. This protecting group is employed for the synthesis of a range of peptides and proteins including teduglutide, ubiquitin, and the low-density lipoprotein class A. This protecting group strategy has the potential to overcome one of the most difficult aspects of modern peptide chemistry.
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Affiliation(s)
- Kevin Neumann
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Jakob Farnung
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Simon Baldauf
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland.
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8602, Japan.
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24
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Hartman K, Mielczarek P, Silberring J. Synthesis of the Novel Covalent Cysteine Proteases Inhibitor with Iodoacetic Functional Group. Molecules 2020; 25:molecules25040813. [PMID: 32069913 PMCID: PMC7070521 DOI: 10.3390/molecules25040813] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/07/2020] [Accepted: 02/12/2020] [Indexed: 01/30/2023] Open
Abstract
This work presents the synthesis of the novel covalent inhibitor of cysteine proteases where epoxide has been replaced by the iodoacetyl functional group. The molecule, similar in action to E-64 and DCG-04, the commonly applied inhibitors, is additionally biotinylated and contains tyrosyl iodination sites. The Fmoc solid phase synthesis has been applied. Conjugation of iodoacetic acid with the peptide was optimized by testing different conjugation agents. The purity of the final product was verified by mass spectrometry and its bioactivity was tested by incubation with a model cysteine protease—staphopain C. Finally, it was shown that the synthesized inhibitor binds to the protein at the ratio of 1:1. More detailed analysis by means of tandem mass spectrometry proved that the inhibitor binds to the cysteine present in the active site of the enzyme.
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Affiliation(s)
- Kinga Hartman
- Department of Biochemistry and Neurobiology, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland; (K.H.); (J.S.)
| | - Przemyslaw Mielczarek
- Department of Biochemistry and Neurobiology, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland; (K.H.); (J.S.)
- Polish Academy of Sciences, Maj Institute of Pharmacology, Laboratory of Proteomics and Mass Spectrometry, Smetna 12, 31-343 Krakow, Poland
- Correspondence: ; Tel.: +48-12-6175083
| | - Jerzy Silberring
- Department of Biochemistry and Neurobiology, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland; (K.H.); (J.S.)
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25
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Abstract
The application of designer peptides in medicinal chemistry, chemical biology, and materials science has generated new interest in synthetic methods for the structural modification of amino acids. Strategies which facilitate the direct diversification of proteinogenic functional groups within unprotected peptide substrates are particularly attractive as they leverage modern solution- and solid-phase protocols-tools which are now both robust and routine-for the synthesis of native peptides. Accordingly, a recent approach to the decarboxylative functionalization of peptidic carboxylic acids, including aspartic/glutamic acid residues and α-carboxylic acids, has proven to be a promising new strategy for peptide modification. This synthetic method merges conventional strategies for the activation of carboxylic acids with transition metal-catalyzed cross-coupling chemistry to forge new C-C bonds for the late-stage introduction of valuable synthetic handles. This chapter details a step-by-step protocol for the activation and nickel-catalyzed decarboxylative alkylation of a simple peptide substrate to highlight the broad utility of this strategy for the synthesis of designer peptides.
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Affiliation(s)
- Meng Yao Zhang
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Lara R Malins
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia.
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26
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Abstract
Octapeptins are naturally derived cyclic lipopeptide antibiotics with activity against a range of Gram-negative pathogens, including highly resistant strains. Octapeptin C4, an exemplar of the class, was synthesized using a combination of Fmoc solid-phase peptide synthesis (SPPS) and solution-phase cyclization. Utilizing H-L-Leu-2-chlorotrityl resin, peptide couplings were performed using HCTU and collidine in DMF. The linear sequence was terminated by N-acylation with 3-(R)-hydroxydecanoic acid. The residue Dab-2 was orthogonally protected with 1-(4,4-dimethyl-2,6-dioxocyclohex-1-ylidene)isovaleryl group (ivDde) to enable selective side-chain deprotection prior to resin cleavage. Resin cleavage was accomplished with hexafluoroisopropanol in DCM, followed by cyclization with diphenylphosphoryl azide (DPPA) and solid sodium bicarbonate in DMF.
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Affiliation(s)
- Karl A Hansford
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia.
| | - Zyta M Ziora
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Matthew A Cooper
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Mark A T Blaskovich
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
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27
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Guidotti N, Fierz B. Semisynthesis and Reconstitution of Nucleosomes Carrying Asymmetric Histone Modifications. Methods Mol Biol 2020; 2133:263-291. [PMID: 32144672 DOI: 10.1007/978-1-0716-0434-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nucleosomes, the basic unit of chromatin, contain a protein core of histone proteins, which are heavily posttranslationally modified. These modifications form a combinatorial language which defines the functional state of the underlying genome. As each histone type exists in two copies in a nucleosome, the modification patterns can differ between the individual histones, resulting in asymmetry and increasing combinatorial complexity. To systematically explore the regulation of chromatin regulatory enzymes (writers, erasers, or readers), chemically defined nucleosomes are required. We have developed strategies to chemically modify histones and control nucleosome assembly, thereby enabling the reconstitution of asymmetric histone modification patterns. Here, we report a detailed protocol for the modular assembly of such nucleosomes. Employing a three-segment ligation strategy for the semisynthesis of H3, coupled with the use of the protease cleavable "lnc-tag," we provide an efficient and traceless method for the controlled semisynthesis and reconstitution of asymmetrically modified nucleosomes.
