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Gibisch M, Müller M, Tauer C, Albrecht B, Hahn R, Cserjan-Puschmann M, Striedner G. A production platform for disulfide-bonded peptides in the periplasm of Escherichia coli. Microb Cell Fact 2024; 23:166. [PMID: 38840157 DOI: 10.1186/s12934-024-02446-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/01/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Recombinant peptide production in Escherichia coli provides a sustainable alternative to environmentally harmful and size-limited chemical synthesis. However, in-vivo production of disulfide-bonded peptides at high yields remains challenging, due to degradation by host proteases/peptidases and the necessity of translocation into the periplasmic space for disulfide bond formation. RESULTS In this study, we established an expression system for efficient and soluble production of disulfide-bonded peptides in the periplasm of E. coli. We chose model peptides with varying complexity (size, structure, number of disulfide bonds), namely parathyroid hormone 1-84, somatostatin 1-28, plectasin, and bovine pancreatic trypsin inhibitor (aprotinin). All peptides were expressed without and with the N-terminal, low molecular weight CASPON™ tag (4.1 kDa), with the expression cassette being integrated into the host genome. During BioLector™ cultivations at microliter scale, we found that most of our model peptides can only be sufficiently expressed in combination with the CASPON™ tag, otherwise expression was only weak or undetectable on SDS-PAGE. Undesired degradation by host proteases/peptidases was evident even with the CASPON™ tag. Therefore, we investigated whether degradation happened before or after translocation by expressing the peptides in combination with either a co- or post-translational signal sequence. Our results suggest that degradation predominantly happened after the translocation, as degradation fragments appeared to be identical independent of the signal sequence, and expression was not enhanced with the co-translational signal sequence. Lastly, we expressed all CASPON™-tagged peptides in two industry-relevant host strains during C-limited fed-batch cultivations in bioreactors. We found that the process performance was highly dependent on the peptide-host-combination. The titers that were reached varied between 0.6-2.6 g L-1, and exceeded previously published data in E. coli. Moreover, all peptides were shown by mass spectrometry to be expressed to completion, including full formation of disulfide bonds. CONCLUSION In this work, we demonstrated the potential of the CASPON™ technology as a highly efficient platform for the production of soluble peptides in the periplasm of E. coli. The titers we show here are unprecedented whenever parathyroid hormone, somatostatin, plectasin or bovine pancreatic trypsin inhibitor were produced in E. coli, thus making our proposed upstream platform favorable over previously published approaches and chemical synthesis.
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Affiliation(s)
- Martin Gibisch
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Matthias Müller
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Christopher Tauer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Bernd Albrecht
- Boehringer-Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, Vienna, Austria
| | - Rainer Hahn
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria.
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
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2
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Kempson J, Zhao R, Pawluczyk J, Wang B, Zhang H, Hou X, Allen MP, Wu DR, Li P, Yip S, Smith A, Traeger SC, Huang S, Cutrone J, Mukherjee S, Sfouggatakis C, Poss M, Scola PM, Meanwell NA, Carter PH, Mathur A. Challenges with the Synthesis of a Macrocyclic Thioether Peptide: From Milligram to Multigram Using Solid Phase Peptide Synthesis (SPPS). J Org Chem 2024; 89:6639-6650. [PMID: 38651358 DOI: 10.1021/acs.joc.4c00429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
We describe an optimization and scale-up of the 45-membered macrocyclic thioether peptide BMS-986189 utilizing solid-phase peptide synthesis (SPPS). Improvements to linear peptide isolation, macrocyclization, and peptide purification were demonstrated to increase the throughput and purification of material on scale and enabled the synthesis and purification of >60 g of target peptide. Taken together, not only these improvements resulted in a 28-fold yield increase from the original SPPS approach, but also the generality of this newly developed SPPS purification sequence has found application in the synthesis and purification of other macrocyclic thioether peptides.
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Affiliation(s)
- James Kempson
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Rulin Zhao
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Joseph Pawluczyk
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Bei Wang
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Huiping Zhang
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Xiaoping Hou
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Martin P Allen
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Dauh-Rurng Wu
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Peng Li
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Shiuhang Yip
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Aaron Smith
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Sarah C Traeger
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Stella Huang
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Jingfang Cutrone
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Subha Mukherjee
- Chemical and Process Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903, United States
| | - Chris Sfouggatakis
- Chemical and Process Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903, United States
| | - Michael Poss
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Paul M Scola
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Nicholas A Meanwell
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Percy H Carter
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
| | - Arvind Mathur
- Research and Early Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States
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3
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Mukherjee S, Rogers A, Creech G, Hang C, Ramirez A, Dummeldinger M, Brueggemeier S, Mapelli C, Zaretsky S, Huang M, Black R, Peddicord MB, Cuniere N, Kempson J, Pawluczyk J, Allen M, Parsons R, Sfouggatakis C. Process Development of a Macrocyclic Peptide Inhibitor of PD-L1. J Org Chem 2024; 89:6651-6663. [PMID: 38663026 DOI: 10.1021/acs.joc.4c00430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
This article outlines the process development leading to the manufacture of 800 g of BMS-986189, a macrocyclic peptide active pharmaceutical ingredient. Multiple N-methylated unnatural amino acids posed challenges to manufacturing due to the lability of the peptide to cleavage during global side chain deprotection and precipitation steps. These issues were exacerbated upon scale-up, resulting in severe yield loss and necessitating careful impurity identification, understanding the root cause of impurity formation, and process optimization to deliver a scalable synthesis. A systematic study of macrocyclization with its dependence on concentration and pH is presented. In addition, a side chain protected peptide synthesis is discussed where the macrocyclic protected peptide is extremely labile to hydrolysis. A computational study explains the root cause of the increased lability of macrocyclic peptide over linear peptide to hydrolysis. A process solution involving the use of labile protecting groups is discussed. Overall, the article highlights the advancements achieved to enable scalable synthesis of an unusually labile macrocyclic peptide by solid-phase peptide synthesis. The sustainability metric indicates the final preparative chromatography drives a significant fraction of a high process mass intensity (PMI).
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Affiliation(s)
- Subha Mukherjee
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Amanda Rogers
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Gardner Creech
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Chao Hang
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Antonio Ramirez
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Michael Dummeldinger
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Shawn Brueggemeier
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Claudio Mapelli
- Discovery Chemistry, Bristol Myers Squibb, Princeton, New Jersey 08540, United States
| | - Serge Zaretsky
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Masano Huang
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Regina Black
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Michael B Peddicord
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Nicolas Cuniere
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - James Kempson
- Discovery Chemistry, Bristol Myers Squibb, Princeton, New Jersey 08540, United States
| | - Joseph Pawluczyk
- Discovery Chemistry, Bristol Myers Squibb, Princeton, New Jersey 08540, United States
| | - Martin Allen
- Discovery Chemistry, Bristol Myers Squibb, Princeton, New Jersey 08540, United States
| | - Rodney Parsons
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Chris Sfouggatakis
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
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4
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Kumar M, Kumar D, Kumar D, Garg Y, Chopra S, Bhatia A. Therapeutic Potential of Nanocarrier Mediated Delivery of Peptides for Wound Healing: Current Status, Challenges and Future Prospective. AAPS PharmSciTech 2024; 25:108. [PMID: 38730090 DOI: 10.1208/s12249-024-02827-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/01/2024] [Indexed: 05/12/2024] Open
Abstract
Wound healing presents a complex physiological process that involves a sequence of events orchestrated by various cellular and molecular mechanisms. In recent years, there has been growing interest in leveraging nanomaterials and peptides to enhance wound healing outcomes. Nanocarriers offer unique properties such as high surface area-to-volume ratio, tunable physicochemical characteristics, and the ability to deliver therapeutic agents in a controlled manner. Similarly, peptides, with their diverse biological activities and low immunogenicity, hold great promise as therapeutics in wound healing applications. In this review, authors explore the potential of peptides as bioactive components in wound healing formulations, focusing on their antimicrobial, anti-inflammatory, and pro-regenerative properties. Despite the significant progress made in this field, several challenges remain, including the need for standardized characterization methods, optimization of biocompatibility and safety profiles, and translation from bench to bedside. Furthermore, developing multifunctional nanomaterial-peptide hybrid systems represents promising avenues for future research. Overall, the integration of nanomaterials made up of natural or synthetic polymers with peptide-based formulations holds tremendous therapeutic potential in advancing the field of wound healing and improving clinical outcomes for patients with acute and chronic wounds.
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Affiliation(s)
- Mohit Kumar
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University (MRSPTU), Bathinda, 151001, Punjab, India
| | - Dikshant Kumar
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University (MRSPTU), Bathinda, 151001, Punjab, India
| | - Devesh Kumar
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University (MRSPTU), Bathinda, 151001, Punjab, India
| | - Yogesh Garg
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University (MRSPTU), Bathinda, 151001, Punjab, India
| | - Shruti Chopra
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University (MRSPTU), Bathinda, 151001, Punjab, India
| | - Amit Bhatia
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University (MRSPTU), Bathinda, 151001, Punjab, India.
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5
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Chaudhary S, Ali Z, Mahfouz M. Molecular farming for sustainable production of clinical-grade antimicrobial peptides. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38685599 DOI: 10.1111/pbi.14344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/26/2024] [Accepted: 03/11/2024] [Indexed: 05/02/2024]
Abstract
Antimicrobial peptides (AMPs) are emerging as next-generation therapeutics due to their broad-spectrum activity against drug-resistant bacterial strains and their ability to eradicate biofilms, modulate immune responses, exert anti-inflammatory effects and improve disease management. They are produced through solid-phase peptide synthesis or in bacterial or yeast cells. Molecular farming, i.e. the production of biologics in plants, offers a low-cost, non-toxic, scalable and simple alternative platform to produce AMPs at a sustainable cost. In this review, we discuss the advantages of molecular farming for producing clinical-grade AMPs, advances in expression and purification systems and the cost advantage for industrial-scale production. We further review how 'green' production is filling the sustainability gap, streamlining patent and regulatory approvals and enabling successful clinical translations that demonstrate the future potential of AMPs produced by molecular farming. Finally, we discuss the regulatory challenges that need to be addressed to fully realize the potential of molecular farming-based AMP production for therapeutics.
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Affiliation(s)
- Shahid Chaudhary
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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6
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García-Gros J, Cajal Y, Marqués AM, Rabanal F. Synthesis of the Antimicrobial Peptide Murepavadin Using Novel Coupling Agents. Biomolecules 2024; 14:526. [PMID: 38785933 PMCID: PMC11117477 DOI: 10.3390/biom14050526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
The problem of antimicrobial resistance is becoming a daunting challenge for human society and healthcare systems around the world. Hence, there is a constant need to develop new antibiotics to fight resistant bacteria, among other important social and economic measures. In this regard, murepavadin is a cyclic antibacterial peptide in development. The synthesis of murepavadin was undertaken in order to optimize the preparative protocol and scale-up, in particular, the use of new activation reagents. In our hands, classical approaches using carbodiimide/hydroxybenzotriazole rendered low yields. The use of novel carbodiimide and reagents based on OxymaPure® and Oxy-B is discussed together with the proper use of chromatographic conditions for the adequate characterization of peptide crudes. Higher yields and purities were obtained. Finally, the antimicrobial activity of different synthetic batches was tested in three Pseudomonas aeruginosa strains, including highly resistant ones. All murepavadin batches yielded the same highly active MIC values and proved that the chiral integrity of the molecule was preserved throughout the whole synthetic procedure.
