1
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Pandurangan S, Easwaramoorthi S, Ayyadurai N. Engineering proteins with catechol chemistry for biotechnological applications. Crit Rev Biotechnol 2024:1-19. [PMID: 39198031 DOI: 10.1080/07388551.2024.2387165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 04/01/2023] [Accepted: 06/27/2023] [Indexed: 09/01/2024]
Abstract
Developing proteins with increased chemical space by expanding the amino acids alphabet has been an emerging technique to compete for the obstacle encountered by their need in various applications. 3,4-Dihydroxyphenylalanine (L-DOPA) catecholic unnatural amino acid is abundantly present in mussels foot proteins through post-translational modification of tyrosine to give a strong adhesion toward wet rocks. L-DOPA forms: bidentate coordination, H-bonding, metal-ligand complexes, long-ranged electrostatic, and van der Waals interactions via a pair of donor hydroxyl groups. Incorporating catechol in proteins through genetic code expansion paved the way for developing: protein-based bio-sensor, implant coating, bio-conjugation, adhesive bio-materials, biocatalyst, metal interaction and nano-biotechnological applications. The increased chemical spaces boost the protein properties by offering a new chemically active interaction ability to the protein. Here, we review the technique employed to develop a genetically expanded organism with catechol to provide novel properties and functionalities; and we highlight the importance of L-DOPA incorporated proteins in biomedical and industrial fields.
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Affiliation(s)
- Suryalakshmi Pandurangan
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research - Central Leather Research Institute, Chennai, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Shanmugam Easwaramoorthi
- Academy of Scientific and Innovative Research, Ghaziabad, India
- Department of Inorganic and Physical Chemistry, Council of Scientific and Industrial Research - Central Leather Research Institute, Chennai, India
| | - Niraikulam Ayyadurai
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research - Central Leather Research Institute, Chennai, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
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2
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Hu L, Zhao J. Ynamide Coupling Reagents: Origin and Advances. Acc Chem Res 2024; 57:855-869. [PMID: 38452397 PMCID: PMC10956395 DOI: 10.1021/acs.accounts.3c00743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024]
Abstract
Since the pioneering work of Curtius and Fischer, chemical peptide synthesis has witnessed a century's development and evolved into a routine technology. However, it is far from perfect. In particular, it is challenged by sustainable development because the state-of-the-art of peptide synthesis heavily relies on legacy reagents and technologies developed before the establishment of green chemistry. Over the past three decades, a broad range of efforts have been made for greening peptide synthesis, among which peptide synthesis using unprotected amino acid represents an ideal and promising strategy because it does not require protection and deprotection steps. Unfortunately, C → N peptide synthesis employing unprotected amino acids has been plagued by undesired polymerization, while N → C inverse peptide synthesis with unprotected amino acids is retarded by severe racemization/epimerization owing to the iterative activation and aminolysis of high racemization/epimerization susceptible peptidyl acids. Consequently, there is an urgent need to develop innovative coupling reagents and strategies with novel mechanisms that can address the long-standing notorious racemization/epimerization issue of peptide synthesis.This Account will describe our efforts in discovery of ynamide coupling reagents and their application in greening peptide synthesis. Over an eight-year journey, ynamide coupling reagents have evolved into a class of general coupling reagents for both amide and ester bond formation. In particular, the superiority of ynamide coupling reagents in suppressing racemization/epimerization enabled them to be effective for peptide fragment condensation, and head-to-tail cyclization, as well as precise incorporation of thioamide substitutions into peptide backbones. The first practical inverse peptide synthesis using unprotected amino acids was successfully accomplished by harnessing such features and taking advantage of a transient protection strategy. Ynamide coupling reagent-mediated ester bond formation enabled efficient intermolecular esterification and macrolactonization with preservation of α-chirality and the configuration of the conjugated α,β-C-C double bond. To make ynamide coupling reagents readily available with reasonable cost and convenience, we have developed a scalable one-step synthetic method from cheap starting materials. Furthermore, a water-removable ynamide coupling reagent was developed, offering a column-free purification of the target coupling product. In addition, the recycle of ynamide coupling reagent was accomplished, thereby paving the way for their sustainable industrial application.As such, this Account presents the whole story of the origin, mechanistic insights, preparation, synthetic applications, and recycle of ynamide coupling reagents with a perspective that highlights their future impact on peptide synthesis.
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Affiliation(s)
- Long Hu
- Affiliated Cancer Hospital, Guangdong
Provincial Key Laboratory of Major Obstetric Diseases, School of Pharmaceutical
Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Junfeng Zhao
- Affiliated Cancer Hospital, Guangdong
Provincial Key Laboratory of Major Obstetric Diseases, School of Pharmaceutical
Sciences, Guangzhou Medical University, Guangzhou, 511436, China
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3
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Chetankumar E, Bharamawadeyar S, Srinivasulu C, Sureshbabu VV. AITF (4-acetamidophenyl triflimide) mediated synthesis of amides, peptides and esters. Org Biomol Chem 2023; 21:8875-8882. [PMID: 37888883 DOI: 10.1039/d3ob01351k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
A simple, broadly applicable protocol for amidation and esterification reactions is described. Thereby, 4-acetamidophenyl triflimide (AITF), a crystalline stable reagent, is employed for the activation of carboxylic acids. The use of AITF as a coupling agent is demonstrated in the synthesis of peptides, amides and esters under mild conditions in good to excellent yields. Notably, peptide segment condensations were also accomplished. A diverse array of synthetic protocols showcasing a broad substrate scope and good functional group compatibility were accomplished. Herein, we systematically summarized the use of AITF in peptide synthesis strategies.
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Affiliation(s)
- Eti Chetankumar
- Peptide Research Laboratory, Department of Studies in Chemistry, Sneha Bhavan, Bangalore University, Jnana Bharathi, Bengaluru 560 056, India.
| | - Swetha Bharamawadeyar
- Peptide Research Laboratory, Department of Studies in Chemistry, Sneha Bhavan, Bangalore University, Jnana Bharathi, Bengaluru 560 056, India.
| | - Chinthaginjala Srinivasulu
- Peptide Research Laboratory, Department of Studies in Chemistry, Sneha Bhavan, Bangalore University, Jnana Bharathi, Bengaluru 560 056, India.
| | - Vommina V Sureshbabu
- Peptide Research Laboratory, Department of Studies in Chemistry, Sneha Bhavan, Bangalore University, Jnana Bharathi, Bengaluru 560 056, India.
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4
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Guimarães CFRC, Félix AS, Brandão TAS, Bemquerer MP, Piló-Veloso D, Verly RM, Resende JM. Optimizing the synthesis of dimeric peptides: influence of the reaction medium and effects that modulate kinetics and reaction yield. Amino Acids 2023; 55:1201-1212. [PMID: 37543997 DOI: 10.1007/s00726-023-03309-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/21/2023] [Indexed: 08/08/2023]
Abstract
Peptides are remarkably interesting alternatives to several applications. In particular, antimicrobial sequences have raised major interest of the scientific community due to the resistance acquired by commonly used antibiotics. Amongst these, some dimeric peptides have shown very promising characteristics as strong biological activities and resistance against degradation by peptidases. However, despite such promising characteristics, a relatively small number of studies address dimeric peptides, mainly due to the synthesis-related obstacles in their production, whereas the well-implemented routines of solid phase peptide synthesis-which includes the possibility of automation-makes life significantly easier. Here, we present kinetic investigations of the dimerization of a cysteine-containing sequence to obtain the homodimeric antimicrobial peptide homotarsinin. Based on the structural and membrane interaction data already available for the dimer and its monomeric chain, we have proposed distinct dimerization protocols in selected environments, namely, aqueous buffer, TFE:H2O and micellar solutions. The experimental results were adjusted by a theoretical model. Both the kinetic profiles and the reaction yields are dependent on the reaction medium, clearly indicating that aggregation, peptide structure, and peptide-membrane interactions play major roles in the formation of the disulfide bond. Finally, the rationalization of the different aspects addressed here is expected to contribute to research and applications that demand the obtainment of dimeric peptides.