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Affiliation(s)
- Nora Guidotti
- École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Beat Fierz
- École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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28
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Dai C, Stephenson RJ, Skwarczynski M, Toth I. Application of Fmoc-SPPS, Thiol-Maleimide Conjugation, and Copper(I)-Catalyzed Alkyne-Azide Cycloaddition "Click" Reaction in the Synthesis of a Complex Peptide-Based Vaccine Candidate Against Group A Streptococcus. Methods Mol Biol 2020; 2103:13-27. [PMID: 31879916 DOI: 10.1007/978-1-0716-0227-0_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fmoc solid-phase peptide synthesis (SPPS) is the most common approach used to synthesize natural and unnatural peptides. However, the synthesis of sequences longer than 30-60 amino acids is associated with a drastic reduction in peptide quality. Thus, large and complex peptides are normally synthesized as fragments, which are then conjugated together. Here, we describe the synthesis of a large, branched peptide, a multi-epitope vaccine candidate against Group A Streptococcus, with the help of microwave-assisted Fmoc-SPPS, thiol-maleimide conjugation, and copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) "click" reaction.
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Affiliation(s)
- Chuankai Dai
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Rachel J Stephenson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Istvan Toth
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia.
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD, Australia.
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29
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Hussein WM, Skwarczynski M, Toth I. An Isodipeptide Building Block for Microwave-Assisted Solid-Phase Synthesis of Difficult Sequence-Containing Peptides. Methods Mol Biol 2020; 2103:139-150. [PMID: 31879923 DOI: 10.1007/978-1-0716-0227-0_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Microwave technology, in conjunction with the isopeptide strategy including Fmoc-based solid-phase peptide synthesis (SPPS), was used to establish a methodology for time-efficient synthesis of peptides containing difficult sequences. A model difficult sequence-containing peptide (8QSer) was synthesized through this method in 1 day, representing a tenfold reduction in synthesis time compared to the isopeptide method combined with classical SPPS.
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Affiliation(s)
- Waleed M Hussein
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Istvan Toth
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia.
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD, Australia.
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30
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Yoshiya T. Synthesis of O-Acyl Isopeptides: Stepwise and Convergent Solid-Phase Synthesis. Methods Mol Biol 2020; 2103:129-138. [PMID: 31879922 DOI: 10.1007/978-1-0716-0227-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The O-acyl isopeptide method was developed for the preparation of difficult sequence-containing peptides, whose hydrophobic nature hampers both peptide chain construction on resin and purification with HPLC after deprotection. In the O-acyl isopeptide method, the target peptide is synthesized in an O-acyl isopeptide form, which contains an O-acyl isopeptide bond instead of the native N-acyl peptide bond at a hydroxy group-containing amino acid residue, such as Ser or Thr. The hydrophilic O-acyl isopeptide can be isolated, e.g., as a lyophilized TFA salt. The target peptide can be quantitatively obtained by a final O-to-N intramolecular acyl migration reaction with exposure to neutral conditions. Additionally, the O-acyl isopeptide is important as a hydrophilic precursor peptide for biological peptide assays that are difficult to handle. This chapter describes the synthesis of such O-acyl isopeptides by stepwise and convergent Fmoc solid-phase peptide synthesis.
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Affiliation(s)
- Taku Yoshiya
- Peptide Institute, Inc., Ibaraki-Shi, Osaka, Japan.
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31
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Abstract
Solubility is a key property of peptides and of central importance to the success of solid-phase peptide synthesis and subsequent peptide purification and handling. Substitution of the backbone amide bond can dramatically increase peptide solubility. Backbone amide bond protection works by preventing the formation of interchain association and can be used both to synthesize aggregation-prone peptide sequences on solid phase and to improve solubility of a peptide post synthesis. Improving peptide solubility by judicial use of backbone protection is of growing importance, particularly for chemical protein synthesis by chemical ligation.
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Affiliation(s)
| | | | | | - John Offer
- The Francis Crick Institute, London, UK.
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32
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Abstract
Glycosylation is one of the most common posttranslational modifications of proteins and can exert profound effects on the inherent properties and biological functions of a given protein. Structurally well-defined homogeneous glycopeptides are highly demanded for functional studies and biomedical applications. Various chemical and chemoenzymatic methods have been reported so far for synthesizing different N- and O-glycopeptides. Among them, the chemoenzymatic method based on an endoglycosidase-catalyzed ligation of free N-glycans and GlcNAc-tagged peptides is emerging as a highly efficient method for constructing large complex N-glycopeptides. This chemoenzymatic approach consists of two key steps. The first step is to prepare the GlcNAc peptide through automated solid-phase peptide synthesis (SPPS) by incorporating an Asn-linked GlcNAc moiety at a predetermined glycosylation site; and the second step is to transfer an N-glycan from the corresponding N-glycan oxazoline en bloc to the GlcNAc peptide by an endoglycosidase or its efficient glycosynthase mutant. In this chapter, we provide detailed procedures of this chemoenzymatic method by demonstrating the synthesis of two HIV-1 V3 glycopeptide antigens carrying a high-mannose-type and a complex-type N-glycan, respectively. The described procedures should be generally applicable for the synthesis of other biologically important N-glycopeptides.