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Affiliation(s)
- Júlia García-Gros
- Section of Organic Chemistry, Department of Inorganic and Organic Chemistry, Faculty of Chemistry, Universitat de Barcelona, 08028 Barcelona, Spain;
| | - Yolanda Cajal
- Department of Pharmacy, Pharmaceutical Technology and Physical Chemistry, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, 08028 Barcelona, Spain;
- Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Ana Maria Marqués
- Laboratory of Microbiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, 08007 Barcelona, Spain;
| | - Francesc Rabanal
- Section of Organic Chemistry, Department of Inorganic and Organic Chemistry, Faculty of Chemistry, Universitat de Barcelona, 08028 Barcelona, Spain;
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7
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Pacini L, Muthyala M, Aguiar L, Zitterbart R, Rovero P, Papini AM. Optimization of peptide synthesis time and sustainability using novel eco-friendly binary solvent systems with induction heating on an automated peptide synthesizer. J Pept Sci 2024:e3605. [PMID: 38660732 DOI: 10.1002/psc.3605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/18/2024] [Accepted: 04/01/2024] [Indexed: 04/26/2024]
Abstract
On December 12th, 2023, the European Commission took regulatory action to amend Annex XVII of REACH, imposing restrictions on the use of N,N-dimethylformamide (DMF) within the EU market owing to its high toxicity. Historically, DMF has been widely considered the gold standard for solid-phase peptide synthesis (SPPS). Being urgent to propose alternative solvents, we tested the suitability of non-hazardous neat and mixed solvents. Notably, binary solvent mixtures containing dimethyl sulfoxide as one of the solvent partners demonstrated high efficacy in solubilizing reagents while maintaining the desired swelling characteristics of common resins. A series of binary solvent mixtures were tested in automated SPPS, both at room temperature and high temperature, employing the PurePep® Chorus synthesizer, which enabled controlled induction heating between 25 and 90°C with oscillation mixing. The performances were assessed in challenging peptide sequences, i.e., ACP (65-74), and in longer and aggregating sequences like SARS-CoV-2 RBM (436-507) and β-amyloid (1-42). Furthermore, as part of the proposed sustainable approach to minimize the utilization of hazardous solvents, we coupled the novel PurePep EasyClean catch-and-release purification technology. This work, addressing regulatory compliance, emphasizes the crucial role of green chemistry in advancing safer and more environmentally friendly practices in SPPS.
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Affiliation(s)
- Lorenzo Pacini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology - Peptlab, MoD&LS Laboratory, University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | | | - Luisa Aguiar
- Gyros Protein Technologies Inc., Tucson, Arizona, USA
| | | | - Paolo Rovero
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
- Department of Neurosciences, Psychology, Drug Research and Child Health, Section of Pharmaceutical Sciences and Nutraceutics, University of Florence, Sesto Fiorentino, Italy
| | - Anna Maria Papini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology - Peptlab, MoD&LS Laboratory, University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
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8
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Wróblewska A, Bak-Sypien II, Paluch P, Wielgus E, Zając J, Jeziorna A, Kaźmierski S, Potrzebowski MJ. Solvent-Free Mechanosynthesis of Oligopeptides by Coupling Peptide Segments of Different Lengths - Elucidating the Role of Cesium Carbonate in Ball Mill Processes. Chemistry 2024:e202400177. [PMID: 38644348 DOI: 10.1002/chem.202400177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/15/2024] [Accepted: 04/17/2024] [Indexed: 04/23/2024]
Abstract
We report an idea for the synthesis of oligopeptides using a solvent-free ball milling approach. Our concept is inspired by block play, in which it is possible to construct different objects using segments (blocks) of different sizes and lengths. We prove that by having a library of short peptides and employing the ball mill mechanosynthesis (BMMS) method, peptides can be easily coupled to form different oligopeptides with the desired functional and biological properties. Optimizing the BMMS process we found that the best yields we obtained when TBTU and cesium carbonate were used as reagents. The role of Cs2CO3 in the coupling mechanism was followed on each stage of synthesis by 1H, 13C and 133Cs NMR employing Magic Angle Spinning (MAS) techniques. It was found that cesium carbonate acts not only as a base but is also responsible for the activation of substrates and intermediates. The unique information about the BMMS mechanism is based on the analysis of 2D NMR data. The power of BMMS is proved by the example of different peptide combinations, 2+2, 3+2, 4+2, 5+2 and 4+4. The tetra-, penta-, hexa-, hepta- and octapeptides obtained under this project were fully characterized by MS and NMR techniques.
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Affiliation(s)
- Aneta Wróblewska
- Division of Structural Studies, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Irena I Bak-Sypien
- Division of Structural Studies, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Piotr Paluch
- Division of Structural Studies, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Ewelina Wielgus
- Division of Structural Studies, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Justyna Zając
- Division of Structural Studies, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Agata Jeziorna
- Division of Structural Studies, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Sławomir Kaźmierski
- Division of Structural Studies, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Marek J Potrzebowski
- Division of Structural Studies, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
- Division of Structural Studies, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
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9
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Kekessie I, Wegner K, Martinez I, Kopach ME, White TD, Tom JK, Kenworthy MN, Gallou F, Lopez J, Koenig SG, Payne PR, Eissler S, Arumugam B, Li C, Mukherjee S, Isidro-Llobet A, Ludemann-Hombourger O, Richardson P, Kittelmann J, Sejer Pedersen D, van den Bos LJ. Process Mass Intensity (PMI): A Holistic Analysis of Current Peptide Manufacturing Processes Informs Sustainability in Peptide Synthesis. J Org Chem 2024; 89:4261-4282. [PMID: 38508870 PMCID: PMC11002941 DOI: 10.1021/acs.joc.3c01494] [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: 07/04/2023] [Revised: 01/17/2024] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
Abstract
Small molecule therapeutics represent the majority of the FDA-approved drugs. Yet, many attractive targets are poorly tractable by small molecules, generating a need for new therapeutic modalities. Due to their biocompatibility profile and structural versatility, peptide-based therapeutics are a possible solution. Additionally, in the past two decades, advances in peptide design, delivery, formulation, and devices have occurred, making therapeutic peptides an attractive modality. However, peptide manufacturing is often limited to solid-phase peptide synthesis (SPPS), liquid phase peptide synthesis (LPPS), and to a lesser extent hybrid SPPS/LPPS, with SPPS emerging as a predominant platform technology for peptide synthesis. SPPS involves the use of excess solvents and reagents which negatively impact the environment, thus highlighting the need for newer technologies to reduce the environmental footprint. Herein, fourteen American Chemical Society Green Chemistry Institute Pharmaceutical Roundtable (ACS GCIPR) member companies with peptide-based therapeutics in their portfolio have compiled Process Mass Intensity (PMI) metrics to help inform the sustainability efforts in peptide synthesis. This includes PMI assessment on 40 synthetic peptide processes at various development stages in pharma, classified according to the development phase. This is the most comprehensive assessment of synthetic peptide environmental metrics to date. The synthetic peptide manufacturing process was divided into stages (synthesis, purification, isolation) to determine their respective PMI. On average, solid-phase peptide synthesis (SPPS) (PMI ≈ 13,000) does not compare favorably with other modalities such as small molecules (PMI median 168-308) and biopharmaceuticals (PMI ≈ 8300). Thus, the high PMI for peptide synthesis warrants more environmentally friendly processes in peptide manufacturing.
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Affiliation(s)
- Ivy Kekessie
- Early Discovery
Biochemistry - Peptide Therapeutics, Genentech,
Inc., A Member of the Roche Group, 1 DNA Way, South San Francisco, California 94080, United States
| | - Katarzyna Wegner
- Active Pharmaceutical
Ingredient Development, Ipsen Manufacturing
Ireland Ltd., Blanchardstown
Industrial Park, Dublin 15, Ireland
| | - Isamir Martinez
- Green Chemistry
Institute, American Chemical Society, 1155 16th St North West, Washington, District of Columbia, 20036, United
States
| | - Michael E. Kopach
- Synthetic
Molecule Design and Development, Eli Lilly
and Company, Indianapolis, Indiana 46285, United States
| | - Timothy D. White
- Synthetic
Molecule Design and Development, Eli Lilly
and Company, Indianapolis, Indiana 46285, United States
| | - Janine K. Tom
- Drug Substance
Technologies, Amgen, Inc., 1 Amgen Center Drive, Thousand
Oaks, California 91320, United States
| | - Martin N. Kenworthy
- Chemical
Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, SK10 2NA, United Kingdom
| | - Fabrice Gallou
- Chemical
& Analytical Development, Novartis Pharma
AG, 4056 Basel, Switzerland
| | - John Lopez
- Chemical
& Analytical Development, Novartis Pharma
AG, 4056 Basel, Switzerland
| | - Stefan G. Koenig
- Small
Molecule
Pharmaceutical Sciences, Genentech, Inc.,
A Member of the Roche Group, 1 DNA Way, South San Francisco, California 94080, United States
| | - Philippa R. Payne
- Outsourced
Manufacturing, Pharmaceutical Development & Manufacturing, Gilead Alberta ULC, 1021 Hayter Rd NW, Edmonton, T6S 1A1, Canada
| | - Stefan Eissler
- Bachem
AG, Hauptstrasse 144, 4416 Bubendorf, Switzerland
| | - Balasubramanian Arumugam
- Chemical
Macromolecule Division, Asymchem Life Science
(Tianjin) Co., Ltd., 71 Seventh Avenue, TEDA Tianjin 300457, China
| | - Changfeng Li
- Chemical
Macromolecule Division, Asymchem Life Science
(Tianjin) Co., Ltd., 71 Seventh Avenue, TEDA Tianjin 300457, China
| | - Subha Mukherjee
- Chemical
Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | | | | | - Paul Richardson
- Chemistry, Pfizer, 10578 Science Center Drive (CB6), San Diego, California 09121, United States
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10
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Kordi M, Talkhounche PG, Vahedi H, Farrokhi N, Tabarzad M. Heterologous Production of Antimicrobial Peptides: Notes to Consider. Protein J 2024; 43:129-158. [PMID: 38180586 DOI: 10.1007/s10930-023-10174-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
Abstract
Heavy and irresponsible use of antibiotics in the last century has put selection pressure on the microbes to evolve even faster and develop more resilient strains. In the confrontation with such sometimes called "superbugs", the search for new sources of biochemical antibiotics seems to have reached the limit. In the last two decades, bioactive antimicrobial peptides (AMPs), which are polypeptide chains with less than 100 amino acids, have attracted the attention of many in the control of microbial pathogens, more than the other types of antibiotics. AMPs are groups of components involved in the immune response of many living organisms, and have come to light as new frontiers in fighting with microbes. AMPs are generally produced in minute amounts within organisms; therefore, to address the market, they have to be either produced on a large scale through recombinant DNA technology or to be synthesized via chemical methods. Here, heterologous expression of AMPs within bacterial, fungal, yeast, plants, and insect cells, and points that need to be considered towards their industrialization will be reviewed.
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Affiliation(s)
- Masoumeh Kordi
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Parnian Ghaedi Talkhounche
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Helia Vahedi
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Naser Farrokhi
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran.
| | - Maryam Tabarzad
- Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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11
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Bae H, Park J, Yoon R, Lee S, Son J. Copper-catalyzed synthesis of primary amides through reductive N-O cleavage of dioxazolones. RSC Adv 2024; 14:9440-9444. [PMID: 38516159 PMCID: PMC10951817 DOI: 10.1039/d4ra00320a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
A new method for the synthesis of primary amides is developed, in which dioxazolones are treated with a copper catalyst under mild reaction conditions. A broad scope of dioxazolones is exhibited as well as dioxazolones containing biologically active structural motifs. These robust and mild reaction conditions allow the transformation of dioxazolones to primary amides, in which sensitive functional groups such as hydroxyl, aldehyde, trialkylsilyl, and unsaturated carbon units are tolerated with excellent chemoselectivity.