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Affiliation(s)
- Carlos F R C Guimarães
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, P.O. Box 486, Belo Horizonte, MG, 31270-901, Brazil
- Present Address: Universidade Nilton Lins, Avenida Professor Nilton Lins, Manaus, AM, 69058-030, Brazil
| | - Amanda S Félix
- Departamento de Química, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG, 39100-000, Brazil
| | - Tiago A S Brandão
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, P.O. Box 486, Belo Horizonte, MG, 31270-901, Brazil
| | - Marcelo P Bemquerer
- Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Embrapa Gado de Leite, Juiz de Fora, MG, 36038-330, Brazil
| | - Dorila Piló-Veloso
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, P.O. Box 486, Belo Horizonte, MG, 31270-901, Brazil
| | - Rodrigo M Verly
- Departamento de Química, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG, 39100-000, Brazil.
| | - Jarbas M Resende
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, P.O. Box 486, Belo Horizonte, MG, 31270-901, Brazil.
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5
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Roubert C, Fontaine E, Upton AM. “Upcycling” known molecules and targets for drug-resistant TB. Front Cell Infect Microbiol 2022; 12:1029044. [PMID: 36275029 PMCID: PMC9582839 DOI: 10.3389/fcimb.2022.1029044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Despite reinvigorated efforts in Tuberculosis (TB) drug discovery over the past 20 years, relatively few new drugs and candidates have emerged with clear utility against drug resistant TB. Over the same period, significant technological advances and learnings around target value have taken place. This has offered opportunities to re-assess the potential for optimization of previously discovered chemical matter against Mycobacterium tuberculosis (M.tb) and for reconsideration of clinically validated targets encumbered by drug resistance. A re-assessment of discarded compounds and programs from the “golden age of antibiotics” has yielded new scaffolds and targets against TB and uncovered classes, for example beta-lactams, with previously unappreciated utility for TB. Leveraging validated classes and targets has also met with success: booster technologies and efforts to thwart efflux have improved the potential of ethionamide and spectinomycin classes. Multiple programs to rescue high value targets while avoiding cross-resistance are making progress. These attempts to make the most of known classes, drugs and targets complement efforts to discover new chemical matter against novel targets, enhancing the chances of success of discovering effective novel regimens against drug-resistant TB.
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6
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Löffler JG, Deniz E, Feid C, Franz VG, Bredenbeck J. Versatile Vibrational Energy Sensors for Proteins. Angew Chem Int Ed Engl 2022; 61:e202200648. [PMID: 35226765 PMCID: PMC9401566 DOI: 10.1002/anie.202200648] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Indexed: 11/10/2022]
Abstract
Vibrational energy transfer (VET) is emerging as key mechanism for protein functions, possibly playing an important role for energy dissipation, allosteric regulation, and enzyme catalysis. A deep understanding of VET is required to elucidate its role in such processes. Ultrafast VIS-pump/IR-probe spectroscopy can detect pathways of VET in proteins. However, the requirement of having a VET donor and a VET sensor installed simultaneously limits the possible target proteins and sites; to increase their number we compare six IR labels regarding their utility as VET sensors. We compare these labels in terms of their FTIR, and VET signature in VET donor-sensor dipeptides in different solvents. Furthermore, we incorporated four of these labels in PDZ3 to assess their capabilities in more complex systems. Our results show that different IR labels can be used interchangeably, allowing for free choice of the right label depending on the system under investigation and the methods available.
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Affiliation(s)
- Jan G. Löffler
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Erhan Deniz
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Carolin Feid
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Valentin G. Franz
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Jens Bredenbeck
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
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7
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Löffler JG, Deniz E, Feid C, Franz VG, Bredenbeck J. Versatile Vibrational Energy Sensors for Proteins. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jan G. Löffler
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Erhan Deniz
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Carolin Feid
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Valentin G. Franz
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Jens Bredenbeck
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
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8
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Adhikari A, Bhattarai BR, Aryal A, Thapa N, Kc P, Adhikari A, Maharjan S, Chanda PB, Regmi BP, Parajuli N. Reprogramming natural proteins using unnatural amino acids. RSC Adv 2021; 11:38126-38145. [PMID: 35498070 PMCID: PMC9044140 DOI: 10.1039/d1ra07028b] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022] Open
Abstract
Unnatural amino acids have gained significant attention in protein engineering and drug discovery as they allow the evolution of proteins with enhanced stability and activity. The incorporation of unnatural amino acids into proteins offers a rational approach to engineer enzymes for designing efficient biocatalysts that exhibit versatile physicochemical properties and biological functions. This review highlights the biological and synthetic routes of unnatural amino acids to yield a modified protein with altered functionality and their incorporation methods. Unnatural amino acids offer a wide array of applications such as antibody-drug conjugates, probes for change in protein conformation and structure-activity relationships, peptide-based imaging, antimicrobial activities, etc. Besides their emerging applications in fundamental and applied science, systemic research is necessary to explore unnatural amino acids with novel side chains that can address the limitations of natural amino acids.
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Affiliation(s)
- Anup Adhikari
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Bibek Raj Bhattarai
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Ashika Aryal
- Department of Chemistry, Birendra Multiple Campus, Tribhuvan University Bharatpur Chitwan Nepal
| | - Niru Thapa
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Puja Kc
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Ashma Adhikari
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Sushila Maharjan
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Prem B Chanda
- Department of Chemistry and Physics, Southeastern Louisiana University Hammond Louisiana 70402 USA
| | - Bishnu P Regmi
- Department of Chemistry, Florida Agricultural and Mechanical University Tallahassee Florida 32307 USA
| | - Niranjan Parajuli
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
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9
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Yi H, Zhang J, Ke F, Guo X, Yang J, Xie P, Liu L, Wang Q, Gao X. Comparative Analyses of the Transcriptome and Proteome of Escherichia coli C321.△A and Further Improving Its Noncanonical Amino Acids Containing Protein Expression Ability by Integration of T7 RNA Polymerase. Front Microbiol 2021; 12:744284. [PMID: 34659179 PMCID: PMC8511705 DOI: 10.3389/fmicb.2021.744284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/30/2021] [Indexed: 01/09/2023] Open
Abstract
Incorporation of noncanonical amino acids (ncAAs) into proteins has been proven to be a powerful tool to manipulate protein structure and function, and to investigate many biological processes. Improving the yields of ncAA-containing proteins is of great significance in industrial-scale applications. Escherichia coli C321.ΔA was generated by the replacement of all known amber codons and the deletion of RF1 in the genome and has been proven to be an ideal host for ncAA-containing protein expression using genetic code expansion. In this study, we investigated the transcriptome and proteome profiles of this first codon reassignment strain and found that some functions and metabolic pathways were differentially expressed when compared with those of its parent strain. Genes involved in carbohydrate and energy metabolism were remarkably downregulated. Our results may provide important clues about the growth defects in E. coli C321.ΔA. Furthermore, we improved the yields of ncAA-containing proteins in E. coli C321.ΔA by integrating the T7 RNA polymerase system.
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Affiliation(s)
- Huawei Yi
- Clinical Laboratory, The First Affiliated Hospital of Yangtze University, Jingzhou, China
| | - Jing Zhang
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Famin Ke
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Xiurong Guo
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Jian Yang
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Peijuan Xie
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Li Liu
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Qin Wang
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Xiaowei Gao
- School of Pharmacy, Southwest Medical University, Luzhou, China.,Department of Chemistry, Zhejiang University, Hangzhou, China
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10
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Le Guen C, Dussouillez C, Kichler A, Chan-Seng D. Insertion of hydrophobic spacers on dodecalysines as potential transfection enhancers. Eur Polym J 2021. [DOI: 10.1016/j.eurpolymj.2021.110654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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11
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Wang Z, Wang X, Wang P, Zhao J. Allenone-Mediated Racemization/Epimerization-Free Peptide Bond Formation and Its Application in Peptide Synthesis. J Am Chem Soc 2021; 143:10374-10381. [PMID: 34191506 DOI: 10.1021/jacs.1c04614] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Allenone has been identified as a highly effective peptide coupling reagent for the first time. The peptide bond was formed with an α-carbonyl vinyl ester as the key intermediate, the formation and subsequent aminolysis of which proceed spontaneously in a racemization-/epimerization-free manner. The allenone coupling reagent not only is effective for the synthesis of simple amides and dipeptides but is also amenable to peptide fragment condensation and solid-phase peptide synthesis (SPPS). The robustness of the allenone-mediated peptide bond formation was showcased incisively by the synthesis of carfilzomib, which involved a rare racemization-/epimerization-free N to C peptide elongation strategy. Furthermore, the successful synthesis of the model difficult peptide ACP (65-74) on a solid support suggested that this method was compatible with SPPS. This method combines the advantages of conventional active esters and coupling reagents, while overcoming the disadvantages of both strategies. Thus, this allenone-mediated peptide bond formation strategy represents a disruptive innovation in peptide synthesis.