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Affiliation(s)
- Guanghui Zong
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA.
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33
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Abstract
Peptide analogs modified with a phosphorus-based moiety (phosphonate, phosphonamidate, or phosphinate) have emerged as invaluable tools in fundamental and medicinal, mechanistic, and inhibitory studies of proteolytic enzymes and other catalytic proteins that process the amino acids and peptides. The first stages of the chemical synthesis of these compounds frequently involve formation of peptide or pseudopeptide bond between a suitably protected α-amino acid and an α-aminoalkyl phosphorus derivative. These preparative protocols are distinct from conventional solution and solid-phase peptide syntheses that have become routine and automatized. In the following chapter, we describe in details the methods and techniques utilized to perform this nonstandard coupling and to obtain P-terminal dipeptidyl phosphonates and pseudodipeptides containing the internal phosphonamidate or phosphinate linkages. Methods of products' purification, the deprotection conditions, and stability issues are also presented and discussed.
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Affiliation(s)
- Artur Mucha
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wrocław, Poland.
| | - Paweł Kafarski
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
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34
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Meschaninova MI, Novopashina DS, Semikolenova OA, Silnikov VN, Venyaminova AG. Novel Convenient Approach to the Solid-Phase Synthesis of Oligonucleotide Conjugates. Molecules 2019; 24:E4266. [PMID: 31771111 PMCID: PMC6930482 DOI: 10.3390/molecules24234266] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 01/03/2023] Open
Abstract
A novel and convenient approach for the solid-phase 5'-functionalization of oligonucleotides is proposed in this article. The approach is based on the activation of free 5'-hydroxyl of polymer support-bound protected oligonucleotides by N,N'-disuccinimidyl carbonate followed by interaction with amino-containing ligands. Novel amino-containing derivatives of closo-dodecaborate, estrone, cholesterol, and α-tocopherol were specially prepared. A wide range of oligonucleotide conjugates bearing closo-dodecaborate, short peptide, pyrene, lipophilic residues (cholesterol, α-tocopherol, folate, estrone), aliphatic diamines, and propargylamine were synthesized and characterized to demonstrate the versatility of the approach. The developed method is suitable for the conjugate synthesis of oligonucleotides of different types (ribo-, deoxyribo-, 2'-O-methylribo-, and others).
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Affiliation(s)
- Mariya I. Meschaninova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova str.2, Novosibirsk 630090, Russia;
| | - Olga A. Semikolenova
- Department of Natural Sciences, Novosibirsk State University, Pirogova str.2, Novosibirsk 630090, Russia;
| | - Vladimir N. Silnikov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
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35
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Dickman R, Mitchell SA, Figueiredo AM, Hansen DF, Tabor AB. Molecular Recognition of Lipid II by Lantibiotics: Synthesis and Conformational Studies of Analogues of Nisin and Mutacin Rings A and B. J Org Chem 2019; 84:11493-11512. [PMID: 31464129 PMCID: PMC6759747 DOI: 10.1021/acs.joc.9b01253] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Indexed: 12/12/2022]
Abstract
In response to the growing threat posed by antibiotic-resistant bacterial strains, extensive research is currently focused on developing antimicrobial agents that target lipid II, a vital precursor in the biosynthesis of bacterial cell walls. The lantibiotic nisin and related peptides display unique and highly selective binding to lipid II. A key feature of the nisin-lipid II interaction is the formation of a cage-like complex between the pyrophosphate moiety of lipid II and the two thioether-bridged rings, rings A and B, at the N-terminus of nisin. To understand the important structural factors underlying this highly selective molecular recognition, we have used solid-phase peptide synthesis to prepare individual ring A and B structures from nisin, the related lantibiotic mutacin, and synthetic analogues. Through NMR studies of these rings, we have demonstrated that ring A is preorganized to adopt the correct conformation for binding lipid II in solution and that individual amino acid substitutions in ring A have little effect on the conformation. We have also analyzed the turn structures adopted by these thioether-bridged peptides and show that they do not adopt the tight α-turn or β-turn structures typically found in proteins.