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Affiliation(s)
- Hyeonwoong Bae
- Department of Chemical Engineering (BK21 FOUR Graduate Program), Dong-A University 37 Nakdong-Daero 550beon-gil, Saha-gu Busan 49315 South Korea
- Department of Chemistry, Dong-A University 37 Nakdong-Daero 550beon-gil, Saha-gu Busan 49315 South Korea
| | - Jinhwan Park
- Department of Chemical Engineering (BK21 FOUR Graduate Program), Dong-A University 37 Nakdong-Daero 550beon-gil, Saha-gu Busan 49315 South Korea
- Department of Chemistry, Dong-A University 37 Nakdong-Daero 550beon-gil, Saha-gu Busan 49315 South Korea
| | - Rahyun Yoon
- Department of Chemistry, Dong-A University 37 Nakdong-Daero 550beon-gil, Saha-gu Busan 49315 South Korea
| | - Seunghoon Lee
- Department of Chemical Engineering (BK21 FOUR Graduate Program), Dong-A University 37 Nakdong-Daero 550beon-gil, Saha-gu Busan 49315 South Korea
- Department of Chemistry, Dong-A University 37 Nakdong-Daero 550beon-gil, Saha-gu Busan 49315 South Korea
| | - Jongwoo Son
- Department of Chemical Engineering (BK21 FOUR Graduate Program), Dong-A University 37 Nakdong-Daero 550beon-gil, Saha-gu Busan 49315 South Korea
- Department of Chemistry, Dong-A University 37 Nakdong-Daero 550beon-gil, Saha-gu Busan 49315 South Korea
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12
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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
ConspectusSince 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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13
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Liu T, Peng Z, Lai M, Hu L, Zhao J. Inverse Peptide Synthesis Using Transient Protected Amino Acids. J Am Chem Soc 2024; 146:4270-4280. [PMID: 38316681 DOI: 10.1021/jacs.4c00314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Peptide therapeutics have experienced a rapid resurgence over the past three decades. While a few peptide drugs are biologically produced, most are manufactured via chemical synthesis. The cycle of prior protection of the amino group of an α-amino acid, activation of its carboxyl group, aminolysis with the free amino group of a growing peptide chain, and deprotection of the N-terminus constitutes the principle of conventional C → N peptide chemical synthesis. The mandatory use of the Nα-protecting group invokes two additional operations for incorporating each amino acid, resulting in poor step- and atom-economy. The burgeoning demand in the peptide therapeutic market necessitates cost-effective and environmentally friendly peptide manufacturing strategies. Inverse peptide chemical synthesis using unprotected amino acids has been proposed as an ideal and appealing strategy. However, it has remained unsuccessful for over 60 years due to severe racemization/epimerization during N → C peptide chain elongation. Herein, this challenge has been successfully addressed by ynamide coupling reagent employing a transient protection strategy. The activation, transient protection, aminolysis, and in situ deprotection were performed in one pot, thus offering a practical peptide chemical synthesis strategy formally using unprotected amino acids as the starting material. Its robustness was exemplified by syntheses of peptide active pharmaceutical ingredients. It is also amenable to fragment condensation and inverse solid-phase peptide synthesis. The compatibility to green solvents further enhances its application potential in large-scale peptide production. This study offered a cost-effective, operational convenient, and environmentally benign approach to peptides.
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Affiliation(s)
- Tao Liu
- Affiliated Cancer Hospital, Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences, Guangzhou Medical University, No.1 Xinzao, Panyu District, Guangzhou 511436, China
| | - Zejun Peng
- Affiliated Cancer Hospital, Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences, Guangzhou Medical University, No.1 Xinzao, Panyu District, Guangzhou 511436, China
| | - Manting Lai
- Affiliated Cancer Hospital, Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences, Guangzhou Medical University, No.1 Xinzao, Panyu District, Guangzhou 511436, China
| | - Long Hu
- Affiliated Cancer Hospital, Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences, Guangzhou Medical University, No.1 Xinzao, Panyu District, Guangzhou 511436, China
| | - Junfeng Zhao
- Affiliated Cancer Hospital, Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences, Guangzhou Medical University, No.1 Xinzao, Panyu District, Guangzhou 511436, China
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14
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Procopio D, Siciliano C, Di Gioia ML. Reactive deep eutectic solvents for EDC-mediated amide synthesis. Org Biomol Chem 2024; 22:1400-1408. [PMID: 38126479 DOI: 10.1039/d3ob01673k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The sustainability of amide bond formation is an ever-present topic in the pharmaceutical industry, as it represents the common motif in many clinically approved drugs. Despite many procedures for accomplishing eco-friendly amide synthesis having been developed, this transformation still remains a contemporary challenge. Herein, we report a greener approach for amide synthesis by using Reactive Deep Eutectic Solvents (RDESs) acting as both the reaction medium and reactants. The procedure not only avoids the use of hazardous solvents but also provides operationally simple product recovery with high purity and efficiency, without chromatographic purification. This approach was efficiently applied to the synthesis of a key intermediate in the production of an active pharmaceutical ingredient like atenolol. The green metrics of the gram-scale procedure were compared to the conventional industrial strategy showing an advancement in the greening of amide synthesis.
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Affiliation(s)
- Debora Procopio
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036, Arcavacata of Rende, Italy.
| | - Carlo Siciliano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036, Arcavacata of Rende, Italy.
| | - Maria Luisa Di Gioia
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036, Arcavacata of Rende, Italy.
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15
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Cruz KG, Eron MH, Makhaik S, Savinov S, Hardy JA. A Non-Active-Site Inhibitor with Selectivity for Zika Virus NS2B-NS3 Protease. ACS Infect Dis 2024; 10:412-425. [PMID: 38265226 PMCID: PMC11099878 DOI: 10.1021/acsinfecdis.3c00330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Flavivirus infection usually results in fever accompanied by headache, arthralgia, and, in some cases, rash. Although the symptoms are mild, full recovery can take several months. Flaviviruses encode seven nonstructural proteins that represent potential drug targets for this viral family. Focusing on the Zika virus NS2B-NS3 protease, we uncovered a unique inhibitor, MH1, composed of aminothiazolopyridine and benzofuran moieties. MH1 inhibits ZVP with a biochemical IC50 of 440 nM and effectively blocks cleavage of ZVP substrates in cells. Surprisingly, MH1 inhibits the other flaviviral proteases at least 18-fold more weakly. This same phenomenon was observed in assays of the viral cytopathic effect, where only Zika virus showed sensitivity to MH1. This selectivity was unexpected since flaviviral proteases have high similarity in sequence and protein structure. MH1 binds at an allosteric site, as demonstrated by its ability to stabilize ZVP synergistically with an active site inhibitor. To understand its selectivity, we constructed a series of hybrid proteases composed of select segments of ZVP, which is sensitive to MH1, and dengue virus protease, which is essentially insensitive to MH1. Our results suggest that MH1 binds to the NS3 protease domain, disrupting its interaction with NS2B. These interactions are essential for substrate binding and cleavage. In particular, the unique dynamic properties of NS2B from Zika seem to be required for the function of MH1. Insights into the mechanism of MH1 function will aid us in developing non-active-site-directed, pan-flaviviral inhibitors, by highlighting the importance of evaluating and considering the dynamics of the NS2B regions.
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Affiliation(s)
| | | | - Sparsh Makhaik
- Department of Chemistry, University of Massachusetts Amherst, MA, US 01002
| | | | - Jeanne A. Hardy
- Department of Chemistry, University of Massachusetts Amherst, MA, US 01002
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16
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Mthembu SN, Chakraborty A, Schönleber R, Albericio F, de la Torre BG. Morpholine, a strong contender for Fmoc removal in solid-phase peptide synthesis. J Pept Sci 2024; 30:e3538. [PMID: 37609959 DOI: 10.1002/psc.3538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/24/2023]
Abstract
Morpholine, which scores 7.5 in terms of greenness and is not a regulated substance, could be considered a strong contender for Fmoc removal in solid-phase peptide synthesis (SPPS). Morpholine in dimethylformamide (DMF) (50%-60%) efficiently removes Fmoc in SPPS, minimizes the formation of diketopiperazine, and almost avoids the aspartimide formation. As a proof of concept, somatostatin has been synthesized using 50% morpholine in DMF with the same purity as when using 20% piperidine-DMF.
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Affiliation(s)
- Sinenhlanhla N Mthembu
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Amit Chakraborty
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
| | | | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, and Department of Organic Chemistry, University of Barcelona, Barcelona, Spain
| | - Beatriz G de la Torre
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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17
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Uehara D, Adachi S, Tsubouchi A, Okada Y, Zhdankin VV, Yoshimura A, Saito A. Peptide coupling using recyclable bicyclic benziodazolone. Chem Commun (Camb) 2024; 60:956-959. [PMID: 38131348 DOI: 10.1039/d3cc04431a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
We report a greener peptide coupling using bicyclic benziodazolone and triarylphosphine as coupling reagents. Bicyclic benziodazolone also works as a base and can be recovered as the corresponding iodine(I) compound after use, which can be converted to the original iodine(III) reagent by electrolytic oxidation.
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Affiliation(s)
- Daigo Uehara
- Division of Applied Chemistry, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Sota Adachi
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Akira Tsubouchi
- Division of Applied Chemistry, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Yohei Okada
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Viktor V Zhdankin
- Department of Chemistry and Biochemistry, University of Minnesota, Duluth, MN, 55812, USA
| | - Akira Yoshimura
- Faculty of Pharmaceutical Sciences, Aomori University, 2-3-1 Kobata, Aomori 030-0943, Japan
| | - Akio Saito
- Division of Applied Chemistry, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
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18
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Sheng ZK, Liu Y, Du LH, Zhang SY, Zhang AY, Xie HJ, Lin H, Yan BL, Xue MM, Ruan ZX, Fu GN, Pan BL, Zhou TY, Luo XP. Development of a green, concise synthesis of nicotinamide derivatives catalysed by Novozym® 435 from Candida antarctica in sustainable continuous-flow microreactors. RSC Adv 2024; 14:131-138. [PMID: 38173597 PMCID: PMC10758761 DOI: 10.1039/d3ra07201k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 11/21/2023] [Indexed: 01/05/2024] Open
Abstract
An increasing number of studies have shown that many nicotinamide derivatives exhibited extensive biological activities, such as anti-inflammatory and antitumor activity. In this paper, a green, concise synthesis of nicotinamide derivatives in sustainable continuous-flow microreactors catalysed by Novozym® 435 from Candida antarctica has been developed. Application of an easily obtainable and reusable lipase in the synthesis of nicotinamide derivatives from methyl nicotinate and amines/benzylamines reacted for 35 min at 50 °C led to high product yields (81.6-88.5%). Environmentally friendly tert-amyl alcohol was applied as a reaction medium. Substantially shorter reaction times as well as a significant increase in the product yield were obtained as compared to the batch process. This innovative approach provides a promising green, efficient and rapid synthesis strategy for pharmaceutical synthesis and further activity research of novel nicotinamide derivatives.