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Affiliation(s)
- Zhengning Wang
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, Guangdong, P. R. China.,College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi, P. R. China
| | - Xuewei Wang
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, Guangdong, P. R. China.,College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi, P. R. China
| | - Penghui Wang
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, Guangdong, P. R. China.,College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi, P. R. China
| | - Junfeng Zhao
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, Guangdong, P. R. China.,School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.,College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi, P. R. China.,State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, People's Republic of China
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12
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Wang X, Li J, Hayashi Y. Oxidative peptide bond formation of glycine-amino acid using 2-(aminomethyl)malononitrile as a glycine unit. Chem Commun (Camb) 2021; 57:4283-4286. [PMID: 33913954 DOI: 10.1039/d1cc00130b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Amide linkage of glycine-amino acid was synthesized by coupling of substituted 2-(aminomethyl)malononitrile as a C-terminal glycine unit and N-terminal amine using CsOAc and O2 in an aqueous solution. This is a coupling reagent-free and catalyst-free peptide synthesis via oxidative amide bond formation. Various tripeptides and tetrapeptides were synthesized efficiently and the sulfide moiety is inert even under an oxygen atmosphere.
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Affiliation(s)
- Xiaoling Wang
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan.
| | - Jing Li
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan.
| | - Yujiro Hayashi
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan.
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13
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Assessing biofilm inhibition and immunomodulatory activity of small amounts of synthetic host defense peptides synthesized using SPOT-array technology. Nat Protoc 2021; 16:1850-1870. [PMID: 33837303 DOI: 10.1038/s41596-021-00500-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022]
Abstract
Peptides are promising drug candidates because of their diversity, biocompatibility and spectrum of activities. Here, we describe a protocol for high-throughput screening of SPOT-peptide arrays to assess the antibiofilm, antimicrobial and immunomodulatory activities of synthetic peptides. It is a Protocol Extension of our previous Nature Protocols article, which describes the synthesis of SPOT-peptide arrays and assays for screening antimicrobial activity. This latest protocol allows the simultaneous assessment of hundreds of synthetic host defense peptides to define their overall activity profiles and identify candidate sequences that are suitable for further characterization and development as anti-infectives. When coupled with the SPOT-array technology for peptide synthesis, the described procedures are rapid, inexpensive and straightforward for peptide library screening. The protocols can be implemented in most microbiology or immunology research laboratories without the need for specialists. The time to complete each step ranges between 1 and 4 h with overnight pauses, and datasets related to the antibiofilm and immunomodulatory activities of a large set of peptide sequences can be generated in a few days.
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14
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Winkler DFH. Automated Solid-Phase Peptide Synthesis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2103:59-94. [PMID: 31879919 DOI: 10.1007/978-1-0716-0227-0_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The development of solid-phase peptide synthesis by Bruce Merrifield paved the way for a synthesis carried out by machines. Automated peptide synthesis is a fast and convenient way of synthesizing many peptides simultaneously. This chapter tries to give a general guidance for the development of synthesis protocols for the peptide synthesizer. It also provides some suggestions for the modification of the synthesized peptides. Additionally, many examples of possible challenges during and after the synthesis are given in order to support the reader in finding the best synthesis strategy. Numerous references are given to many of the described matters.
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15
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Ahangarpour M, Kavianinia I, Harris PWR, Brimble MA. Photo-induced radical thiol-ene chemistry: a versatile toolbox for peptide-based drug design. Chem Soc Rev 2021; 50:898-944. [PMID: 33404559 DOI: 10.1039/d0cs00354a] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While the global market for peptide/protein-based therapeutics is witnessing significant growth, the development of peptide drugs remains challenging due to their low oral bioavailability, poor membrane permeability, and reduced metabolic stability. However, a toolbox of chemical approaches has been explored for peptide modification to overcome these obstacles. In recent years, there has been a revival of interest in photoinduced radical thiol-ene chemistry as a powerful tool for the construction of therapeutic peptides.
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Affiliation(s)
- Marzieh Ahangarpour
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand.
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16
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Murugan NA, Raja KMP, Saraswathi NT. Peptide-Based Antiviral Drugs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:261-284. [PMID: 34258744 DOI: 10.1007/978-981-16-0267-2_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Three types of chemical entities, namely, small organic molecules (organics), peptides, and biologics, are mainly used as drug candidates for the treatment of various diseases. Even though the peptide drugs are known since 1920 in association with the clinical use of insulin, only a limited number of peptides are currently used for therapeutics due to various disadvantages associated with them such as limited serum and blood stability, oral bioavailability, and permeability. Since, through chemical modifications and structure tuning, many of these limitations can be overcome, peptide-based drugs are gaining attention in pharmaceutical research. As of today, there are more than 60 peptide-based drugs approved by FDA, and over 150 peptides are in the advanced clinical studies. In this book chapter, the peptide-based lead compounds and drugs available for treating various viral diseases and their advantages and disadvantages when compared to small molecules drugs are discussed.
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Affiliation(s)
- N Arul Murugan
- Department of Theoretical Chemistry and Biology, School of Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - K Muruga Poopathi Raja
- Chemical Biology and Biophysics Laboratory, Department of Physical Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai, Tamilnadu, India.
| | - N T Saraswathi
- School of Chemical & Biotechnology, Sastra Deemed University, Thanjavur, Tamil Nadu, India
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17
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Braun GA, Pogostin BH, Pucetaite M, Londergan CH, Åkerfeldt KS. Deuterium-Enhanced Raman Spectroscopy for Histidine pK a Determination in a pH-Responsive Hydrogel. Biophys J 2020; 119:1701-1705. [PMID: 33080220 DOI: 10.1016/j.bpj.2020.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022] Open
Abstract
We report here a method for the determination of the pKa of histidine in complex or heterogeneous systems amenable to neither solid-state nor solution NMR spectroscopy. Careful synthesis of a fluorenylmethyloxycarbonyl- and trityl-protected, C2-deuterated histidine produces a vibrational-probe-equipped amino acid that can readily be incorporated into any peptide accessible by standard solid-phase methods. The frequency of the unique, Raman-active stretching vibration of this C2-D probe is a clear reporter of the protonation state of histidine. We investigate here a pH-sensitive peptide that self-assembles to form a hydrogel at neutral pH. The pKa of the lone histidine residue in the peptide, which is likely responsible for this pH-dependent behavior, cannot be investigated by NMR spectroscopy because of the supramolecular, soft nature of the gel. However, after synthesizing a C2-deuterated-histidine-containing peptide, we were able to follow the protonation state of histidine throughout a pH titration using Raman difference spectroscopy, thereby precisely determining the pKa of interest.