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Affiliation(s)
- Rachael Dickman
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Serena A. Mitchell
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Angelo M. Figueiredo
- Institute
of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K.
| | - D. Flemming Hansen
- Institute
of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K.
| | - Alethea B. Tabor
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
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36
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Okarvi SM, AlJammaz I. Development of the Tumor-Specific Antigen-Derived Synthetic Peptides as Potential Candidates for Targeting Breast and Other Possible Human Carcinomas. Molecules 2019; 24:molecules24173142. [PMID: 31470531 PMCID: PMC6749314 DOI: 10.3390/molecules24173142] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/09/2019] [Accepted: 07/16/2019] [Indexed: 01/26/2023] Open
Abstract
The human epidermal growth factor receptor 2 (HER2) represents one of the most studied tumor-associated antigens for cancer immunotherapy. The receptors for HER2 are overexpressed in various human cancers, such as breast and ovarian cancer. The relatively low expression of this antigen on normal tissues makes it a clinically useful molecular target for tumor imaging and targeted therapy. HER2 overexpression is correlated with aggressive tumor behavior and poor clinical outcomes. Thus, HER2 has become an important prognostic and predictive factor, as well as a potential molecular target. Due to the heterogeneity of breast cancer and possible discordance in HER2 status between primary tumors and distant metastases, assessment of HER2 expression by noninvasive imaging is important. Molecular imaging of HER2 expression may provide essential prognostic and predictive information concerning disseminated cancer and aid in the selection of an optimal therapy. Another tumor-specific antigen is MUC1, which is silent on normal tissues, but overexpressed in almost all human epithelial cell cancers, including >90% of human breast, ovarian, pancreatic, colorectal, lung, prostate, and gastric cancers and is a promising tumor antigen with diagnostic as well as the therapeutic potential of cancer. Radiolabeled small peptide ligands are attractive as probes for molecular imaging, as they reach and bind the target receptor efficiently and clear from blood and non-target organs faster than bulky antibodies. In this study, HER2 and MUC1-based peptides were synthesized and preclinically evaluated in an effort to develop peptide-based SPECT radiopharmaceuticals derived from tumor-associated antigens for the detection of breast cancer. Our findings demonstrate that the tumor antigen peptides radiolabeled efficiently with 99mTc and showed high metabolic stability in human plasma in vitro. The data from breast tumor cell binding confirmed the high affinity (in low nanomolar range) towards respective breast cancer cell lines. In healthy mice, 99mTc-labeled peptides displayed favorable pharmacokinetics, with high excretion by the renal system. In tumor xenografts nude mice models, good uptake by the SKBR3, MCF7, and T47D tumors were found, with good tumor-to-blood and tumor to muscle ratios. Additionally, tumor lesions can be seen in γ-camera imaging. Our data suggest that based on its ability to detect HER2- and MUC1-positive breast cancer cells in vivo, 99mTc-HER2 and 99mTc-MUC1-targeted peptides may be promising tumor imaging probes and warrant further investigation.
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Affiliation(s)
- Subhani M Okarvi
- Cyclotron and Radiopharmaceuticals Department, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia.
| | - Ibrahim AlJammaz
- Cyclotron and Radiopharmaceuticals Department, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia
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37
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Rodrigues F, Georgelin T, Gabant G, Rigaud B, Gaslain F, Zhuang G, Gardênnia da Fonseca M, Valtchev V, Touboul D, Jaber M. Confinement and Time Immemorial: Prebiotic Synthesis of Nucleotides on a Porous Mineral Nanoreactor. J Phys Chem Lett 2019; 10:4192-4196. [PMID: 31305079 DOI: 10.1021/acs.jpclett.9b01448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We report the successful one-pot synthesis of adenosine mono-, di-, and triphosphate in the confined space of a mordenite zeolite. This is also the first report of ATP synthesized onto a porous mineral surface. The results revealed a plausible prebiotic route to ribonucleotides and highlighted the contribution of microporous minerals in the origins of life.