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Affiliation(s)
- Zhi-Kai Sheng
- College of Pharmaceutical Science, ZheJiang University of Technology Zhejiang Hangzhou 310014 China +86 571 88320903 +86-189-690-693-99
| | - Yi Liu
- College of Pharmaceutical Science, ZheJiang University of Technology Zhejiang Hangzhou 310014 China +86 571 88320903 +86-189-690-693-99
| | - Li-Hua Du
- College of Pharmaceutical Science, ZheJiang University of Technology Zhejiang Hangzhou 310014 China +86 571 88320903 +86-189-690-693-99
| | - Shi-Yi Zhang
- College of Pharmaceutical Science, ZheJiang University of Technology Zhejiang Hangzhou 310014 China +86 571 88320903 +86-189-690-693-99
| | - Ao-Ying Zhang
- College of Pharmaceutical Science, ZheJiang University of Technology Zhejiang Hangzhou 310014 China +86 571 88320903 +86-189-690-693-99
| | - Han-Jia Xie
- College of Pharmaceutical Science, ZheJiang University of Technology Zhejiang Hangzhou 310014 China +86 571 88320903 +86-189-690-693-99
| | - Hang Lin
- College of Pharmaceutical Science, ZheJiang University of Technology Zhejiang Hangzhou 310014 China +86 571 88320903 +86-189-690-693-99
| | - Bing-Lin Yan
- College of Pharmaceutical Science, ZheJiang University of Technology Zhejiang Hangzhou 310014 China +86 571 88320903 +86-189-690-693-99
| | - Miao-Miao Xue
- College of Pharmaceutical Science, ZheJiang University of Technology Zhejiang Hangzhou 310014 China +86 571 88320903 +86-189-690-693-99
| | - Zhi-Xuan Ruan
- College of Pharmaceutical Science, ZheJiang University of Technology Zhejiang Hangzhou 310014 China +86 571 88320903 +86-189-690-693-99
| | - Guo-Neng Fu
- College of Pharmaceutical Science, ZheJiang University of Technology Zhejiang Hangzhou 310014 China +86 571 88320903 +86-189-690-693-99
| | - Bing-Le Pan
- College of Pharmaceutical Science, ZheJiang University of Technology Zhejiang Hangzhou 310014 China +86 571 88320903 +86-189-690-693-99
| | - Tong-Yao Zhou
- College of Pharmaceutical Science, ZheJiang University of Technology Zhejiang Hangzhou 310014 China +86 571 88320903 +86-189-690-693-99
| | - Xi-Ping Luo
- Zhejiang Provincial Key Laboratory of Chemical Utilization of Forestry Biomass, Zhejiang A&F University Zhejiang Hangzhou 311300 China
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19
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Schnatbaum K, Holenya P, Pfeil S, Drosch M, Eckey M, Reimer U, Wenschuh H, Kern F. An Overview of Peptides and Peptide Pools for Antigen-Specific Stimulation in T-Cell Assays. Methods Mol Biol 2024; 2768:29-50. [PMID: 38502386 DOI: 10.1007/978-1-0716-3690-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
The analysis of antigen-specific T-cell responses has become routine in many laboratories. Functional T-cell assays like enzyme-linked-immuno-spot (ELISPOT), which depend on antigen-specific stimulation, increasingly use peptides to represent the antigen of interest. Besides single peptides, mixtures of peptides (peptide pools) are very frequently applied. Such peptide pools may, for example, represent entire proteins (with overlapping peptides covering a protein sequence) or include noncontiguous peptides such as a collection of T-cell-stimulating peptides. The optimum specification of single peptides or peptide pools for T-cell stimulation assays will depend on the purpose of the test, the target T-cell population, the availability of sample, requirements regarding reproducibility, and, last but not least, the available budget, to mention only the most important factors. Because of the way peptides are produced, they will always contain certain amounts of impurities such as peptides with deletions or truncated peptides, and there may be additional by-products of peptide synthesis. Optimized synthesis protocols as well as purification help reduce impurities that might otherwise cause false-positive assay results. However, specific requirements with respect to purity will vary depending on the purpose of an assay. Finally, storage conditions significantly affect the shelf life of peptides, which is relevant especially for longitudinal studies. The present book chapter addresses all of these aspects in detail. It should provide the researcher with all necessary background knowledge for making the right decisions when it comes to choosing, using, and storing peptides for ELISPOT and other T-cell stimulation assays.
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Affiliation(s)
| | | | | | | | | | - Ulf Reimer
- JPT Peptide Technologies, Berlin, Germany
| | | | - Florian Kern
- JPT Peptide Technologies, Berlin, Germany.
- Brighton and Sussex Medical School, Brighton, UK.
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20
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Collins JM, Singh SK, White TA, Cesta DJ, Simpson CL, Tubb LJ, Houser CL. Total wash elimination for solid phase peptide synthesis. Nat Commun 2023; 14:8168. [PMID: 38071224 PMCID: PMC10710472 DOI: 10.1038/s41467-023-44074-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
We present a process for solid phase peptide synthesis (SPPS) that completely eliminates all solvent intensive washing steps during each amino acid addition cycle. A key breakthrough is the removal of a volatile Fmoc deprotection base through bulk evaporation at elevated temperature while preventing condensation on the vessel surfaces with a directed headspace gas flushing. This process was demonstrated at both research and production scales without any impact on product quality and when applied to a variety of challenging sequences (up to 89 amino acids in length). The overall result is an extremely fast, high purity, scalable process with a massive waste reduction (up to 95%) while only requiring 10-15% of the standard amount of base used. This transformation of SPPS represents a step-change in peptide manufacturing process efficiency, and should encourage expanded access to peptide-based therapeutics.
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Affiliation(s)
- Jonathan M Collins
- Peptide Synthesis Research, CEM Corporation, 3100 Smith Farm Rd, Matthews, NC, 28104, USA.
| | - Sandeep K Singh
- Peptide Synthesis Research, CEM Corporation, 3100 Smith Farm Rd, Matthews, NC, 28104, USA
| | - Travis A White
- Peptide Synthesis Research, CEM Corporation, 3100 Smith Farm Rd, Matthews, NC, 28104, USA
| | - Drew J Cesta
- Peptide Synthesis Research, CEM Corporation, 3100 Smith Farm Rd, Matthews, NC, 28104, USA
| | - Colin L Simpson
- Peptide Synthesis Research, CEM Corporation, 3100 Smith Farm Rd, Matthews, NC, 28104, USA
| | - Levi J Tubb
- Peptide Synthesis Research, CEM Corporation, 3100 Smith Farm Rd, Matthews, NC, 28104, USA
| | - Christopher L Houser
- Peptide Synthesis Research, CEM Corporation, 3100 Smith Farm Rd, Matthews, NC, 28104, USA
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21
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Zhong W, Wan C, Zhou Z, Dai C, Zhang Y, Lu F, Yin F, Li Z. 4-Iodine N-Methylpyridinium-Mediated Peptide Synthesis. Org Lett 2023; 25:8661-8665. [PMID: 38009639 DOI: 10.1021/acs.orglett.3c03539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Through systematic optimization of halopyridinium compounds, we established a peptide coupling protocol utilizing 4-iodine N-methylpyridinium (4IMP) for solid-phase peptide synthesis (SPPS). The 4IMP coupling reagent is easily prepared, bench stable, and cost-effective. Employing 4IMP in the SPPS process has showcased remarkable chemoselectivity and efficiency, effectively eliminating racemization and epimerization. This achievement has been substantiated through the successful synthesis of a range of peptides via the direct utilization of commercially available amino acid substrates for SPPS.
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Affiliation(s)
- Wanjin Zhong
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Chuan Wan
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118, China
| | - Ziyuan Zhou
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Chuan Dai
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Yichi Zhang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Fei Lu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, China
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22
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Duengo S, Muhajir MI, Hidayat AT, Musa WJA, Maharani R. Epimerisation in Peptide Synthesis. Molecules 2023; 28:8017. [PMID: 38138507 PMCID: PMC10745333 DOI: 10.3390/molecules28248017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/11/2023] [Accepted: 10/23/2023] [Indexed: 12/24/2023] Open
Abstract
Epimerisation is basically a chemical conversion that includes the transformation of an epimer into another epimer or its chiral partner. Epimerisation of amino acid is a side reaction that sometimes happens during peptide synthesis. It became the most avoided reaction because the process affects the overall conformation of the molecule, eventually even altering the bioactivity of the peptide. Epimerised products have a high similarity of physical characteristics, thus making it difficult for them to be purified. In regards to amino acids, epimerisation is very important in keeping the chirality of the assembled amino acids unchanged during the peptide synthesis and obtaining the desirable product without any problematic purification. In this review, we report several factors that induce epimerisation during peptide synthesis, including how to characterise and affect the bioactivities. To avoid undesirable epimerisation, we also describe several methods of suppressing the process.
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Affiliation(s)
- Suleman Duengo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia; (S.D.); (M.I.M.); (A.T.H.)
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Negeri Gorontalo, Gorontalo 96128, North Sulawesi, Indonesia;
| | - Muhamad Imam Muhajir
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia; (S.D.); (M.I.M.); (A.T.H.)
| | - Ace Tatang Hidayat
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia; (S.D.); (M.I.M.); (A.T.H.)
- Central Laboratory, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia
| | - Weny J. A. Musa
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Negeri Gorontalo, Gorontalo 96128, North Sulawesi, Indonesia;
| | - Rani Maharani
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia; (S.D.); (M.I.M.); (A.T.H.)
- Central Laboratory, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia
- Research Collaboration Centre for Theranostic Radiopharmaceutical, National Research and Innovation Agency (BRIN), Sumedang 45363, West Java, Indonesia
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23
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Uth C, Englert S, Avrutina O, Kolmar H, Knauer S. Novel amino-Li resin for water-based solid-phase peptide synthesis. J Pept Sci 2023; 29:e3527. [PMID: 37322567 DOI: 10.1002/psc.3527] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/17/2023]
Abstract
We report the first application of a novel amino-Li resin to water-based solid-phase peptide synthesis (SPPS) applying the Smoc-protecting group approach. We demonstrated that it is a suitable support for the sustainable water-based alternative to a classical SPPS approach. The resin possesses good swelling properties in aqueous milieu, provides significant coupling sites, and may be applicable to the synthesis of difficult sequences and aggregation-prone peptides.
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Affiliation(s)
| | | | - Olga Avrutina
- Clemens-Schöpf Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Harald Kolmar
- Clemens-Schöpf Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
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24
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Grąźlewska W, Holec-Gąsior L, Sołowińska K, Chmielewski T, Fiecek B, Contreras M. Epitope Mapping of BmpA and BBK32 Borrelia burgdorferi Sensu Stricto Antigens for the Design of Chimeric Proteins with Potential Diagnostic Value. ACS Infect Dis 2023; 9:2160-2172. [PMID: 37803965 PMCID: PMC10722512 DOI: 10.1021/acsinfecdis.3c00258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Indexed: 10/08/2023]
Abstract
Lyme disease is a tick-borne zoonosis caused by Gram-negative bacteria belonging to the Borrelia burgdorferi sensu lato (s.l.) group. In this study, IgM- and IgG-specific linear epitopes of two B. burgdorferi sensu stricto (s.s.) antigens BmpA and BBK32 were mapped using a polypeptide array. Subsequently, two chimeric proteins BmpA-BBK32-M and BmpA-BBK32-G were designed to validate the construction of chimeras using the identified epitopes for the detection of IgM and IgG, respectively, by ELISA. IgG-ELISA based on the BmpA-BBK32-G antigen showed 71% sensitivity and 95% specificity, whereas a slightly lower diagnostic utility was obtained for IgM-ELISA based on BmpA-BBK32-M, where the sensitivity was also 71% but the specificity decreased to 89%. The reactivity of chimeric proteins with nondedicated antibodies was much lower. These results suggest that the identified epitopes may be useful in the design of new forms of antigens to increase the effectiveness of Lyme disease serodiagnosis. It has also been proven that appropriate selection of epitopes enables the construction of chimeric proteins exhibiting reactivity with a specific antibody isotype.