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Affiliation(s)
- Gabriel A Braun
- Department of Chemistry, Haverford College, Haverford, Pennsylvania; Centre for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden, Lund University, Lund, Sweden.
| | - Brett H Pogostin
- Department of Chemistry, Haverford College, Haverford, Pennsylvania
| | - Milda Pucetaite
- Centre for Environmental and Climate Research, Lund University, Lund, Sweden
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18
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Affiliation(s)
- Zachary P. Gates
- p53 Lab, Agency for Science, Technology and Research (A*STAR) Singapore Singapore
| | - Nina Hartrampf
- Department of Chemistry University of Zurich Zurich Switzerland
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19
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Ya’u Sabo Ajingi, Nujarin Jongruja. Antimicrobial Peptide Engineering: Rational Design, Synthesis, and Synergistic Effect. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020040044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Mueller LK, Baumruck AC, Zhdanova H, Tietze AA. Challenges and Perspectives in Chemical Synthesis of Highly Hydrophobic Peptides. Front Bioeng Biotechnol 2020; 8:162. [PMID: 32195241 PMCID: PMC7064641 DOI: 10.3389/fbioe.2020.00162] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/18/2020] [Indexed: 12/31/2022] Open
Abstract
Solid phase peptide synthesis (SPPS) provides the possibility to chemically synthesize peptides and proteins. Applying the method on hydrophilic structures is usually without major drawbacks but faces extreme complications when it comes to "difficult sequences." These includes the vitally important, ubiquitously present and structurally demanding membrane proteins and their functional parts, such as ion channels, G-protein receptors, and other pore-forming structures. Standard synthetic and ligation protocols are not enough for a successful synthesis of these challenging sequences. In this review we highlight, summarize and evaluate the possibilities for synthetic production of "difficult sequences" by SPPS, native chemical ligation (NCL) and follow-up protocols.
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Affiliation(s)
- Lena K. Mueller
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt University of Technology, Darmstadt, Germany
| | - Andreas C. Baumruck
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt University of Technology, Darmstadt, Germany
| | - Hanna Zhdanova
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Alesia A. Tietze
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
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21
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Hasanin MS, Moustafa GO. New potential green, bioactive and antimicrobial nanocomposites based on cellulose and amino acid. Int J Biol Macromol 2020; 144:441-448. [DOI: 10.1016/j.ijbiomac.2019.12.133] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/15/2019] [Accepted: 12/15/2019] [Indexed: 12/16/2022]
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22
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Okamoto R, Nomura K, Maki Y, Kajihara Y. A Chemoselective Peptide Bond Formation by Amino Thioacid Coupling. CHEM LETT 2019. [DOI: 10.1246/cl.190607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ryo Okamoto
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Project Research Center for Fundamental Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kota Nomura
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuta Maki
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Project Research Center for Fundamental Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhiro Kajihara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Project Research Center for Fundamental Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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23
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Díaz‐Perlas C, Varese M, Guardiola S, Sánchez‐Navarro M, García J, Teixidó M, Giralt E. Protein Chemical Synthesis Combined with Mirror‐Image Phage Display Yields
d
‐Peptide EGF Ligands that Block the EGF–EGFR Interaction. Chembiochem 2019; 20:2079-2084. [DOI: 10.1002/cbic.201900355] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Cristina Díaz‐Perlas
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
| | - Monica Varese
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
| | - Salvador Guardiola
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
| | - Macarena Sánchez‐Navarro
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
| | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
| | - Meritxell Teixidó
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
- Department of Inorganic and Organic ChemistryUniversity of Barcelona Martí I Franqués 1–11 Barcelona 08028 Spain
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24
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Comandè A, Greco M, Belsito EL, Liguori A, Leggio A. A titanium tetrachloride-based effective methodology for the synthesis of dipeptides. RSC Adv 2019; 9:22137-22142. [PMID: 35518841 PMCID: PMC9066614 DOI: 10.1039/c9ra04058g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/09/2019] [Indexed: 11/21/2022] Open
Abstract
A series of dipeptide systems have been easily achieved through a TiCl4-assisted condensation reaction. The reaction of N-protected amino acids with amino acid methyl esters in pyridine and in the presence of TiCl4 furnished the corresponding dipeptides with high yields and diastereoselectivity. The reaction was successfully applied to amino acids protected on the α-amino function with different protecting groups. The adopted experimental conditions allowed preserving both the protecting groups on the α-amino function and on the side chain functionalities. Furthermore, the preservation of the stereochemical integrity at the amino acid chiral centres has been verified.
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Affiliation(s)
- Alessandra Comandè
- Dipartimento di Farmacia e Scienze della Salute e della Nutrizione, Università della Calabria Edificio Polifunzionale I-87036 Arcavacata di Rende CS Italy +39 984 493265 +39 984 493199
| | - Marianna Greco
- Dipartimento di Farmacia e Scienze della Salute e della Nutrizione, Università della Calabria Edificio Polifunzionale I-87036 Arcavacata di Rende CS Italy +39 984 493265 +39 984 493199
| | - Emilia Lucia Belsito
- Dipartimento di Farmacia e Scienze della Salute e della Nutrizione, Università della Calabria Edificio Polifunzionale I-87036 Arcavacata di Rende CS Italy +39 984 493265 +39 984 493199
| | - Angelo Liguori
- Dipartimento di Farmacia e Scienze della Salute e della Nutrizione, Università della Calabria Edificio Polifunzionale I-87036 Arcavacata di Rende CS Italy +39 984 493265 +39 984 493199
| | - Antonella Leggio
- Dipartimento di Farmacia e Scienze della Salute e della Nutrizione, Università della Calabria Edificio Polifunzionale I-87036 Arcavacata di Rende CS Italy +39 984 493265 +39 984 493199
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25
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Elhenawy AA, Al-Harbi LM, Moustafa GO, El-Gazzar MA, Abdel-Rahman RF, Salim AE. Synthesis, comparative docking, and pharmacological activity of naproxen amino acid derivatives as possible anti-inflammatory and analgesic agents. Drug Des Devel Ther 2019; 13:1773-1790. [PMID: 31213767 PMCID: PMC6540076 DOI: 10.2147/dddt.s196276] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/04/2019] [Indexed: 11/23/2022] Open
Abstract
Background and aim: Naproxen is a member of the Nonsteroidal anti-inflammatory drugs (NSAIDs). This work aimed to synthesize a safe NSAID agent based on a peptide derivative. Methods: The structure of compounds 5–20 was established on the basis of spectral data. Frontier molecular orbitals and chemical reactivity were discussed to clarify inter- and intramolecular interactions among tested compounds. We applied competitive molecular docking using polynomial logarithms to identify the most accurate algorithm for pharmacological activity prediction for the tested compounds. The docking protocol with the lowest RMSD was selected for analyzing binding affinity. Results: Docking results illustrated that the binding interaction increased after introduction of an acidic fragment to the parent compound. These compounds were selected for additional study against adsorption, distribution, metabolism, excretion, and toxicity (ADMET) in silico. The compounds tested had good oral bioavailability without any carcinogenesis effect; no marked health effects were observed via rodent toxicity. Compounds passed through docking and ADMET profiles for them (5–16) were examined as anti-inflammatory and analgesic agents. Compounds 8 and 16 showed higher anti-inflammatory potency than the reference drug and tested compounds. Compounds 8, 10, and 14 exhibited the highest analgesic potency compared to the other tested compounds. Conclusion: The tested compounds have shown negligible ulcerogenic effects, and may be considered safer drugs than naproxen for treating inflammatory conditions.
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Affiliation(s)
- Ahmed A Elhenawy
- Chemistry Department, Faculty of Science, Al-Azhar University (Boys' Branch), Nasr City, Cairo, Egypt
| | - L M Al-Harbi
- King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Gaber O Moustafa
- Peptide Chemistry Department, Chemical Industries Research Division, National Research Centre, Dokki, Giza 12622, Egypt
| | - M A El-Gazzar
- Chemistry Department, Faculty of Science, Al-Azhar University (Boys' Branch), Nasr City, Cairo, Egypt
| | | | - Abd Elhamid Salim
- Chemistry Department, Faculty of Science, Al-Azhar University (Boys' Branch), Nasr City, Cairo, Egypt
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26
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Synthetic Evaluation of Standard and Microwave-Assisted Solid Phase Peptide Synthesis of a Long Chimeric Peptide Derived from Four Plasmodium falciparum Proteins. Molecules 2018; 23:molecules23112877. [PMID: 30400576 PMCID: PMC6278645 DOI: 10.3390/molecules23112877] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 11/17/2022] Open
Abstract
An 82-residue-long chimeric peptide was synthesised by solid phase peptide synthesis (SPPS), following the Fmoc protocol. Microwave (MW) radiation-assisted synthesis was compared to standard synthesis using low loading (0.20 mmol/g) of polyethylene glycol (PEG) resin. Similar synthetic difficulties were found when the chimeric peptide was obtained via these two reaction conditions, indicating that such difficulties were inherent to the sequence and could not be resolved using MW; by contrast, the number of coupling cycles and total reaction time became reduced whilst crude yield and percentage recovery after purification were higher for MW radiation-assisted synthesis.