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Affiliation(s)
- Francisco Rodrigues
- Sorbonne University , CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale , 4 Place Jussieu , F-75005 Paris , France
- Department of Chemistry , State University of Paraíba , UEPB, Campina Grande , Paraíba 58429-500, Brazil
| | - Thomas Georgelin
- Centre de Biophysique Moléculaire , CNRS, Rue Charles Sadron, 45000 Orléans , France
| | - Guillaume Gabant
- Centre de Biophysique Moléculaire , CNRS, Rue Charles Sadron, 45000 Orléans , France
| | - Baptiste Rigaud
- CNRS Institut des Matériaux de Paris Centre (FR2482) , 4 Place Jussieu , 75005 Paris , France
| | - Fabrice Gaslain
- MINES ParisTech , PSL - Research University , MAT - Centre des Matériaux, CNRS UMR 7633, BP 87, F-91003 Evry , France
| | - Guanzheng Zhuang
- Sorbonne University , CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale , 4 Place Jussieu , F-75005 Paris , France
| | - Maria Gardênnia da Fonseca
- Department of Chemistry , Federal University of Paraíba , UFPB, João Pessoa , Paraíba 58059-900 , Brazil
| | - Valentin Valtchev
- Normandy University , Laboratoire Catalyse & Spectrochimie, ENSICAEN , 6 bl Maréchal Juin , 14050 Caen , France
| | - David Touboul
- CNRS-Institut de Chimie des Substances Naturelles, UPR2301 , Université Paris-Saclay , 91198 Gif-sur-Yvette cedex, France
| | - Maguy Jaber
- Sorbonne University , CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale , 4 Place Jussieu , F-75005 Paris , France
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38
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Fedorczyk B, Lipiński PFJ, Puszko AK, Tymecka D, Wilenska B, Dudka W, Perret GY, Wieczorek R, Misicka A. Triazolopeptides Inhibiting the Interaction between Neuropilin-1 and Vascular Endothelial Growth Factor-165. Molecules 2019; 24:molecules24091756. [PMID: 31064153 PMCID: PMC6539594 DOI: 10.3390/molecules24091756] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/03/2019] [Accepted: 05/04/2019] [Indexed: 12/11/2022] Open
Abstract
Inhibiting the interaction of neuropilin-1 (NRP-1) with vascular endothelial growth factor (VEGF) has become an interesting mechanism for potential anticancer therapies. In our previous works, we have obtained several submicromolar inhibitors of this interaction, including branched pentapeptides of general structure Lys(Har)-Xxx-Xxx-Arg. With the intent to improve the proteolytic stability of our inhibitors, we turned our attention to 1,4-disubstituted 1,2,3-triazoles as peptide bond isosteres. In the present contribution, we report the synthesis of 23 novel triazolopeptides along with their inhibitory activity. The compounds were synthesized using typical peptide chemistry methods, but with a conversion of amine into azide completely on solid support. The inhibitory activity of the synthesized derivatives spans from 9.2% to 58.1% at 10 μM concentration (the best compound Lys(Har)-GlyΨ[Trl]GlyΨ[Trl]Arg, 3, IC50 = 8.39 μM). Synthesized peptidotriazoles were tested for stability in human plasma and showed remarkable resistance toward proteolysis, with half-life times far exceeding 48 h. In vitro cell survival test resulted in no significant impact on bone marrow derived murine cells 32D viability. By means of molecular dynamics, we were able to propose a binding mode for compound 3 and discuss the observed structure–activity relationships.
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Affiliation(s)
| | - Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland.
| | - Anna K Puszko
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Dagmara Tymecka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Beata Wilenska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Wioleta Dudka
- Laboratory of Cytometry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland.
| | - Gerard Y Perret
- Université Paris 13, Sorbonne Paris Cité, INSERM U1125, 74 rue Marcel Cachin, 93017 Bobigny, France.
| | - Rafal Wieczorek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Aleksandra Misicka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
- Department of Neuropeptides, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland.
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39
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Swiontek M, Fraczyk J, Wasko J, Chaberska A, Pietrzak L, Kaminski ZJ, Szymanski L, Wiak S, Kolesinska B. Search for New Aggregable Fragments of Human Insulin. Molecules 2019; 24:molecules24081600. [PMID: 31018524 PMCID: PMC6514721 DOI: 10.3390/molecules24081600] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/18/2019] [Accepted: 04/20/2019] [Indexed: 11/16/2022] Open
Abstract
In this study, three independent methods were used to identify short fragment of both chains of human insulin which are prone for aggregation. In addition, circular dichroism (CD) research was conducted to understand the progress of aggregation over time. The insulin fragments (deca- and pepta-peptides) were obtained by solid-phase synthesis using 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium toluene-4-sulfonate (DMT/NMM/TosO-) as a coupling reagent. Systematic studies allowed identification of the new fragments, expected to be engaged in triggering aggregation of the entire structure of human insulin under physiological conditions. It was found that the aggregation process occurs through various structural conformers and may favor the formation of a fibrous structure of aggregate.
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Affiliation(s)
- Monika Swiontek
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
| | - Justyna Fraczyk
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
| | - Joanna Wasko
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
| | - Agata Chaberska
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
| | - Lukasz Pietrzak
- Institute of Mechatronics and Information Systems, Faculty of Electrical, Electronic, Computer and Control Engineering, Lodz University of Technology, Stefanowskiego 18/22, 90-924 Lodz, Poland.
| | - Zbigniew J Kaminski
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
| | - Lukasz Szymanski
- Institute of Mechatronics and Information Systems, Faculty of Electrical, Electronic, Computer and Control Engineering, Lodz University of Technology, Stefanowskiego 18/22, 90-924 Lodz, Poland.
| | - Slawomir Wiak
- Institute of Mechatronics and Information Systems, Faculty of Electrical, Electronic, Computer and Control Engineering, Lodz University of Technology, Stefanowskiego 18/22, 90-924 Lodz, Poland.
| | - Beata Kolesinska
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
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40
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Antopolsky M. Synthetic Oligonucleotides in SPECT/CT In Vivo Imaging: Chemical Modifications, In 111 Complex Formation, Incorporation into Drug Delivery Systems. Methods Mol Biol 2019; 1943:73-82. [PMID: 30838610 DOI: 10.1007/978-1-4939-9092-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Here in we describe a solid phase synthesis of oligonucleotides bearing unnatural moiety appropriate for complex formation with In111 as well as their deprotection, isolation, and purification. We also present methods for oligonucleotides/In111 complex formulation with single and double stranded oligonucleotides of RNA nature and give an example of preparation method for one supramolecular drug delivery system (DDS) consisting of radiolabeled siRNA and positively charged peptide.