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Affiliation(s)
- Weronika Grąźlewska
- Department
of Molecular Biotechnology and Microbiology, Faculty of Chemistry, University of Gdańsk Technology, 80-233 Gdańsk, Poland
- SaBio,
Instituto de Investigación en Recursos Cinegéticos IREC−CSIC-UCLM-JCCM, 13005 Ciudad Real, Spain
| | - Lucyna Holec-Gąsior
- Department
of Molecular Biotechnology and Microbiology, Faculty of Chemistry, University of Gdańsk Technology, 80-233 Gdańsk, Poland
| | - Karolina Sołowińska
- Department
of Molecular Biotechnology and Microbiology, Faculty of Chemistry, University of Gdańsk Technology, 80-233 Gdańsk, Poland
| | - Tomasz Chmielewski
- Department
of Parasitology and Diseases Transmitted by Vectors, National Institute of Public Health NIH - National Research Institute, 00-791 Warsaw, Poland
| | - Beata Fiecek
- Department
of Parasitology and Diseases Transmitted by Vectors, National Institute of Public Health NIH - National Research Institute, 00-791 Warsaw, Poland
| | - Marinela Contreras
- SaBio,
Instituto de Investigación en Recursos Cinegéticos IREC−CSIC-UCLM-JCCM, 13005 Ciudad Real, Spain
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25
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Rahaman KA, Muresan AR, Hasan ML, Joung YK, Min H, Son J, Kang MJ, Kwon OS. Detection and quantification of the metabolite Ac-Tβ 1-14 in in vitro experiments and urine of rats treated with Ac-Tβ4: A potential biomarker of Ac-Tβ4 for doping tests. Drug Test Anal 2023; 15:1454-1467. [PMID: 37515313 DOI: 10.1002/dta.3552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023]
Abstract
Thymosin β4 (Tβ4) was reported to exert various beneficial bioactivities such as tissue repair, anti-inflammation, and reduced scar formation, and it is listed on the prohibited substances in sports by the World Anti-Doping Agency. However, no metabolism studies of Tβ4 were reported yet. Previously, our lab reported in in vitro experiment that a total of 13 metabolites were found by using multiple enzymes, and six metabolites (Ac-Tβ31-43 , Ac-Tβ17-43 , Ac-Tβ1-11 , Ac-Tβ1-14 , Ac-Tβ1-15 , and Ac-Tβ1-17 ) were confirmed by comparing with the synthetic standards. This study was aimed at identifying new metabolites of Tβ4 leucine aminopeptidase (LAP), human kidney microsomes (HKM), cultured huvec cells, and rats after administration of Tβ4 protein to develop biomarkers for detecting doping drugs in sports. A method for detecting and quantifying Ac-Tβ1-14 was developed and validated using Q-Exactive orbitrap mass spectrometry. The limit of detection (LOD) and limit of quantification (LOQ) of the Ac-Tβ1-14 were 0.19 and 0.58 ng/mL, respectively, and showed a good linearity (r2 = 0.9998). As a result, among the six metabolites above, Ac-Tβ1-14 , as a common metabolite, was found in LAP, HKM, huvec cells exposed to Tβ4, and the urine of rats intraperitoneally treated with 20-mg/kg Tβ4. And the metabolite Ac-Tβ1-14 was quantitatively determined by 48 h in rats, with the highest concentration occurring between 0 and 6 h. Ac-Tβ1-14 was not detected in non-treated control groups, including human blank urine. These results suggest that Ac-Tβ1-14 in urine is a potential biomarker for screening the parent Tβ4 in doping tests.
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Affiliation(s)
- Khandoker Asiqur Rahaman
- Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul, South Korea
- Doping Control Center, Korea Institute of Science and Technology, Seoul, South Korea
| | - Anca Raluca Muresan
- Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul, South Korea
- Doping Control Center, Korea Institute of Science and Technology, Seoul, South Korea
| | - Md Lemon Hasan
- Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul, South Korea
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, South Korea
| | - Yoon Ki Joung
- Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul, South Korea
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, South Korea
| | - Hophil Min
- Doping Control Center, Korea Institute of Science and Technology, Seoul, South Korea
| | - Junghyun Son
- Doping Control Center, Korea Institute of Science and Technology, Seoul, South Korea
| | - Min-Jung Kang
- Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul, South Korea
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology, Seoul, South Korea
| | - Oh-Seung Kwon
- Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul, South Korea
- Doping Control Center, Korea Institute of Science and Technology, Seoul, South Korea
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26
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Pereira-Dias L, Oliveira-Pinto PR, Fernandes JO, Regalado L, Mendes R, Teixeira C, Mariz-Ponte N, Gomes P, Santos C. Peptaibiotics: Harnessing the potential of microbial secondary metabolites for mitigation of plant pathogens. Biotechnol Adv 2023; 68:108223. [PMID: 37536466 DOI: 10.1016/j.biotechadv.2023.108223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Agricultural systems are in need of low-cost, safe antibiotics to protect crops from pests and diseases. Peptaibiotics, a family of linear, membrane-active, amphipathic polypeptides, have been shown to exhibit antibacterial, antifungal, and antiviral activity, and to be inducers of plant resistance against a wide range of phytopathogens. Peptaibiotics belong to the new generation of alternatives to agrochemicals, aligned with the United Nations Sustainable Development Goals and the One Health approach toward ensuring global food security and safety. Despite that, these fungi-derived, non-ribosomal peptides remain surprisingly understudied, especially in agriculture, where only a small number has been tested against a reduced number of phytopathogens. This lack of adoption stems from peptaibiotics' poor water solubility and the difficulty to synthesize and purify them in vitro, which compromises their delivery and inclusion in formulations. In this review, we offer a comprehensive analysis of peptaibiotics' classification, biosynthesis, relevance to plant protection, and mode of action against phytopathogens, along with the techniques enabling researchers to extract, purify, and elucidate their structure, and the databases holding such valuable data. It is also discussed how chemical synthesis and ionic liquids could increase their solubility, how genetic engineering and epigenetics could boost in vitro production, and how omics can reduce screenings' workload through in silico selection of the best candidates. These strategies could turn peptaibiotics into effective, ultra-specific, biodegradable tools for phytopathogen control.
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Affiliation(s)
- Leandro Pereira-Dias
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022, Valencia, Spain.
| | - Paulo R Oliveira-Pinto
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Juliana O Fernandes
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Laura Regalado
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rafael Mendes
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Cátia Teixeira
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Nuno Mariz-Ponte
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Paula Gomes
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Conceição Santos
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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27
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Tatsumi T, Sasamoto K, Matsumoto T, Hirano R, Oikawa K, Nakano M, Yoshida M, Oisaki K, Kanai M. Practical N-to-C peptide synthesis with minimal protecting groups. Commun Chem 2023; 6:231. [PMID: 37884638 PMCID: PMC10603086 DOI: 10.1038/s42004-023-01030-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
Accessible drug modalities have continued to increase in number in recent years. Peptides play a central role as pharmaceuticals and biomaterials in these new drug modalities. Although traditional peptide synthesis using chain-elongation from C- to N-terminus is reliable, it produces large quantities of chemical waste derived from protecting groups and condensation reagents, which place a heavy burden on the environment. Here we report an alternative N-to-C elongation strategy utilizing catalytic peptide thioacid formation and oxidative peptide bond formation with main chain-unprotected amino acids under aerobic conditions. This method is applicable to both iterative peptide couplings and convergent fragment couplings without requiring elaborate condensation reagents and protecting group manipulations. A recyclable N-hydroxy pyridone additive effectively suppresses epimerization at the elongating chain. We demonstrate the practicality of this method by showcasing a straightforward synthesis of the nonapeptide DSIP. This method further opens the door to clean and atom-efficient peptide synthesis.
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Affiliation(s)
- Toshifumi Tatsumi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koki Sasamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takuya Matsumoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ryo Hirano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kazuki Oikawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Masato Nakano
- Interdisciplinary Research Center for Catalytic Chemistry (IRC3), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5-2, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Masaru Yoshida
- Interdisciplinary Research Center for Catalytic Chemistry (IRC3), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5-2, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Kounosuke Oisaki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Interdisciplinary Research Center for Catalytic Chemistry (IRC3), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5-2, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan.
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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28
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Thomas JA, Hinton ZR, Korley LTJ. Peptide-polyurea hybrids: a platform for tunable, thermally-stable, and injectable hydrogels. SOFT MATTER 2023; 19:7912-7922. [PMID: 37706333 PMCID: PMC10615840 DOI: 10.1039/d3sm00780d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Drawing inspiration from natural systems, such as the highly segmented structures found in silk fibroin, is an important strategy when designing strong, yet dynamic biomaterials. Polymer-peptide hybrids aim to incorporate the benefits of hierarchical polypeptide structures into synthetic platforms that are promising materials for hydrogel systems due to aspects such as their biocompatibility and structural tunability. In this work, we demonstrated the utility of poly(ethylene glycol) (PEG) peptide-polyurea hybrids as self-assembled hydrogels. Specifically, poly(ε-carbobenzyloxy-L-lysine)-b-PEG-b-poly(ε-carbobenzyloxy-L-lysine) and poly(β-benzyl-L-aspartate)-b-PEG-b-poly(β-benzyl-L-aspartate) triblock copolymers were used as the soft segments in linear peptide-polyurea (PPU) hybrids. We systematically examined the effect of peptide secondary structure and peptide segment length on hydrogelation, microstructure, and rheological properties of our PPU hydrogels. Polymers containing α-helical secondary structures resulted in rapid gelation upon the addition of water, as driven by hierarchical assembly of the peptide segments. Peptide segment length dictated gel strength and resistance to deformation via complex relationships. Simulated injection experiments demonstrated that PPU hydrogels recover their original gel network within 10 s of cessation of high shear. Finally, we showed that PPU hydrogels remain solid-like within the range of 10 to 80 °C; however, a unique softening transition occurs at temperatures corresponding to slight melting of secondary structures. Overall, this bioinspired PPU hybrid platform provides opportunities to design synthetic, bioinspired polymers for hydrogels with tunable microstructure and mechanics for a wide range of thermal and injection-based applications.
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Affiliation(s)
- Jessica A Thomas
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA.
| | - Zachary R Hinton
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA.
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - LaShanda T J Korley
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA.
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
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29
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Mattellone A, Corbisiero D, Cantelmi P, Martelli G, Palladino C, Tolomelli A, Cabri W, Ferrazzano L. Fast Solution-Phase and Liquid-Phase Peptide Syntheses (SolPSS and LPPS) Mediated by Biomimetic Cyclic Propylphosphonic Anhydride (T3P ®). Molecules 2023; 28:7183. [PMID: 37894662 PMCID: PMC10609394 DOI: 10.3390/molecules28207183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The growing applications of peptide-based therapeutics require the development of efficient protocols from the perspective of an industrial scale-up. T3P® (cyclic propylphosphonic anhydride) promotes amidation in the solution-phase through a biomimetic approach, similar to the activation of carboxylic moiety catalyzed by ATP-grasp enzymes in metabolic pathways. The T3P® induced coupling reaction was applied in this study to the solution-phase peptide synthesis (SolPPS). Peptide bond formation occurred in a few minutes with high efficiency and no epimerization, generating water-soluble by-products, both using N-Boc or N-Fmoc amino acids. The optimized protocol, which was successfully applied to the iterative synthesis of a pentapeptide, also allowed for a decrease in the solvent volume, thus improving process sustainability. The protocol was finally extended to the liquid-phase peptide synthesis (LPPS), where the isolation of the peptide was performed using precipitation, thus also showing the suitability of this coupling reagent to this emerging technique.
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Affiliation(s)
- Alexia Mattellone
- Tolomelli-Cabri/P4I Lab—Peptidomimetics and Peptides Targeting Protein-Protein Interaction, Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum—University of Bologna, Via Gobetti 87, 40129 Bologna, Italy; (A.M.); (D.C.); (P.C.); (G.M.); (C.P.); (L.F.)
| | - Dario Corbisiero
- Tolomelli-Cabri/P4I Lab—Peptidomimetics and Peptides Targeting Protein-Protein Interaction, Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum—University of Bologna, Via Gobetti 87, 40129 Bologna, Italy; (A.M.); (D.C.); (P.C.); (G.M.); (C.P.); (L.F.)
| | - Paolo Cantelmi
- Tolomelli-Cabri/P4I Lab—Peptidomimetics and Peptides Targeting Protein-Protein Interaction, Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum—University of Bologna, Via Gobetti 87, 40129 Bologna, Italy; (A.M.); (D.C.); (P.C.); (G.M.); (C.P.); (L.F.)
| | - Giulia Martelli
- Tolomelli-Cabri/P4I Lab—Peptidomimetics and Peptides Targeting Protein-Protein Interaction, Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum—University of Bologna, Via Gobetti 87, 40129 Bologna, Italy; (A.M.); (D.C.); (P.C.); (G.M.); (C.P.); (L.F.)
| | - Chiara Palladino
- Tolomelli-Cabri/P4I Lab—Peptidomimetics and Peptides Targeting Protein-Protein Interaction, Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum—University of Bologna, Via Gobetti 87, 40129 Bologna, Italy; (A.M.); (D.C.); (P.C.); (G.M.); (C.P.); (L.F.)
| | - Alessandra Tolomelli
- Tolomelli-Cabri/P4I Lab—Peptidomimetics and Peptides Targeting Protein-Protein Interaction, Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum—University of Bologna, Via Gobetti 87, 40129 Bologna, Italy; (A.M.); (D.C.); (P.C.); (G.M.); (C.P.); (L.F.)