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27
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Amino acids and peptides as reactants in multicomponent reactions: modification of peptides with heterocycle backbones through combinatorial chemistry. Mol Divers 2018; 23:317-331. [PMID: 30187297 DOI: 10.1007/s11030-018-9861-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 08/02/2018] [Indexed: 12/11/2022]
Abstract
In this study, amino acids and peptides were used as reactants in a Hantzsch multicomponent reaction in order to synthesize new structurally diverse molecules containing these synthons. As well, an applicable strategy for modification of these natural molecules with heterocycle backbones such as pyrimidine, xanthene and acridine is introduced. Using this method, a set of new amino acid- and peptide-functionalized heterocycles were synthesized in good to excellent yields under mild conditions. Furthermore, carbohydrates were used as substrates in the synthesis of some derivatives. Overall, this methodology allows the possibility of synthesis of large numbers of natural product-based libraries, using amino acids, peptides and carbohydrates through combinatorial chemistry.
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28
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Moustafa G, Khalaf H, Naglah A, Al-Wasidi A, Al-Jafshar N, Awad H. The Synthesis of Molecular Docking Studies, In Vitro Antimicrobial and Antifungal Activities of Novel Dipeptide Derivatives Based on N-(2-(2-Hydrazinyl-2-oxoethylamino)-2-oxoethyl)-nicotinamide. Molecules 2018; 23:molecules23040761. [PMID: 29584635 PMCID: PMC6017860 DOI: 10.3390/molecules23040761] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/14/2018] [Accepted: 03/20/2018] [Indexed: 11/16/2022] Open
Abstract
A series of linear dipeptide derivatives (4–10) were prepared and evaluated as antimicrobial agents via the synthesis of N-(2-(2-hydrazinyl-2-oxoethylamino)-2-oxoethyl) nicotinamide (4). Compound 4 was reacted with 4-chlorobenzaldehyde or 4-hydroxybenzaldehyde, to give the hydrazones 5 and 6, respectively. On the other hand, Compound 4 was coupled with phenylisocyanate or methylisothiocyanate to give Compounds 7 and 8, respectively. The latter compounds (7 and 8) were coupled with chloroacetic acid to give oxazolidine (9) and thiazolidine (10), respectively. The newly synthesized dipeptide compounds were confirmed by means of their spectral data. The antimicrobial activity of the newly synthesized compounds 4–10 was evaluated by agar well diffusion, and they showed good activity. Compounds 4, 5, and 9 gave the most promising activity in this study. Most of the tested compounds possessed MIC values ranging from 50 to 500 µg/mL. Furthermore, docking studies were carried out on enoyl reductase from E. coli and cytochrome P450 14 α-sterol demethylase (Cyp51) from Candida albicans active sites. The MolDock scores of the seven tested compounds ranged between −117 and −171 and between −107 and −179, respectively.
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Affiliation(s)
- Gaber Moustafa
- Peptide Chemistry Department, Chemical Industries Research Division, National Research Centre, Dokki 12622, Cairo, Egypt.
| | - Hemat Khalaf
- Chemistry Department, College of Science and Arts-Qurayat, Jouf University, Sakaka 72388, Saudi Arabia.
- Photochemistry Department, Chemical Industries Research Division, National Research Centre, Dokki 12622, Cairo, Egypt.
| | - Ahmed Naglah
- Peptide Chemistry Department, Chemical Industries Research Division, National Research Centre, Dokki 12622, Cairo, Egypt.
- Department of Pharmaceutical Chemistry, Drug Exploration and Development Chair (DEDC), College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Asma Al-Wasidi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia.
| | - Nawal Al-Jafshar
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia.
| | - Hassan Awad
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Div., National Research Centre, Dokki 12622, Cairo, Egypt.
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29
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Jaradat DMM. Thirteen decades of peptide synthesis: key developments in solid phase peptide synthesis and amide bond formation utilized in peptide ligation. Amino Acids 2017; 50:39-68. [PMID: 29185032 DOI: 10.1007/s00726-017-2516-0] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/21/2017] [Indexed: 12/27/2022]
Abstract
A historical overview of peptide chemistry from T. Curtius to E. Fischer to M. Bergmann and L. Zervas is first presented. Next, the fundamentals of peptide synthesis with a focus on solid phase peptide synthesis by R. B. Merrifield are described. Immobilization strategies to attach the first amino acid to the resin, coupling strategies in stepwise peptide chain elongation, and approaches to synthesize difficult peptide sequences are also shown. A brief comparison between tert-butyloxycarbonyl (Boc)/benzyl (Bzl) strategy and 9-fluorenylmethoxycarbonyl (Fmoc)/tert-butyl (t -Bu) strategy utilized in solid phase peptide synthesis is given with an emphasis on the latter. Finally, the review focuses on the discovery and development of peptide ligation and the latest advances in this field including native amide bond formation strategies, these include the native chemical ligation, α-ketoacid-hydroxylamine ligation, and serine/threonine ligation which are the most commonly used chemoselective ligation methods that provide amide bond at the ligation site. This review provides an overview of the literature concerning the most important advances in the chemical synthesis of proteins and peptides covering the period from 1882 to 2017.
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Affiliation(s)
- Da'san M M Jaradat
- Department of Chemistry, Faculty of Science, Al-Balqa Applied University, P.O. Box 19117, Al-Salt, Jordan.
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30
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Taskova M, Mantsiou A, Astakhova K. Synthetic Nucleic Acid Analogues in Gene Therapy: An Update for Peptide-Oligonucleotide Conjugates. Chembiochem 2017; 18:1671-1682. [PMID: 28614621 DOI: 10.1002/cbic.201700229] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Indexed: 12/29/2022]
Abstract
The main objective of this work is to provide an update on synthetic nucleic acid analogues and nanoassemblies as tools in gene therapy. In particular, the synthesis and properties of peptide-oligonucleotide conjugates (POCs), which have high potential in research and as therapeutics, are described in detail. The exploration of POCs has already led to fruitful results in the treatment of neurological diseases, lung disorders, cancer, leukemia, viral, and bacterial infections. However, delivery and in vivo stability are the major barriers to the clinical application of POCs and other analogues that still have to be overcome. This review summarizes recent achievements in the delivery and in vivo administration of synthetic nucleic acid analogues, focusing on POCs, and compares their efficiency.
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Affiliation(s)
- Maria Taskova
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Anna Mantsiou
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Kira Astakhova
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.,Technical University of Denmark, Department of Chemistry, Kemitorvet, 2800, Kongens Lyngby, Denmark
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31
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Pifferi C, Daskhan GC, Fiore M, Shiao TC, Roy R, Renaudet O. Aminooxylated Carbohydrates: Synthesis and Applications. Chem Rev 2017; 117:9839-9873. [PMID: 28682060 DOI: 10.1021/acs.chemrev.6b00733] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Among other classes of biomolecules, carbohydrates and glycoconjugates are widely involved in numerous biological functions. In addition to addressing the related synthetic challenges, glycochemists have invested intense efforts in providing access to structures that can be used to study, activate, or inhibit these biological processes. Over the past few decades, aminooxylated carbohydrates have been found to be key building blocks for achieving these goals. This review provides the first in-depth overview covering several aspects related to the syntheses and applications of aminooxylated carbohydrates. After a brief introduction to oxime bonds and their relative stabilities compared to related C═N functions, synthetic aspects of oxime ligation and methodologies for introducing the aminooxy functionality onto both glycofuranosyls and glycopyranosyls are described. The subsequent section focuses on biological applications involving aminooxylated carbohydrates as components for the construcion of diverse architectures. Mimetics of natural structures represent useful tools for better understanding the features that drive carbohydrate-receptor interaction, their biological output and they also represent interesting structures with improved stability and tunable properties. In the next section, multivalent structures such as glycoclusters and glycodendrimers obtained through oxime ligation are described in terms of synthetic design and their biological applications such as immunomodulators. The second-to-last section discusses miscellaneous applications of oxime-based glycoconjugates, such as enantioselective catalysis and glycosylated oligonucleotides, and conclusions and perspectives are provided in the last section.