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Affiliation(s)
- Maxim Antopolsky
- Teaching and Scientific Consulting, FGBPOU "Medical College", Moscow, Russian Federation.
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41
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Abstract
Chemical cytometry, sensitive analytical measurements of single cells, reveals inherent heterogeneity of cells within a population which is masked or averaged out when using bulk analysis techniques. A particular challenge of chemical cytometry is the development of a suitable reporter or probe for the desired measurement. These reporters must be sufficiently specific for measuring the desired process; possess a lifetime long enough to accomplish the measurement; and have the ability to be loaded into single cells. This chapter details our approach to rationally design and improve peptide substrates as reporters of enzyme activity utilizing chemical cytometry. This method details the iterative approach used to design, characterize, and identify a peptidase-resistant peptide reporter which acts as a kinase substrate within intact cells. Small-scale, rationally designed peptide libraries are generated to rapidly and economically screen candidate reporter peptides for substrate suitability and peptidase resistance. Also detailed are strategies to characterize and validate the designed reporters by determining kinetic parameters, intracellular substrate specificity, resistance to degradation by intracellular peptidases, and behavior within lysates and intact cells.
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Affiliation(s)
- Angela Proctor
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States
| | - Qunzhao Wang
- Department of Chemical Biology and Medicinal Chemistry, School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States
| | - David S Lawrence
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States; Department of Chemical Biology and Medicinal Chemistry, School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States
| | - Nancy L Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States; Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill; North Carolina State University, Raleigh, NC, United States.
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42
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Flood DT, Hintzen JCJ, Bird MJ, Cistrone PA, Chen JS, Dawson PE. Leveraging the Knorr Pyrazole Synthesis for the Facile Generation of Thioester Surrogates for use in Native Chemical Ligation. Angew Chem Int Ed Engl 2018; 57:11634-11639. [PMID: 29908104 PMCID: PMC6126375 DOI: 10.1002/anie.201805191] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/14/2018] [Indexed: 12/12/2022]
Abstract
Facile synthesis of C-terminal thioesters is integral to native chemical ligation (NCL) strategies for chemical protein synthesis. We introduce a new method of mild peptide activation, which leverages solid-phase peptide synthesis (SPPS) on an established resin linker and classical heterocyclic chemistry to convert C-terminal peptide hydrazides into their corresponding thioesters via an acyl pyrazole intermediate. Peptide hydrazides, synthesized on established trityl chloride resins, can be activated in solution with stoichiometric acetyl acetone (acac), readily proceed to the peptide acyl pyrazoles. Acyl pyrazoles are mild acylating agents and are efficiently exchanged with an aryl thiol, which can then be directly utilized in NCL. The mild, chemoselective, and stoichiometric activating conditions allow this method to be utilized through multiple sequential ligations without intermediate purification steps.
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Affiliation(s)
- Dillon T. Flood
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Jordi C. J. Hintzen
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Michael J. Bird
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Philip A. Cistrone
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Jason S. Chen
- Director of the Automated Synthesis Facility, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Philip E. Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 (USA),
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43
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Neves R, Stephens K, Smith-Carpenter JE. Synthesis and Characterization of 1,2-Dithiolane Modified Self-Assembling Peptides. J Vis Exp 2018:58135. [PMID: 30176010 PMCID: PMC6128216 DOI: 10.3791/58135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
This report focuses on the synthesis of an N-terminus 1,2-dithiolane modified self-assembling peptide and the characterization of the resulting self-assembled supramolecular structures. The synthetic route takes advantage of solid-phase peptide synthesis with the on-resin coupling of the dithiolane precursor molecule, 3-(acetylthio)-2-(acetylthiomethyl)propanoic acid, and the microwave-assisted thioacetate deprotection of the peptide N-terminus before final cleavage from the resin to yield the 1,2-dithiolane modified peptide. After the high-performance liquid chromatography (HPLC) purification of the 1,2-dithiolane peptide, derived from the nucleating core of the Aβ peptide associated with Alzheimer's disease, the peptide is shown to self-assemble into cross-β amyloid fibers. Protocols to characterize the amyloid fibers by Fourier-transform infrared spectroscopy (FT-IR), circular dichroism spectroscopy (CD) and transmission electron microscopy (TEM) are presented. The methods of N-terminal modification with a 1,2-dithiolane moiety to well-characterized self-assembling peptides can now be explored as model systems to develop post-assembly modification strategies and explore dynamic covalent chemistry on supramolecular peptide nanofiber surfaces.