- Consorzio C.I.N.M.P.I.S. (National Interuniversity Research Consortium in Innovative Synthesis Methodologies and Processes) c/o, Alma Mater Studiorum—University of Bologna, Via Gobetti 87, 40129 Bologna, Italy
| | - Walter Cabri
- Tolomelli-Cabri/P4I Lab—Peptidomimetics and Peptides Targeting Protein-Protein Interaction, Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum—University of Bologna, Via Gobetti 87, 40129 Bologna, Italy; (A.M.); (D.C.); (P.C.); (G.M.); (C.P.); (L.F.)
- Consorzio C.I.N.M.P.I.S. (National Interuniversity Research Consortium in Innovative Synthesis Methodologies and Processes) c/o, Alma Mater Studiorum—University of Bologna, Via Gobetti 87, 40129 Bologna, Italy
| | - Lucia Ferrazzano
- Tolomelli-Cabri/P4I Lab—Peptidomimetics and Peptides Targeting Protein-Protein Interaction, Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum—University of Bologna, Via Gobetti 87, 40129 Bologna, Italy; (A.M.); (D.C.); (P.C.); (G.M.); (C.P.); (L.F.)
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30
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Rossino G, Marchese E, Galli G, Verde F, Finizio M, Serra M, Linciano P, Collina S. Peptides as Therapeutic Agents: Challenges and Opportunities in the Green Transition Era. Molecules 2023; 28:7165. [PMID: 37894644 PMCID: PMC10609221 DOI: 10.3390/molecules28207165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/05/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Peptides are at the cutting edge of contemporary research for new potent, selective, and safe therapeutical agents. Their rise has reshaped the pharmaceutical landscape, providing solutions to challenges that traditional small molecules often cannot address. A wide variety of natural and modified peptides have been obtained and studied, and many others are advancing in clinical trials, covering multiple therapeutic areas. As the demand for peptide-based therapies grows, so does the need for sustainable and environmentally friendly synthesis methods. Traditional peptide synthesis, while effective, often involves environmentally draining processes, generating significant waste and consuming vast resources. The integration of green chemistry offers sustainable alternatives, prioritizing eco-friendly processes, waste reduction, and energy conservation. This review delves into the transformative potential of applying green chemistry principles to peptide synthesis by discussing relevant examples of the application of such approaches to the production of active pharmaceutical ingredients (APIs) with a peptide structure and how these efforts are critical for an effective green transition era in the pharmaceutical field.
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Affiliation(s)
- Giacomo Rossino
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Emanuela Marchese
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
- Department of Health Sciences, University “Magna Graecia”, Viale Europa, 88100 Catanzaro, Italy
| | - Giovanni Galli
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Francesca Verde
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Matteo Finizio
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Massimo Serra
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Pasquale Linciano
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Simona Collina
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
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31
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Wang S, Teng H, Wang L, Li P, Yuan X, Sang X, Wu J, Yang L, Xu G. A Simple Screening and Optimization Bioprocess for Long-Chain Peptide Catalysts Applied to Asymmetric Aldol Reaction. Molecules 2023; 28:6985. [PMID: 37836827 PMCID: PMC10574572 DOI: 10.3390/molecules28196985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Peptides have demonstrated their efficacy as catalysts in asymmetric aldol reactions. But the constraints inherent in chemical synthesis have imposed limitations on the viability of long-chain peptide catalysts. A noticeable dearth of tools has impeded the swift and effective screening of peptide catalysts using biological methods. To address this, we introduce a straightforward bioprocess for the screening of peptide catalysts for asymmetric aldol reactions. We synthesized several peptides through this method and obtained a 15-amino acid peptide. This peptide exhibited asymmetric aldol catalytic activity, achieving 77% ee in DMSO solvent and 63% ee with over an 80.8% yield in DMSO mixed with a pH 9.0 buffer solution. The successful application of our innovative approach not only represents an advancement but also paves the way for currently unexplored research avenues.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Gang Xu
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
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32
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Oyebamiji AK, Akintelu SA, Akintayo ET, Akintayo CO, Aworinde HO, Adekunle OD. Dataset on substituents effect on biological activities of linear RGD-containing peptides as potential anti-angiotensin converting enzyme. Data Brief 2023; 50:109478. [PMID: 37600591 PMCID: PMC10432606 DOI: 10.1016/j.dib.2023.109478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/22/2023] Open
Abstract
The angiotensin converting enzyme inhibiting activity of linear rgd-containing peptides was investigated using in silico approach. The synthesized compound (parent compound) using experimental approach as well as its derivatives was subjected to computational examination using appropriate software. The investigated compounds were optimized using Spartan 14 while the docking study was executed via Pymol, AutoDock Tool, AutoDock Vina and discovery studio. The descriptors obtained (2D and 3D) were screened and the descriptor with highest capacity (squared correlation coefficient) was correlated to the calculated binding affinity. More so, the docking analysis was performed on the investigated linear rgd-containing peptides and angiotensin converting enzyme (PDB ID: 3nxq) via docking software and the resulted scoring and the types of the interaction observed were presented. Furthermore, (S)-dimethyl 2-(2-((S)-2-((R)-1-((S)-2-((S)-2-((S)-3-(4-chlorophenyl)-2-(1,3-dioxoisoindolin-2-yl)propanamido)-4-(methylthio)butanamido)-4-methylpentanoyl)pyrrolidine-2-carboxamido)-5-(3-((2,2,4,5,7-pentamethyl-2,3-dihydrobenzofuran-6-yl)sulfonyl)guanidino)pentanamido)acetamido)succinate (AB5) (compound with lowest binding affinity) and metformin were subjected to ADMET analysis and the resulted outcome were reported appropriately.
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Affiliation(s)
- Abel Kolawole Oyebamiji
- Computational Chemistry Research Laboratory, Industrial Chemistry Programme, Bowen University, Iwo, Osun State, Nigeria
| | - Sunday Adewale Akintelu
- Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Oyo State, Nigeria
| | - Emmanuel Temitope Akintayo
- Computational Chemistry Research Laboratory, Industrial Chemistry Programme, Bowen University, Iwo, Osun State, Nigeria
- Department of Chemistry, Ekiti State University, Ado-Ekiti, Nigeria
| | - Cecillia Olufunke Akintayo
- Computational Chemistry Research Laboratory, Industrial Chemistry Programme, Bowen University, Iwo, Osun State, Nigeria
- Department of Chemistry, Federal University, Oye-Ekiti, Nigeria
| | | | - Oluwatobi D. Adekunle
- Computational Chemistry Research Laboratory, Industrial Chemistry Programme, Bowen University, Iwo, Osun State, Nigeria
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33
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Zhou Y, Li H, Huang Y, Li J, Deng G, Chen G, Xi Z, Zhou C. Suppression of alpha-carbon racemization in peptide synthesis based on a thiol-labile amino protecting group. Nat Commun 2023; 14:5324. [PMID: 37658053 PMCID: PMC10474026 DOI: 10.1038/s41467-023-41115-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/22/2023] [Indexed: 09/03/2023] Open
Abstract
In conventional solid-phase peptide synthesis (SPPS), α-amino groups are protected with alkoxycarbonyl groups (e.g., 9-fluorenylmethoxycarbonyl [Fmoc]). However, during SPPS, inherent side reactions of the protected amino acids (e.g., α-C racemization and aspartimide formation) generate by-products that are hard to remove. Herein, we report a thiol-labile amino protecting group for SPPS, the 2,4-dinitro-6-phenyl-benzene sulfenyl (DNPBS) group, which is attached to the α-amino group via a S-N bond and can be quantitatively removed in minutes under nearly neutral conditions (1 M p-toluenethiol/pyridine). The use of DNPBS greatly suppresses the main side reactions observed during conventional SPPS. Although DNPBS SPPS is not as efficient as Fmoc SPPS, especially for synthesis of long peptides, DNPBS and Fmoc are orthogonal protecting groups; and thus DNPBS SPPS and Fmoc SPPS can be combined to synthesize peptides that are otherwise difficult to obtain.
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Affiliation(s)
- Yifei Zhou
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Hongjun Li
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Yi Huang
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Jiahui Li
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Guiyu Deng
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Gong Chen
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China.
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Lepori M, Schmid S, Barham JP. Photoredox catalysis harvesting multiple photon or electrochemical energies. Beilstein J Org Chem 2023; 19:1055-1145. [PMID: 37533877 PMCID: PMC10390843 DOI: 10.3762/bjoc.19.81] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/07/2023] [Indexed: 08/04/2023] Open
Abstract
Photoredox catalysis (PRC) is a cutting-edge frontier for single electron-transfer (SET) reactions, enabling the generation of reactive intermediates for both oxidative and reductive processes via photon activation of a catalyst. Although this represents a significant step towards chemoselective and, more generally, sustainable chemistry, its efficacy is limited by the energy of visible light photons. Nowadays, excellent alternative conditions are available to overcome these limitations, harvesting two different but correlated concepts: the use of multi-photon processes such as consecutive photoinduced electron transfer (conPET) and the combination of photo- and electrochemistry in synthetic photoelectrochemistry (PEC). Herein, we review the most recent contributions to these fields in both oxidative and reductive activations of organic functional groups. New opportunities for organic chemists are captured, such as selective reactions employing super-oxidants and super-reductants to engage unactivated chemical feedstocks, and scalability up to gram scales in continuous flow. This review provides comparisons between the two techniques (multi-photon photoredox catalysis and PEC) to help the reader to fully understand their similarities, differences and potential applications and to therefore choose which method is the most appropriate for a given reaction, scale and purpose of a project.
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Affiliation(s)
- Mattia Lepori
- Fakultät für Chemie und Pharmazie, Universität Regensburg, Universitatsstraße 31, 93040 Regensburg, Germany
| | - Simon Schmid
- Fakultät für Chemie und Pharmazie, Universität Regensburg, Universitatsstraße 31, 93040 Regensburg, Germany
| | - Joshua P Barham
- Fakultät für Chemie und Pharmazie, Universität Regensburg, Universitatsstraße 31, 93040 Regensburg, Germany
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35
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Alizadeh AA, Rasouli S, Jamshidi Kandjani O, Hemmati S, Dastmalchi S. Expression, Purification and Characterization of Functional Teduglutide Using GST Fusion System in Prokaryotic Cells. Adv Pharm Bull 2023; 13:592-600. [PMID: 37646058 PMCID: PMC10460804 DOI: 10.34172/apb.2023.064] [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: 05/28/2022] [Revised: 11/15/2022] [Accepted: 12/04/2022] [Indexed: 09/01/2023] Open
Abstract
Purpose Teduglutide is the first and only FDA-approved drug for long-term treatment of short bowel syndrome (SBS). The current study aimed to present an approach for production of teduglutide using recombinant DNA technology. Methods The coding gene for teduglutide was cloned into pGEX-2T vector, where coding sequence for factor Xa cleavage site was added between GST and teduglutide coding genes. The GST-teduglutide protein was overexpressed in E. coli BL21 (DE3) strain and affinity purified using glutathione sepharose affinity column. Results On-column proteolytic activity of factor Xa followed by size exclusion chromatography resulted in the pure teduglutide. Circular dichroism (CD) spectropolarimetry showed that the produced teduglutide folds into mainly α-helical structure (>50%), as expected. In mass spectroscopy analysis, the fragments of teduglutide resulted by cyanogen bromide cleavage as well as those expected theoretically due to mass fragmentation were identified. The functionality of the produced peptide was evaluated by measuring its proliferative effect on Caco2 intestinal epithelial cells, and the results indicated that produced teduglutide induces cell proliferation by 19±0.30 and 33±7.82 % at 1.21 and 3.64 µM concentrations, respectively, compared to untreated cells. Conclusion Teduglutide was successfully expressed and purified and its functionality and structural integrity were confirmed by in vitro experiments. We believe that the experimental-scale method presented in the current study can be useful for pilot-scale and also industrial-scale production of teduglutide.