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Affiliation(s)
- Carlo Pifferi
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France
| | - Gour Chand Daskhan
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France
| | - Michele Fiore
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France
| | - Tze Chieh Shiao
- Pharmaqam, Department of Chemistry, Université du Québec à Montreal , P.O. Box 8888, Succursale Centre-ville, Montréal, Québec H3C 3P8, Canada
| | - René Roy
- Pharmaqam, Department of Chemistry, Université du Québec à Montreal , P.O. Box 8888, Succursale Centre-ville, Montréal, Québec H3C 3P8, Canada
| | - Olivier Renaudet
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France.,Institut Universitaire de France , 103 Boulevard Saint-Michel, 75005 Paris, France
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32
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Kozma E, Demeter O, Kele P. Bio-orthogonal Fluorescent Labelling of Biopolymers through Inverse-Electron-Demand Diels-Alder Reactions. Chembiochem 2017; 18:486-501. [PMID: 28070925 PMCID: PMC5363342 DOI: 10.1002/cbic.201600607] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Indexed: 02/06/2023]
Abstract
Bio-orthogonal labelling schemes based on inverse-electron-demand Diels-Alder (IEDDA) cycloaddition have attracted much attention in chemical biology recently. The appealing features of this reaction, such as the fast reaction kinetics, fully bio-orthogonal nature and high selectivity, have helped chemical biologists gain deeper understanding of biochemical processes at the molecular level. Listing the components and discussing the possibilities and limitations of these reagents, we provide a recent snapshot of the field of IEDDA-based biomolecular manipulation with special focus on fluorescent modulation approaches through the use of bio-orthogonalized building blocks. At the end, we discuss challenges that need to be addressed for further developments in order to overcome recent limitations and to enable researchers to answer biomolecular questions in more detail.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research GroupInstitute of Organic ChemistryResearch Centre for Natural SciencesHungarian Academy of Sciences1117 Magyar tudósok krt. 2BudapestHungary
| | - Orsolya Demeter
- Chemical Biology Research GroupInstitute of Organic ChemistryResearch Centre for Natural SciencesHungarian Academy of Sciences1117 Magyar tudósok krt. 2BudapestHungary
| | - Péter Kele
- Chemical Biology Research GroupInstitute of Organic ChemistryResearch Centre for Natural SciencesHungarian Academy of Sciences1117 Magyar tudósok krt. 2BudapestHungary
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33
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Luna OF, Gomez J, Cárdenas C, Albericio F, Marshall SH, Guzmán F. Deprotection Reagents in Fmoc Solid Phase Peptide Synthesis: Moving Away from Piperidine? Molecules 2016; 21:molecules21111542. [PMID: 27854291 PMCID: PMC6274427 DOI: 10.3390/molecules21111542] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/08/2016] [Accepted: 11/12/2016] [Indexed: 12/31/2022] Open
Abstract
The deprotection step is crucial in order to secure a good quality product in Fmoc solid phase peptide synthesis. 9-Fluorenylmethoxycarbonyl (Fmoc) removal is achieved by a two-step mechanism reaction favored by the use of cyclic secondary amines; however, the efficiency of the reaction could be affected by side reactions and by-product formation. Several aspects have to be taken into consideration when selecting a deprotection reagent: its physicochemical behavior, basicity (pKa) and polarity, concentration, and time of reaction, toxicity and disposability of residues and, finally, availability of reagents. This report presents a comparison of the performance of three strategies for deprotection using microwave-assisted Fmoc peptide synthesis. Four peptide sequences were synthesized using Rink amide resin with a Liberty Blue™ automated synthesizer and 4-methylpiperidine (4MP), piperidine (PP), and piperazine (PZ) as Fmoc removal reagents. In the first instance all three reagents behaved similarly. A detailed analysis showed a correlation between the hydrophobicity and size of the peptide with the yield and purity of the obtained product. The three reagents are interchangeable, and replacement of piperidine could be advantageous regarding toxicity and reagent handling.
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Affiliation(s)
- Omar F Luna
- Fraunhofer Chile Research, Santiago 7550296, Chile.
| | - Johana Gomez
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile.
| | - Constanza Cárdenas
- Fraunhofer Chile Research, Santiago 7550296, Chile.
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile.
| | - Fernando Albericio
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, University of Barcelona, Barcelona 08028, Spain.
- Department of Organic Chemistry, University of Barcelona, Barcelona 08028, Spain.
- School of Chemistry, University of KwaZulu-Natal, Durban 4001, South Africa.
| | - Sergio H Marshall
- Fraunhofer Chile Research, Santiago 7550296, Chile.
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile.
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile.
| | - Fanny Guzmán
- Fraunhofer Chile Research, Santiago 7550296, Chile.
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile.
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Abstract
The present review offers an overview of nonclassical (e.g., with no pre- or in situ activation of a carboxylic acid partner) approaches for the construction of amide bonds. The review aims to comprehensively discuss relevant work, which was mainly done in the field in the last 20 years. Organization of the data follows a subdivision according to substrate classes: catalytic direct formation of amides from carboxylic and amines ( section 2 ); the use of carboxylic acid surrogates ( section 3 ); and the use of amine surrogates ( section 4 ). The ligation strategies (NCL, Staudinger, KAHA, KATs, etc.) that could involve both carboxylic acid and amine surrogates are treated separately in section 5 .
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Affiliation(s)
- Renata Marcia de Figueiredo
- Institut Charles Gerhardt de Montpellier (ICGM), UMR 5253-CNRS-UM-ENSCM, Ecole Nationale Supérieure de Chimie , 8 rue de l'Ecole Normale, 34296 Montpellier Cedex 5, France
| | - Jean-Simon Suppo
- Institut Charles Gerhardt de Montpellier (ICGM), UMR 5253-CNRS-UM-ENSCM, Ecole Nationale Supérieure de Chimie , 8 rue de l'Ecole Normale, 34296 Montpellier Cedex 5, France
| | - Jean-Marc Campagne
- Institut Charles Gerhardt de Montpellier (ICGM), UMR 5253-CNRS-UM-ENSCM, Ecole Nationale Supérieure de Chimie , 8 rue de l'Ecole Normale, 34296 Montpellier Cedex 5, France
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35
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Kou KGM, Li BX, Lee JC, Gallego GM, Lebold TP, DiPasquale AG, Sarpong R. Syntheses of Denudatine Diterpenoid Alkaloids: Cochlearenine, N-Ethyl-1α-hydroxy-17-veratroyldictyzine, and Paniculamine. J Am Chem Soc 2016; 138:10830-3. [PMID: 27525345 PMCID: PMC5076861 DOI: 10.1021/jacs.6b07268] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The denudatine-type diterpenoid alkaloids cochlearenine, N-ethyl-1α-hydroxy-17-veratroyldictyzine, and paniculamine have been synthesized for the first time (25, 26, and 26 steps from 16, respectively). These syntheses take advantage of a common intermediate (8) that we have previously employed in preparing aconitine-type natural products. The syntheses reported herein complete the realization of a unified strategy for the preparation of C20, C19, and C18 diterpenoid alkaloids.
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Affiliation(s)
- Kevin G. M. Kou
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Beryl X. Li
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | | | | | | | - Antonio G. DiPasquale
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Richmond Sarpong
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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36
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Lücke D, Dalton T, Ley SV, Wilson ZE. Synthesis of Natural and Unnatural Cyclooligomeric Depsipeptides Enabled by Flow Chemistry. Chemistry 2016; 22:4206-17. [PMID: 26844421 PMCID: PMC4797712 DOI: 10.1002/chem.201504457] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Indexed: 11/21/2022]
Abstract
Flow chemistry has been successfully integrated into the synthesis of a series of cyclooligomeric depsipeptides of three different ring sizes including the natural products beauvericin (1 a), bassianolide (2 b) and enniatin C (1 b). A reliable flow chemistry protocol was established for the coupling and macrocyclisation to form challenging N‐methylated amides. This flexible approach has allowed the rapid synthesis of both natural and unnatural depsipeptides in high yields, enabling further exploration of their promising biological activity.