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Affiliation(s)
- Ruben Neves
- Department of Chemistry and Biochemistry, Fairfield University
| | - Kailyn Stephens
- Department of Chemistry and Biochemistry, Fairfield University
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44
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Kijewska M, Waliczek M, Cal M, Jaremko Ł, Jaremko M, Król M, Kołodziej M, Lisowski M, Stefanowicz P, Szewczuk Z. Solid-phase synthesis of peptides containing aminoadipic semialdehyde moiety and their cyclisations. Sci Rep 2018; 8:10462. [PMID: 29993003 PMCID: PMC6041278 DOI: 10.1038/s41598-018-28798-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/29/2018] [Indexed: 11/23/2022] Open
Abstract
Pathological levels of oxidative stress (OS) have been implicated in many diseases including diabetes mellitus, neurodegenerative diseases, inflammatory diseases, atherosclerosis, and cancer. Studies of oxidative stress are however complicated by the low concentration of oxidation products. To resolve this problem, we tested a new derivative of aminoadipic semialdehyde (Fmoc-Aea-OH) in the solid-phase synthesis of carbonylated peptides. We prepared a series of peptides with free and acetylated N-terminal amino groups using the Fmoc-Aea-OH reagent. LC-MS, ESI-MS, and MS/MS spectra confirmed the sequences of the modified peptides, although the LC-MS and ESI-MS spectra were dominated by signals corresponding to dehydration products. NMR studies of acetylated products revealed that the dominant product formed in this reaction contains a 1,2,3,4-tetrahydropyridine-2-carboxylic acid residue. Another side reaction in this system was the cleavage of the amide bond between the Aea residue and the amino acid moiety preceding it resulting in the formation of a side product with a six-membered ring at the N-terminus (2,3,4,5-tetrahydropyridine-2-carboxylic acid residue). We found that, depending on the peptide sequence, one of those side products is predominant. Our work suggests new methods for the solid-state synthesis of peptides containing unnatural amino acids.
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Affiliation(s)
- Monika Kijewska
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland.
| | - Mateusz Waliczek
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Marta Cal
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Łukasz Jaremko
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Mariusz Jaremko
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia.
| | - Maria Król
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Marta Kołodziej
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Marek Lisowski
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Zbigniew Szewczuk
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
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45
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Prior AM, Hori T, Fishman A, Sun D. Recent Reports of Solid-Phase Cyclohexapeptide Synthesis and Applications. Molecules 2018; 23:molecules23061475. [PMID: 29912160 PMCID: PMC6100019 DOI: 10.3390/molecules23061475] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/11/2018] [Accepted: 06/16/2018] [Indexed: 12/31/2022] Open
Abstract
Macrocyclic peptides are privileged scaffolds for drug development and constitute a significant portion of macrocyclic drugs on the market today in fields spanning from infectious disease to oncology. Developing orally bioavailable peptide-based drugs remains a challenging task; however, macrocyclization of linear peptides can be an effective strategy to improve membrane permeability, proteolytic stability, oral bioavailability, and overall drug-like characteristics for this class. Significant advances in solid-phase peptide synthesis (SPPS) have enabled the efficient construction of macrocyclic peptide and peptidomimetic libraries with macrolactamization being performed on-resin or in solution phase. The primary goal of this review is to summarize solid-phase cyclohexapeptide synthesis using the on-resin and solution-phase macrocyclization methodologies published since 2013. We also highlight their broad applications ranging from natural product total synthesis, synthetic methodology development, and medicinal chemistry, to drug development and analyses of conformational and physiochemical properties.
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Affiliation(s)
- Allan M Prior
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 34 Rainbow Drive, Hilo, Hawaii, HI 96720, USA.
| | - Taylor Hori
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 34 Rainbow Drive, Hilo, Hawaii, HI 96720, USA.
| | - Ashriel Fishman
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 34 Rainbow Drive, Hilo, Hawaii, HI 96720, USA.
| | - Dianqing Sun
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 34 Rainbow Drive, Hilo, Hawaii, HI 96720, USA.
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46
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Zimmermann T, Christensen SB, Franzyk H. Preparation of Enzyme-Activated Thapsigargin Prodrugs by Solid-Phase Synthesis. Molecules 2018; 23:molecules23061463. [PMID: 29914143 PMCID: PMC6100299 DOI: 10.3390/molecules23061463] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 06/05/2018] [Accepted: 06/12/2018] [Indexed: 11/20/2022] Open
Abstract
Since cells in solid tumors divide less rapidly than cells in the bone marrow or cells of the immune system, mitotic inhibitors often cause severe side effects when used for treatment of diseases like prostate cancer and breast cancer. One approach to overcome this problem involves attempts at developing drugs based on general cytotoxins, like calicheamicin and thapsigargin, which kill cells at all phases of the cell cycle. However, such toxins can only be used when efficient targeting to the malignant tissue is possible. In the case of thapsigargin, selectivity for tumor-associated cells is achieved by conjugating the drug to a peptide that is only cleaved in the vicinity of tumors to release the cytotoxic drug or an analog with retained activity. Solid-phase synthesis protocols were developed for preparation of three already validated prodrugs of thapsigargin: one prodrug cleavable by human kallikrein 2, one prodrug cleavable by prostate-specific antigen, and one prodrug cleavable by prostate-specific membrane antigen.