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Affiliation(s)
- Ali Akbar Alizadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saba Rasouli
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Salar Hemmati
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
- Faculty of Pharmacy, Near East University, Po.Box: 99138, Nicosia, North Cyprus, Mersin 10, Turkey
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36
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Nakahara H, Sennari G, Noguchi Y, Hirose T, Sunazuka T. Development of a nitrogen-bound hydrophobic auxiliary: application to solid/hydrophobic-tag relay synthesis of calpinactam. Chem Sci 2023; 14:6882-6889. [PMID: 37389244 PMCID: PMC10306108 DOI: 10.1039/d3sc01432k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 04/28/2023] [Indexed: 07/01/2023] Open
Abstract
In the last couple of decades, technologies and strategies for peptide synthesis have advanced rapidly. Although solid-phase peptide synthesis (SPPS) and liquid-phase peptide synthesis (LPPS) have contributed significantly to the development of the field, there have been remaining challenges for C-terminal modifications of peptide compounds in SPPS and LPPS. Orthogonal to the current standard approach that relies on installation of a carrier molecule at the C-terminus of amino acids, we developed a new hydrophobic-tag carbonate reagent which facilitated robust preparation of nitrogen-tag-supported peptide compounds. This auxiliary was easily installed on a variety of amino acids including oligopeptides that have a broad range of noncanonical residues, allowing simple purification of the products by crystallization and filtration. We demonstrated a de novo solid/hydrophobic-tag relay synthesis (STRS) strategy using the nitrogen-bound auxiliary for total synthesis of calpinactam.
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Affiliation(s)
- Hiroki Nakahara
- Ōmura Satoshi Memorial Institute and Graduate School of Infection Control Sciences, Kitasato University 5-9-1 Shirokane, Minato-ku Tokyo 108-8641 Japan
| | - Goh Sennari
- Ōmura Satoshi Memorial Institute and Graduate School of Infection Control Sciences, Kitasato University 5-9-1 Shirokane, Minato-ku Tokyo 108-8641 Japan
| | - Yoshihiko Noguchi
- Ōmura Satoshi Memorial Institute and Graduate School of Infection Control Sciences, Kitasato University 5-9-1 Shirokane, Minato-ku Tokyo 108-8641 Japan
| | - Tomoyasu Hirose
- Ōmura Satoshi Memorial Institute and Graduate School of Infection Control Sciences, Kitasato University 5-9-1 Shirokane, Minato-ku Tokyo 108-8641 Japan
| | - Toshiaki Sunazuka
- Ōmura Satoshi Memorial Institute and Graduate School of Infection Control Sciences, Kitasato University 5-9-1 Shirokane, Minato-ku Tokyo 108-8641 Japan
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37
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Sugisawa N, Ando A, Fuse S. Rapid and column-chromatography-free peptide chain elongation via a one-flow, three-component coupling approach. Chem Sci 2023; 14:6986-6991. [PMID: 37389269 PMCID: PMC10306071 DOI: 10.1039/d3sc01333b] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/04/2023] [Indexed: 07/01/2023] Open
Abstract
Short peptides are extremely important as drugs and building blocks for the syntheses of longer peptides. Both solid- and liquid-phase peptide syntheses suffer from a large number of synthetic steps, high cost, and/or tedious purification. Here, we developed a rapid, mild, inexpensive, and column-chromatography-free peptide chain elongation via a one-flow, three-component coupling (3CC) approach that is the first to use α-amino acid N-carboxy anhydrides (α-NCAs) both as electrophiles and nucleophiles. We demonstrated the high-yielding and column-chromatography-free syntheses of 17 tripeptides, as well as a gram-scale synthesis of a tripeptide. The total synthesis of beefy meaty peptide was achieved by repeating the 3CC approach with the addition of only one column chromatographic purification. We also demonstrated a one-flow tripeptide synthesis via in situ preparation of α-NCA starting from three readily available protected amino acids. With this study, we achieved dramatic reductions in both time and cost compared with typical solid-phase synthesis.
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Affiliation(s)
- Naoto Sugisawa
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University Nagoya 464-8601 Japan
| | - Akira Ando
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University Nagoya 464-8601 Japan
| | - Shinichiro Fuse
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University Nagoya 464-8601 Japan
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38
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Vivenzio G, Scala MC, Marino P, Manfra M, Campiglia P, Sala M. Dipropyleneglycol Dimethylether, New Green Solvent for Solid-Phase Peptide Synthesis: Further Challenges to Improve Sustainability in the Development of Therapeutic Peptides. Pharmaceutics 2023; 15:1773. [PMID: 37376220 DOI: 10.3390/pharmaceutics15061773] [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: 05/30/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
In recent years, peptides have gained more success as therapeutic compounds. Nowadays, the preferred method to obtain peptides is solid-phase peptide synthesis (SPPS), which does not respect the principles of green chemistry due to the large number of toxic reagents and solvents used. The aim of this work was to research and study an environmentally sustainable solvent able to replace dimethylformamide (DMF) in fluorenyl methoxycarbonyl (Fmoc) solid-phase peptide synthesis. Herein, we report the use of dipropyleneglycol dimethylether (DMM), a well-known green solvent with low human toxicity following oral, inhalant, and dermal exposure and that is easily biodegradable. Some tests were needed to evaluate its applicability to all the steps of SPPS, such as amino acid solubility, resin swelling, deprotection kinetics, and coupling tests. Once the best green protocol was established, it was applied to the synthesis of different length peptides to study some of the fundamental parameters of green chemistry, such as PMI (process mass intensity) and the recycling of solvent. It was revealed that DMM is a valuable alternative to DMF in all steps of solid-phase peptide synthesis.
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Affiliation(s)
- Giovanni Vivenzio
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084 Salerno, Italy
| | - Maria Carmina Scala
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084 Salerno, Italy
| | - Pasquale Marino
- Department of Sciences, University of Basilicata, Via dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Michele Manfra
- Department of Sciences, University of Basilicata, Via dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084 Salerno, Italy
| | - Marina Sala
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084 Salerno, Italy
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Chen D, Xu L, Ren B, Wang Z, Liu C. Triflylpyridinium as Coupling Reagent for Rapid Amide and Ester Synthesis. Org Lett 2023. [PMID: 37290965 DOI: 10.1021/acs.orglett.3c01598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
An effective method has been developed to facilitate the synthesis of amides and esters at ambient temperature within 5 min, in which a stable and easily accessible triflylpyridinium reagent is used. Remarkably, this method not only has a wide range of substrate compatibility but also could realize the scalable synthesis of peptide and ester via a continuous flow process. Moreover, excellent chirality retentions are presented during activation of carboxylic acid.
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Affiliation(s)
- Du Chen
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangxuan Xu
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bowen Ren
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zian Wang
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Liu
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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40
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Kazmirchuk TDD, Bradbury-Jost C, Withey TA, Gessese T, Azad T, Samanfar B, Dehne F, Golshani A. Peptides of a Feather: How Computation Is Taking Peptide Therapeutics under Its Wing. Genes (Basel) 2023; 14:1194. [PMID: 37372372 DOI: 10.3390/genes14061194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Leveraging computation in the development of peptide therapeutics has garnered increasing recognition as a valuable tool to generate novel therapeutics for disease-related targets. To this end, computation has transformed the field of peptide design through identifying novel therapeutics that exhibit enhanced pharmacokinetic properties and reduced toxicity. The process of in-silico peptide design involves the application of molecular docking, molecular dynamics simulations, and machine learning algorithms. Three primary approaches for peptide therapeutic design including structural-based, protein mimicry, and short motif design have been predominantly adopted. Despite the ongoing progress made in this field, there are still significant challenges pertaining to peptide design including: enhancing the accuracy of computational methods; improving the success rate of preclinical and clinical trials; and developing better strategies to predict pharmacokinetics and toxicity. In this review, we discuss past and present research pertaining to the design and development of in-silico peptide therapeutics in addition to highlighting the potential of computation and artificial intelligence in the future of disease therapeutics.
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Affiliation(s)
- Thomas David Daniel Kazmirchuk
- Department of Biology, and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Calvin Bradbury-Jost
- Department of Biology, and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Taylor Ann Withey
- Department of Biology, and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Tadesse Gessese
- Department of Biology, and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Taha Azad
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC J1H 5N4, Canada
| | - Bahram Samanfar
- Department of Biology, and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, ON K1S 5B6, Canada
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, ON K1A 0C6, Canada
| | - Frank Dehne
- School of Computer Science, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Ashkan Golshani
- Department of Biology, and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, ON K1S 5B6, Canada
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41
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Wu A, Yamamoto H. Super silyl-based stable protecting groups for both the C- and N-terminals of peptides: applied as effective hydrophobic tags in liquid-phase peptide synthesis. Chem Sci 2023; 14:5051-5061. [PMID: 37206381 PMCID: PMC10189889 DOI: 10.1039/d3sc01239e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Tag-assisted liquid-phase peptide synthesis (LPPS) is one of the important processes in peptide synthesis in pharmaceutical discovery. Simple silyl groups have positive effects when incorporated in the tags due to their hydrophobic properties. Super silyl groups contain several simple silyl groups and play an important role in modern aldol reactions. In view of the unique structural architecture and hydrophobic properties of the super silyl groups, herein, two new types of stable super silyl-based groups (tris(trihexylsilyl)silyl group and propargyl super silyl group) were developed as hydrophobic tags to increase the solubility in organic solvents and the reactivity of peptides during LPPS. The tris(trihexylsilyl)silyl group can be installed at the C-terminal of the peptides in ester form and N-terminal in carbamate form for peptide synthesis and it is compatible with hydrogenation conditions (Cbz chemistry) and Fmoc-deprotection conditions (Fmoc chemistry). The propargyl super silyl group is acid-resistant, which is compatible with Boc chemistry. Both tags are complementary to each other. The preparation of these tags requires less steps than previously reported tags. Nelipepimut-S was synthesized successfully with different strategies using these two types of super silyl tags.
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Affiliation(s)
- An Wu
- Peptide Research Centre, Chubu University 1200 Matsumoto-cho Kasugai Aichi 487-8501 Japan
| | - Hisashi Yamamoto
- Peptide Research Centre, Chubu University 1200 Matsumoto-cho Kasugai Aichi 487-8501 Japan
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42
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Ouellet S, Ferguson L, Lau AZ, Lim TKY. CysPresso: a classification model utilizing deep learning protein representations to predict recombinant expression of cysteine-dense peptides. BMC Bioinformatics 2023; 24:200. [PMID: 37193950 PMCID: PMC10189939 DOI: 10.1186/s12859-023-05327-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/08/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Cysteine-dense peptides (CDPs) are an attractive pharmaceutical scaffold that display extreme biochemical properties, low immunogenicity, and the ability to bind targets with high affinity and selectivity. While many CDPs have potential and confirmed therapeutic uses, synthesis of CDPs is a challenge. Recent advances have made the recombinant expression of CDPs a viable alternative to chemical synthesis. Moreover, identifying CDPs that can be expressed in mammalian cells is crucial in predicting their compatibility with gene therapy and mRNA therapy. Currently, we lack the ability to identify CDPs that will express recombinantly in mammalian cells without labour intensive experimentation. To address this, we developed CysPresso, a novel machine learning model that predicts recombinant expression of CDPs based on primary sequence. RESULTS We tested various protein representations generated by deep learning algorithms (SeqVec, proteInfer, AlphaFold2) for their suitability in predicting CDP expression and found that AlphaFold2 representations possessed the best predictive features. We then optimized the model by concatenation of AlphaFold2 representations, time series transformation with random convolutional kernels, and dataset partitioning. CONCLUSION Our novel model, CysPresso, is the first to successfully predict recombinant CDP expression in mammalian cells and is particularly well suited for predicting recombinant expression of knottin peptides. When preprocessing the deep learning protein representation for supervised machine learning, we found that random convolutional kernel transformation preserves more pertinent information relevant for predicting expressibility than embedding averaging. Our study showcases the applicability of deep learning-based protein representations, such as those provided by AlphaFold2, in tasks beyond structure prediction.