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Affiliation(s)
- Daniel Lücke
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Toryn Dalton
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Steven V Ley
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Zoe E Wilson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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37
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Mangelschots J, Bibian M, Gardiner J, Waddington L, Van Wanseele Y, Van Eeckhaut A, Acevedo MMD, Van Mele B, Madder A, Hoogenboom R, Ballet S. Mixed α/β-Peptides as a Class of Short Amphipathic Peptide Hydrogelators with Enhanced Proteolytic Stability. Biomacromolecules 2016; 17:437-45. [DOI: 10.1021/acs.biomac.5b01319] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - James Gardiner
- CSIRO Manufacturing
Flagship, Bayview Avenue, Clayton, VIC 3169, Australia
| | - Lynne Waddington
- CSIRO Manufacturing
Flagship, Bayview Avenue, Clayton, VIC 3169, Australia
| | - Yannick Van Wanseele
- Department
of Pharmaceutical Chemistry and Drug Analysis, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Ann Van Eeckhaut
- Department
of Pharmaceutical Chemistry and Drug Analysis, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
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38
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Groß A, Hashimoto C, Sticht H, Eichler J. Synthetic Peptides as Protein Mimics. Front Bioeng Biotechnol 2016; 3:211. [PMID: 26835447 PMCID: PMC4717299 DOI: 10.3389/fbioe.2015.00211] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/22/2015] [Indexed: 12/21/2022] Open
Abstract
The design and generation of molecules capable of mimicking the binding and/or functional sites of proteins represents a promising strategy for the exploration and modulation of protein function through controlled interference with the underlying molecular interactions. Synthetic peptides have proven an excellent type of molecule for the mimicry of protein sites because such peptides can be generated as exact copies of protein fragments, as well as in diverse chemical modifications, which includes the incorporation of a large range of non-proteinogenic amino acids as well as the modification of the peptide backbone. Apart from extending the chemical and structural diversity presented by peptides, such modifications also increase the proteolytic stability of the molecules, enhancing their utility for biological applications. This article reviews recent advances by this and other laboratories in the use of synthetic protein mimics to modulate protein function, as well as to provide building blocks for synthetic biology.
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Affiliation(s)
- Andrea Groß
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Chie Hashimoto
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
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39
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Roberts AG, Johnston EV, Shieh JH, Sondey JP, Hendrickson RC, Moore MAS, Danishefsky SJ. Fully Synthetic Granulocyte Colony-Stimulating Factor Enabled by Isonitrile-Mediated Coupling of Large, Side-Chain-Unprotected Peptides. J Am Chem Soc 2015; 137:13167-75. [PMID: 26401918 PMCID: PMC4617663 DOI: 10.1021/jacs.5b08754] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human granulocyte colony-stimulating factor (G-CSF) is an endogenous glycoprotein involved in hematopoiesis. Natively glycosylated and nonglycosylated recombinant forms, lenograstim and filgrastim, respectively, are used clinically to manage neutropenia in patients undergoing chemotherapeutic treatment. Despite their comparable therapeutic potential, the purpose of O-linked glycosylation at Thr133 remains a subject of controversy. In light of this, we have developed a synthetic platform to prepare G-CSF aglycone with the goal of enabling access to native and designed glycoforms with site-selectivity and glycan homogeneity. To address the synthesis of a relatively large, aggregation-prone sequence, we advanced an isonitrile-mediated ligation method. The chemoselective activation and coupling of C-terminal peptidyl Gly thioacids with the N-terminus of an unprotected peptide provide ligated peptides directly in a manner complementary to that with conventional native chemical ligation-desulfurization strategies. Herein, we describe the details and application of this method as it enabled the convergent total synthesis of G-CSF aglycone.
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Affiliation(s)
- Andrew G. Roberts
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
| | - Eric V. Johnston
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
| | - Jae-Hung Shieh
- Cell Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
| | - Joseph P. Sondey
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
| | - Ronald C. Hendrickson
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
| | - Malcolm A. S. Moore
- Cell Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
| | - Samuel J. Danishefsky
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
- Cell Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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40
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Silva JG, Arruda LM, Pinheiro GS, Lima CL, Melo FEA, Ayala AP, Filho JM, Freire PTC. The temperature-dependent single-crystal Raman spectroscopy of a model dipeptide: L-Alanyl-L-alanine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 148:244-249. [PMID: 25897718 DOI: 10.1016/j.saa.2015.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/04/2015] [Accepted: 04/07/2015] [Indexed: 06/04/2023]
Abstract
A single-crystal of peptide L-alanyl-L-alanine (C6H12N2O3) was studied by Raman spectroscopy at low-temperature, and a tentative assignment of the normal modes was given. Evidence of a second order structural phase transition was found through Raman spectroscopy between the temperatures of 80K and 60K. Group theory considerations suggest that the transition leads the sample from the tetragonal to a monoclinic structure. Additionally, our study suggests that the mechanism for the structural phase transition is governed by the occupation of non-equivalent C1 local symmetry sites by the CH3 molecular groups. Analysis based on group theory suggests L-alanyl-L-alanine presents C2 symmetry at low temperatures.
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Affiliation(s)
- J G Silva
- Departamento de Física, Universidade Federal do Ceará, C.P. 6030, CEP 60455-760 Fortaleza, CE, Brazil
| | - L M Arruda
- Departamento de Física, Universidade Federal do Ceará, C.P. 6030, CEP 60455-760 Fortaleza, CE, Brazil
| | - G S Pinheiro
- Departamento de Física, Universidade Federal do Ceará, C.P. 6030, CEP 60455-760 Fortaleza, CE, Brazil; Departamento de Física, Campus Ministro Petrônio Portella, Universidade Federal do Piauí, CEP 64049-550 Teresina, PI, Brazil.
| | - C L Lima
- Departamento de Física, Campus Ministro Petrônio Portella, Universidade Federal do Piauí, CEP 64049-550 Teresina, PI, Brazil
| | - F E A Melo
- Departamento de Física, Universidade Federal do Ceará, C.P. 6030, CEP 60455-760 Fortaleza, CE, Brazil
| | - A P Ayala
- Departamento de Física, Universidade Federal do Ceará, C.P. 6030, CEP 60455-760 Fortaleza, CE, Brazil
| | - J Mendes Filho
- Departamento de Física, Universidade Federal do Ceará, C.P. 6030, CEP 60455-760 Fortaleza, CE, Brazil
| | - P T C Freire
- Departamento de Física, Universidade Federal do Ceará, C.P. 6030, CEP 60455-760 Fortaleza, CE, Brazil
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41
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Synthesis, molecular docking and anticancer studies of peptides and iso-peptides. Bioorg Med Chem Lett 2015; 25:2980-4. [PMID: 26048799 DOI: 10.1016/j.bmcl.2015.05.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 05/08/2015] [Accepted: 05/12/2015] [Indexed: 11/23/2022]
Abstract
Chiral peptides and iso-peptides were synthesized in excellent yield by using benzotriazole mediated solution phase synthesis. Benzotriazole acted both as activating and leaving group, eliminating frequent use of protection and subsequent deprotection. The procedure was based on the hypothesis that epimerization should be suppressed in solution due to a faster coupling rate than SPPS. All the synthesized peptides complied with Lipinski's Ro5 except for the rotatable bonds. Inhibition of cell proliferation of cancer cell lines is one of the most commonly used methods to study the effectiveness of any anticancer agents. Synthesized peptides and iso-peptides were tested against three cancer cell lines (MCF-7, MDA-MB 231) to determine their anti-proliferative potential. NFkB was also determined. Molecular docking studies were also carried out to complement the experimental results.