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Affiliation(s)
- Tomas Zimmermann
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.
| | - Søren Brøgger Christensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.
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47
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Liu J, Cheng R, Rozovsky S. Synthesis and semisynthesis of selenopeptides and selenoproteins. Curr Opin Chem Biol 2018; 46:41-47. [PMID: 29723718 DOI: 10.1016/j.cbpa.2018.04.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/09/2018] [Accepted: 04/16/2018] [Indexed: 11/19/2022]
Abstract
The versatile chemistry of the genetically encoded amino acid selenocysteine (Sec) is employed in Nature to expand the reactivity of enzymes. In addition to, its role in biology, Sec is used in protein engineering to modify folding, stability, and reactivity of proteins, to introduce conjugations and to facilitate reactions. However, due to limitations related to Sec's insertion mechanism in Nature, much of the production of Sec containing peptides and proteins relies on synthesis and semisynthesis. Here, we review recent advances that have enabled the assembly of complicated selenoproteins, including novel uses of protecting groups for solid phase peptide synthesis, rapid selenoester driven chemical ligations and versatile expressed protein ligations.
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Affiliation(s)
- Jun Liu
- University of California, San Francisco, Department of Pharmaceutical Chemistry, 555 Mission Bay Blvd. South, San Francisco, CA 94158, United States.
| | - Rujin Cheng
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19716, United States
| | - Sharon Rozovsky
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19716, United States.
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48
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Wilson TA, Tokarski RJ, Sullivan P, Demoret RM, Orjala J, Rakotondraibe LH, Fuchs JR. Total Synthesis of Scytonemide A Employing Weinreb AM Solid-Phase Resin. J Nat Prod 2018; 81:534-542. [PMID: 29400964 PMCID: PMC5866229 DOI: 10.1021/acs.jnatprod.7b00912] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The human 20S proteasome inhibitor scytonemide A (1), a macrocyclic imine originally isolated from the cyanobacterium Scytonema hofmanni, was synthesized via a biomimetic solid-phase peptide synthesis (SPPS) approach employing the Weinreb AM resin. Utilizing this approach, cyclization of the protected heptapeptide via formation of the imine bond occurred spontaneously upon cleavage from the resin in the presence of a reducing agent and subsequent aqueous workup. The final deprotection step necessary to produce the natural product was accomplished under slightly basic conditions, facilitating cleavage of the silyl ether group while leaving the macrocycle intact. Purification of the synthetic scytonemide A was accomplished via normal-phase flash column chromatography, potentially facilitating larger scale preparation of the compound necessary for future mechanistic and SAR studies. The structure of the target compound was confirmed by NMR spectroscopy, which also shed light on differences in the spectroscopic data obtained for the synthetic and natural scytonemide A samples for some of the amide and alcohol signals in the 1H NMR spectrum.
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Affiliation(s)
- Tyler A. Wilson
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Robert J. Tokarski
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Peter Sullivan
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, United States
| | - Robert M. Demoret
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Jimmy Orjala
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, United States
| | - L. Harinantenaina Rakotondraibe
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - James R. Fuchs
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
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49
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Abstract
One-bead-one-compound (OBOC) libraries constructed by solid-phase split-and-pool synthesis are a valuable source of protein ligands. Most OBOC libraries are comprised of oligoamides, particularly peptides, peptoids, and peptoid-inspired molecules. Further diversification of the chemical space covered by OBOC libraries is desirable. Toward this end, we report here the efficient proline-catalyzed asymmetric Mannich reaction between immobilized aldehydes and soluble ketones and anilines. The reaction conditions do not compromise the amplification of DNA by the PCR. Thus, this chemistry will likely be useful for the construction of novel DNA-encoded libraries by solid-phase synthesis.
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Affiliation(s)
- Nam Tran-Hoang
- Department of Chemistry The Scripps Research Institute 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Department of Chemistry The Scripps Research Institute 130 Scripps Way, Jupiter, Florida 33458, United States
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50
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Abstract
Synthetic mono-ADPr-peptides are useful for structural, biochemical, and proteomics studies. We describe here a protocol for the preparation of mono-ADPr-peptides based on a fairly standard Fmoc-based solid-phase synthesis. Phosphoribosylated precursor building blocks are introduced into the peptide chain on solid-phase and subsequently converted to ADPr-sites by chemical phosphorylation with adenosine phosphoramidite. Suitably protected phosphoribosylated glutamine, asparagine, and citrulline building blocks described in this protocol allow introduction of ADP-Gln, ADPr-Asn, and ADPr-Cit into peptide chains as demonstrated for three peptides. Trifunctional amino acids, for which base-sensitive side-chain protection is available, can be accommodated in the sequences flanking the ADPr-cites.
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Affiliation(s)
- Hans A V Kistemaker
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Universiteit Leiden, Leiden, The Netherlands
| | - Jim Voorneveld
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Universiteit Leiden, Leiden, The Netherlands
| | - Dmitri V Filippov
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Universiteit Leiden, Leiden, The Netherlands.
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