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Affiliation(s)
| | - Larissa Ferguson
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Angus Z Lau
- Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Physical Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Tony K Y Lim
- , Vancouver, Canada.
- Department of Pharmacology, University of Cambridge, Cambridge, UK.
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43
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Verma V, Bade I, Karde V, Heng JYY. Experimental Elucidation of Templated Crystallization and Secondary Processing of Peptides. Pharmaceutics 2023; 15:pharmaceutics15041288. [PMID: 37111774 PMCID: PMC10142637 DOI: 10.3390/pharmaceutics15041288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The crystallization of peptides offers a sustainable and inexpensive alternative to the purification process. In this study, diglycine was crystallised in porous silica, showing the porous templates' positive yet discriminating effect. The diglycine induction time was reduced by five-fold and three-fold upon crystallising in the presence of silica with pore sizes of 6 nm and 10 nm, respectively. The diglycine induction time had a direct relationship with the silica pore size. The stable form (α-form) of diglycine was crystallised in the presence of porous silica, with the diglycine crystals obtained associated with the silica particles. Further, we studied the mechanical properties of diglycine tablets for their tabletability, compactability, and compressibility. The mechanical properties of the diglycine tablets were similar to those of pure MCC, even with the presence of diglycine crystals in the tablets. The diffusion studies of the tablets using the dialysis membrane presented an extended release of diglycine through the dialysis membrane, confirming that the peptide crystal can be used for oral formulation. Hence, the crystallization of peptides preserved their mechanical and pharmacological properties. More data on different peptides can help us produce oral formulation peptides faster than usual.
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Affiliation(s)
- Vivek Verma
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Isha Bade
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Vikram Karde
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Jerry Y Y Heng
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
- Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, UK
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44
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Edson CB, Liu M, Totsingan F, O’Berg E, Salvucci J, Dao U, Khare SD, Gross RA. Monomer Choice Influences N-Acryloyl Amino Acid Grafter Conversion via Protease Catalysis. Biomacromolecules 2023; 24:1798-1809. [PMID: 36996092 PMCID: PMC10139737 DOI: 10.1021/acs.biomac.3c00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
End-capped peptides modified with reactive functional groups on the N-terminus provide a route to prepare peptide-polymer conjugates for a broad range of applications. Unfortunately, current chemical methods to construct modified peptides rely largely on solid-phase peptide synthesis (SPPS), which lacks green preparative characteristics and is costly, thus limiting its applicability to specialty applications such as regenerative medicine. This work evaluates N-terminally modified N-acryloyl-glutamic acid diethyl ester, N-acryloyl-leucine ethyl ester, and N-acryloyl-alanine ethyl ester as grafters and papain as the protease for the direct addition of amino acid ethyl ester (AA-OEt) monomers via protease-catalyzed peptide synthesis (PCPS) and the corresponding formation of N-acryloyl-functionalized oligopeptides in a one-pot aqueous reaction. It was hypothesized that by building N-acryloyl grafters from AA-OEt monomers that are known to be good substrates for papain in PCPS, the corresponding grafters would yield high grafter conversions, high ratio of grafter-oligopeptide to free NH2-oligopeptide, and high overall yield. However, this work demonstrates based on the grafter/monomers studied herein that the dominant factor in N-acryloyl-AA-OEt grafter conversion is the co-monomer used in co-oligomerizations. Computational modeling using Rosetta qualitatively recapitulates the results and provides insight into the structural and energetic bases underlying substrate selectivity. The findings herein expand our knowledge of factors that determine the efficiency of preparing N-acryloyl-terminated oligopeptides by PCPS that could provide practical routes to peptide macromers for conjugation to polymers and surfaces for a broad range of applications.
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Affiliation(s)
- Cody B. Edson
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8 St. Troy, NY 12180
| | - Melinda Liu
- Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Filbert Totsingan
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8 St. Troy, NY 12180
| | - Evan O’Berg
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8 St. Troy, NY 12180
| | - John Salvucci
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8 St. Troy, NY 12180
| | - Uyen Dao
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8 St. Troy, NY 12180
| | - Sagar D. Khare
- Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Richard A. Gross
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8 St. Troy, NY 12180
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45
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Protease-catalyzed synthesis of α-poly-L-Lysine and amphiphilic poly(L-lysine-co-L-phenylalanine) in a neat non-toxic organic solvent. Bioprocess Biosyst Eng 2023; 46:515-522. [PMID: 36539643 DOI: 10.1007/s00449-022-02836-3] [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: 10/12/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
Subtilisin Carlsberg (alkaline protease from Bacillus licheniformis) catalyzes the syntheses of high molecular weights (ca. 20 KDa) cationic α-poly-L-lysine and amphiphilic poly(α-L-lysine-co-L-phenylalanine) in neat organic solvent. The synthesis is conducted in liquid 1,1,1,2-tetrafluoroethane solvent, which is a hydrophobic non-toxic gas that does not deplete the ozone layer and approved for pharmaceutical applications. Solubility of substrates and adequate protease activity in this system with low water environment limits the reaction of hydrolysis of the growing peptide chains. The pressurization of this organic compressed fluid to liquid has low-pressure requirements (25 bar, 40 ºC), and its complete evaporation at atmospheric pressure after completing the reaction ensures solvent-free residues in products. The resulting polypeptides present null cytotoxicity according to MTT and NR analyses, as well as Calcein/EthD-1 assay in human cells.
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46
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Agrawal P, Wilkstein K, Guinn E, Mason M, Serrano Martinez CI, Saylae J. A Review of Tangential Flow Filtration: Process Development and Applications in the Pharmaceutical Industry. Org Process Res Dev 2023. [DOI: 10.1021/acs.oprd.2c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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47
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Harel O, Jbara M. Chemical Synthesis of Bioactive Proteins. Angew Chem Int Ed Engl 2023; 62:e202217716. [PMID: 36661212 DOI: 10.1002/anie.202217716] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/21/2023]
Abstract
Nature has developed a plethora of protein machinery to operate and maintain nearly every task of cellular life. These processes are tightly regulated via post-expression modifications-transformations that modulate intracellular protein synthesis, folding, and activation. Methods to prepare homogeneously and precisely modified proteins are essential to probe their function and design new bioactive modalities. Synthetic chemistry has contributed remarkably to protein science by allowing the preparation of novel biomacromolecules that are often challenging or impractical to prepare via common biological means. The ability to chemically build and precisely modify proteins has enabled the production of new molecules with novel physicochemical properties and programmed activity for biomedical research, diagnostic, and therapeutic applications. This minireview summarizes recent developments in chemical protein synthesis to produce bioactive proteins, with emphasis on novel analogs with promising in vitro and in vivo activity.
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Affiliation(s)
- Omer Harel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Muhammad Jbara
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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48
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Jackson MA, Xie J, Nguyen LTT, Wang X, Yap K, Harvey PJ, Gilding EK, Craik DJ. Plant-based production of an orally active cyclotide for the treatment of multiple sclerosis. Transgenic Res 2023; 32:121-133. [PMID: 36930229 PMCID: PMC10102037 DOI: 10.1007/s11248-023-00341-1] [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: 01/30/2023] [Accepted: 02/24/2023] [Indexed: 03/18/2023]
Abstract
Multiple sclerosis (MS) is a debilitating disease that requires prolonged treatment with often severe side effects. One experimental MS therapeutic currently under development is a single amino acid mutant of a plant peptide termed kalata B1, of the cyclotide family. Like all cyclotides, the therapeutic candidate [T20K]kB1 is highly stable as it contains a cyclic backbone that is cross-linked by three disulfide bonds in a knot-like structure. This stability is much sought after for peptide drugs, which despite exquisite selectivity for their targets, are prone to rapid degradation in human serum. In preliminary investigations, it was found that [T20K]kB1 retains oral activity in experimental autoimmune encephalomyelitis, a model of MS in mice, thus opening up opportunities for oral dosing of the peptide. Although [T20K]kB1 can be synthetically produced, a recombinant production system provides advantages, specifically for reduced scale-up costs and reductions in chemical waste. In this study, we demonstrate the capacity of the Australian native Nicotiana benthamiana plant to produce a structurally identical [T20K]kB1 to that of the synthetic peptide. By optimizing the co-expressed cyclizing enzyme, precursor peptide arrangements, and transgene regulatory regions, we demonstrate a [T20K]kB1 yield in crude peptide extracts of ~ 0.3 mg/g dry mass) in whole plants and close to 1.0 mg/g dry mass in isolated infiltrated leaves. With large-scale plant production facilities coming on-line across the world, the sustainable and cost-effective production of cyclotide-based therapeutics is now within reach.
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Affiliation(s)
- Mark A Jackson
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jing Xie
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Linh T T Nguyen
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Xiaohan Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peta J Harvey
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia.
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Chaudhary S, Ali Z, Tehseen M, Haney EF, Pantoja-Angles A, Alshehri S, Wang T, Clancy GJ, Ayach M, Hauser C, Hong PY, Hamdan SM, Hancock REW, Mahfouz M. Efficient in planta production of amidated antimicrobial peptides that are active against drug-resistant ESKAPE pathogens. Nat Commun 2023; 14:1464. [PMID: 36928189 PMCID: PMC10020429 DOI: 10.1038/s41467-023-37003-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
Antimicrobial peptides (AMPs) are promising next-generation antibiotics that can be used to combat drug-resistant pathogens. However, the high cost involved in AMP synthesis and their short plasma half-life render their clinical translation a challenge. To address these shortcomings, we report efficient production of bioactive amidated AMPs by transient expression of glycine-extended AMPs in Nicotiana benthamiana line expressing the mammalian enzyme peptidylglycine α-amidating mono-oxygenase (PAM). Cationic AMPs accumulate to substantial levels in PAM transgenic plants compare to nontransgenic N. benthamiana. Moreover, AMPs purified from plants exhibit robust killing activity against six highly virulent and antibiotic resistant ESKAPE pathogens, prevent their biofilm formation, analogous to their synthetic counterparts and synergize with antibiotics. We also perform a base case techno-economic analysis of our platform, demonstrating the potential economic advantages and scalability for industrial use. Taken together, our experimental data and techno-economic analysis demonstrate the potential use of plant chassis for large-scale production of clinical-grade AMPs.
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Affiliation(s)
- Shahid Chaudhary
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Muhammad Tehseen
- Laboratory of DNA Replication and Recombination, Division of Biological Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Evan F Haney
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Aarón Pantoja-Angles
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Salwa Alshehri
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Biochemistry Department, Faculty of Science, University of Jeddah, Jeddah, 21577, Saudi Arabia
| | - Tiannyu Wang
- Water Desalination and Reuse Center, Division of Biological Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Gerard J Clancy
- Analytical Chemistry Core Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Maya Ayach
- Imaging & Characterization Core Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Charlotte Hauser
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, Division of Biological Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Division of Biological Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Robert E W Hancock
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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50
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Digal LD, Kirkeby EK, Austin MJ, Roberts AG. Design and Evaluation of Ambiphilic Aryl Thiol-Iminium-Based Molecules for Organocatalyzed Thioacyl Aminolysis. ACS OMEGA 2023; 8:9319-9325. [PMID: 36936301 PMCID: PMC10018527 DOI: 10.1021/acsomega.2c07586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Progress toward the design and synthesis of ambiphilic aryl thiol-iminium-based small molecules for organocatalyzed thioacyl aminolysis is reported. Here we describe the synthesis of a novel tetrahydroisoquinoline-derived scaffold, bearing both thiol and iminium functionalities, capable of promoting the transthioesterification and subsequent amine capture reactions necessary to achieve organocatalyzed thioacyl aminolysis. Model studies demonstrate the ability of this designed organocatalyst to deliver critical intermediates capable of undergoing these individual reactions necessary for the proposed process. Future design improvements and directions toward cysteine-independent organocatalyzed native chemical ligation are discussed.
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