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42
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Chen M, Heimer P, Imhof D. Synthetic strategies for polypeptides and proteins by chemical ligation. Amino Acids 2015; 47:1283-99. [DOI: 10.1007/s00726-015-1982-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/02/2015] [Indexed: 11/30/2022]
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43
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Salvador CEM, Pieber B, Neu PM, Torvisco A, Kleber Z Andrade C, Kappe CO. A sequential Ugi multicomponent/Cu-catalyzed azide-alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. J Org Chem 2015; 80:4590-602. [PMID: 25842982 DOI: 10.1021/acs.joc.5b00445] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of a continuous flow multistep strategy for the synthesis of linear peptoids and their subsequent macrocyclization via Click chemistry is described. The central transformation of this process is an Ugi four-component reaction generating the peptidomimetic core structure. In order to avoid exposure to the often toxic and malodorous isocyanide building blocks, the continuous approach was telescoped by the dehydration of the corresponding formamide. In a concurrent operation, the highly energetic azide moiety required for the subsequent intramolecular copper-catalyzed azide-alkyne cycloaddition (Click reaction) was installed by nucleophilic substitution from a bromide precursor. All steps yielding to the linear core structures can be conveniently coupled without the need for purification steps resulting in a single process generating the desired peptidomimetics in good to excellent yields within a 25 min reaction time. The following macrocyclization was realized in a coil reactor made of copper without any additional additive. A careful process intensification study demonstrated that this transformation occurs quantitatively within 25 min at 140 °C. Depending on the resulting ring strain, either a dimeric or a monomeric form of the cyclic product was obtained.
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Affiliation(s)
- Carlos Eduardo M Salvador
- †Institute of Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria.,‡Laboratório de Química Metodológica e Orgânica Sintética, Instituto de Química, Universidade de Brasília, Campus Universitário Darcy Ribeiro, C.P. 4478, 70904-970, Brasília-DF, Brazil
| | - Bartholomäus Pieber
- †Institute of Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - Philipp M Neu
- †Institute of Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - Ana Torvisco
- §Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Carlos Kleber Z Andrade
- ‡Laboratório de Química Metodológica e Orgânica Sintética, Instituto de Química, Universidade de Brasília, Campus Universitário Darcy Ribeiro, C.P. 4478, 70904-970, Brasília-DF, Brazil
| | - C Oliver Kappe
- †Institute of Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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44
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Rahbek Knudsen K, Ladlow M, Bandpey Z, Ley S. Fully Automated Sequence-Specific Synthesis of α-Peptides Using Flow Chemistry. J Flow Chem 2015. [DOI: 10.1556/jfc-d-13-00033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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45
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Odar C, Winkler M, Wiltschi B. Fluoro amino acids: A rarity in nature, yet a prospect for protein engineering. Biotechnol J 2015; 10:427-46. [DOI: 10.1002/biot.201400587] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/08/2014] [Accepted: 01/09/2015] [Indexed: 01/01/2023]
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46
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Barbakadze NN, Jones RA, Rosario NR, Nadaraia NS, Kakhabrishvili ML, Dennis Hall C, Katritzky AR. Chemical modification of oximes with N-protected amino acids. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.07.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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47
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Thapa P, Zhang RY, Menon V, Bingham JP. Native chemical ligation: a boon to peptide chemistry. Molecules 2014; 19:14461-83. [PMID: 25221869 PMCID: PMC6271921 DOI: 10.3390/molecules190914461] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/02/2014] [Accepted: 09/02/2014] [Indexed: 11/16/2022] Open
Abstract
The use of chemical ligation within the realm of peptide chemistry has opened various opportunities to expand the applications of peptides/proteins in biological sciences. Expansion and refinement of ligation chemistry has made it possible for the entry of peptides into the world of viable oral therapeutic drugs through peptide backbone cyclization. This progression has been a journey of chemical exploration and transition, leading to the dominance of native chemical ligation in the present advances of peptide/protein applications. Here we illustrate and explore the historical and current nature of peptide ligation, providing a clear indication to the possibilities and use of these novel methods to take peptides outside their typically defined boundaries.
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Affiliation(s)
- Parashar Thapa
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Rui-Yang Zhang
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Vinay Menon
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
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48
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Kemayo Koumkoua P, Aisenbrey C, Salnikov E, Rifi O, Bechinger B. On the design of supramolecular assemblies made of peptides and lipid bilayers. J Pept Sci 2014; 20:526-36. [PMID: 24909405 DOI: 10.1002/psc.2656] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/29/2014] [Accepted: 04/29/2014] [Indexed: 02/02/2023]
Abstract
Peptides confer interesting properties to materials, supramolecular assemblies and to lipid membranes and are used in analytical devices or within delivery vehicles. Their relative ease of production combined with a high degree of versatility make them attractive candidates to design new such products. Here, we review and demonstrate how CD- and solid-state NMR spectroscopic approaches can be used to follow the reconstitution of peptides into membranes and to describe some of their fundamental characteristics. Whereas CD spectroscopy is used to monitor secondary structure in different solvent systems and thereby aggregation properties of the highly hydrophobic domain of p24, a protein involved in vesicle trafficking, solid-state NMR spectroscopy was used to deduce structural information and the membrane topology of a variety of peptide sequences found in nature or designed. (15)N chemical shift solid-state NMR spectroscopy indicates that the hydrophobic domain of p24 as well as a designed sequence of 19 hydrophobic amino acid residues adopt transmembrane alignments in phosphatidylcholine membranes. In contrast, the amphipathic antimicrobial peptide magainin 2 and the designed sequence LK15 align parallel to the bilayer surface. Additional angular information is obtained from deuterium solid-state NMR spectra of peptide sites labelled with (2)H3-alanine, whereas (31)P and (2)H solid-state NMR spectra of the lipids furnish valuable information on the macroscopic order and phase properties of the lipid matrix. Using these approaches, peptides and reconstitution protocols can be elaborated in a rational manner, and the analysis of a great number of peptide sequences is reviewed. Finally, a number of polypeptides with membrane topologies that are sensitive to a variety of environmental conditions such as pH, lipid composition and peptide-to-lipid ratio will be presented.
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Affiliation(s)
- Patricia Kemayo Koumkoua
- Université de Strasbourg / CNRS, UMR7177, Institut de Chimie, 1, rue Blaise Pascal, 67070, Strasbourg, France
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49
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Lang K, Chin JW. Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem Rev 2014; 114:4764-806. [PMID: 24655057 DOI: 10.1021/cr400355w] [Citation(s) in RCA: 797] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kathrin Lang
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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50
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Simon MD, Heider PL, Adamo A, Vinogradov AA, Mong SK, Li X, Berger T, Policarpo RL, Zhang C, Zou Y, Liao X, Spokoyny AM, Jensen KF, Pentelute BL. Rapid flow-based peptide synthesis. Chembiochem 2014; 15:713-20. [PMID: 24616230 PMCID: PMC4045704 DOI: 10.1002/cbic.201300796] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Indexed: 11/06/2022]
Abstract
A flow-based solid-phase peptide synthesis methodology that enables the incorporation of an amino acid residue every 1.8 min under automatic control or every 3 min under manual control is described. This is accomplished by passing a stream of reagent through a heat exchanger into a low volume, low backpressure reaction vessel, and through a UV detector. These features enable continuous delivery of heated solvents and reagents to the solid support at high flow rate, thereby maintaining maximal concentration of reagents in the reaction vessel, quickly exchanging reagents, and eliminating the need to rapidly heat reagents after they have been added to the vessel. The UV detector enables continuous monitoring of the process. To demonstrate the broad applicability and reliability of this method, it was employed in the total synthesis of a small protein, as well as dozens of peptides. The quality of the material obtained with this method is comparable to that for traditional batch methods, and, in all cases, the desired material was readily purifiable by RP-HPLC. The application of this method to the synthesis of the 113-residue Bacillus amyloliquefaciens RNase and the 130-residue DARPin pE59 is described in the accompanying manuscript.
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Affiliation(s)
- Mark D. Simon
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Patrick L. Heider
- Department of Chemical Engeneering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Andrea Adamo
- Department of Chemical Engeneering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Alexander A. Vinogradov
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Surin K. Mong
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Xiyuan Li
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Tatiana Berger
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Rocco L. Policarpo
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Chi Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Yekui Zou
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Xiaoli Liao
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Alexander M. Spokoyny
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Klavs F. Jensen
- Department of Chemical Engeneering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Bradley L. Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
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