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Yan C, Fyfe C, Minty L, Barrington H, Jamieson C, Reid M. Computer vision as a new paradigm for monitoring of solution and solid phase peptide synthesis. Chem Sci 2023; 14:11872-11880. [PMID: 37920332 PMCID: PMC10619640 DOI: 10.1039/d3sc01383a] [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: 03/15/2023] [Accepted: 10/04/2023] [Indexed: 11/04/2023] Open
Abstract
We report a strategy for the camera-enabled non-contact colourimetric reaction monitoring and optimisation of amide bond formation, mediated by coupling reagents. For amide bond formation in solution phase, investigation of reactions mediated by HATU, PyAOP, and DIC/Oxyma evidenced correlations between colour parameters extracted from video data and conversion to amide product measured by off-line HPLC analysis of concentration. These correlations, supported by mutual information analysis, were further investigated using video recordings of solid phase peptide synthesis (SPPS), co-analysed by off-line HPLC to track remaining unreacted substrate in solution. An optimisation method of coupling time in SPPS was derived from ΔE (a measurement of colour contrast), giving comparable isolated peptide yield and purity at 65-95% reduced overall reaction time. The same colour data enabled data-rich monitoring of reaction rate attenuation, consisted with computationally-derived measures of amino acid steric bulk. These findings provide a foundation for exploring the use of camera technology and computer vision towards automated and online mechanistic profiling of SPPS.
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Affiliation(s)
- Chunhui Yan
- WestCHEM Department of Pure & Applied Chemistry, University of Strathclyde Glasgow UK
| | - Calum Fyfe
- WestCHEM Department of Pure & Applied Chemistry, University of Strathclyde Glasgow UK
| | - Laura Minty
- WestCHEM Department of Pure & Applied Chemistry, University of Strathclyde Glasgow UK
| | - Henry Barrington
- WestCHEM Department of Pure & Applied Chemistry, University of Strathclyde Glasgow UK
| | - Craig Jamieson
- WestCHEM Department of Pure & Applied Chemistry, University of Strathclyde Glasgow UK
| | - Marc Reid
- WestCHEM Department of Pure & Applied Chemistry, University of Strathclyde Glasgow UK
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de la Torre BG, Ramkisson S, Albericio F, Lopez J. Refractive Index: The Ultimate Tool for Real-Time Monitoring of Solid-Phase Peptide Synthesis. Greening the Process. Org Process Res Dev 2021. [DOI: 10.1021/acs.oprd.1c00051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Beatriz G. de la Torre
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Shaveer Ramkisson
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, and Department of Organic Chemistry, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - John Lopez
- Novartis Pharma AG, Lichtstrasse 35, 4056 Basel, Switzerland
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Chandra K, Naoum JN, Roy TK, Gilon C, Gerber RB, Friedler A. Mechanistic studies of malonic acid-mediated in situ acylation. Biopolymers 2015; 104:495-505. [PMID: 25846609 DOI: 10.1002/bip.22654] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/13/2015] [Accepted: 03/30/2015] [Indexed: 11/05/2022]
Abstract
We have previously introduced an easy to perform, cost-effective and highly efficient acetylation technique for solid phase synthesis (SPPS). Malonic acid is used as a precursor and the reaction proceeds via a reactive ketene that acetylates the target amine. Here we present a detailed mechanistic study of the malonic acid-mediated acylation. The influence of reaction conditions, peptide sequence and reagents was systematically studied. Our results show that the methodology can be successfully applied to different types of peptides and nonpeptidic molecules irrespective of their structure, sequence, or conformation. Using alkyl, phenyl, and benzyl malonic acid, we synthesized various acyl peptides with almost quantitative yields. The ketenes obtained from the different malonic acid derived precursors were characterized by in situ (1) H-NMR. The reaction proceeded in short reaction times and resulted in excellent yields when using uronium-based coupling agents, DIPEA as a base, DMF/DMSO/NMP as solvents, Rink amide/Wang/Merrifield resins, temperature of 20°C, pH 8-12 and 5 min preactivation at inert atmosphere. The reaction was unaffected by Lewis acids, transition metal ions, surfactants, or salt. DFT studies support the kinetically favorable concerted mechanism for CO2 and ketene formation that leads to the thermodynamically stable acylated products. We conclude that the malonic acid-mediated acylation is a general method applicable to various target molecules.
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Affiliation(s)
- Koushik Chandra
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Johnny N Naoum
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Tapta Kanchan Roy
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel.,The Fritz Haber Research Center, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Chaim Gilon
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - R Benny Gerber
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel.,The Fritz Haber Research Center, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel.,Department of Chemistry, University of California, Irvine, California, 92697
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
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Chandra K, Roy TK, Naoum JN, Gilon C, Gerber RB, Friedler A. A highly efficient in situ N-acetylation approach for solid phase synthesis. Org Biomol Chem 2014; 12:1879-84. [DOI: 10.1039/c3ob42096e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In situ peptide acetylation.
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Affiliation(s)
- Koushik Chandra
- Institute of Chemistry
- The Hebrew University of Jerusalem
- Givat Ram, Israel
| | - Tapta Kanchan Roy
- Institute of Chemistry
- The Hebrew University of Jerusalem
- Givat Ram, Israel
- The Fritz Haber Research Center
- The Hebrew University of Jerusalem
| | - Johnny N. Naoum
- Institute of Chemistry
- The Hebrew University of Jerusalem
- Givat Ram, Israel
| | - Chaim Gilon
- Institute of Chemistry
- The Hebrew University of Jerusalem
- Givat Ram, Israel
| | - R. Benny Gerber
- Institute of Chemistry
- The Hebrew University of Jerusalem
- Givat Ram, Israel
- The Fritz Haber Research Center
- The Hebrew University of Jerusalem
| | - Assaf Friedler
- Institute of Chemistry
- The Hebrew University of Jerusalem
- Givat Ram, Israel
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5
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Furbert P, Lu C, Winograd N, DeLouise L. Label-free optical detection of peptide synthesis on a porous silicon scaffold/sensor. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:2908-15. [PMID: 18247639 PMCID: PMC2573388 DOI: 10.1021/la703053h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Mesoporous porous silicon (PSi) microcavity sensors are used to conduct conventional solid-phase peptide synthesis. The sensor optical response provides a convenient means to monitor the synthesis reaction in a nondestructive manner. Measurements indicate that peptide synthesis occurs only when the PSi sensor/scaffold is amine-terminated using, for example, the amino silane or deprotected acid-labile Rink linker. Equivalent coupling efficiencies of the first amino acid to both amine terminations are observed. Kinetic studies indicate that coupling reactions are 90% complete in 1 h. Quantitative analysis of the optical response following the synthesis of homo-oligopeptides (4-mers) suggests that coupling efficiencies and/or optical thickness changes depend on the peptide length. The synthesis of the cell adhesive oligopeptide (RGD) was monitored by the optical sensor response and validated by the cell culture of primary dermal fibroblasts. Secondary ion mass spectrometry (SIMS) analysis successfully detected peptide on the silicon wafer adjacent to the PSi. Our findings suggest the potential to exploit the high surface area, efficient coupling, and intrinsic optical detection properties of PSi for label-free high-throughput screening.
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Affiliation(s)
- Patrick Furbert
- Department of Microbiology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, New York 14642, USA
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Bagno A, Bicciato S, Dettin M, Di Bello C. A novel algorithm for the coupling control in solid-phase peptide synthesis. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1997; 50:231-7. [PMID: 9309587 DOI: 10.1111/j.1399-3011.1997.tb01189.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This paper describes a new method for the evaluation of conductimetric data collected during the in-line monitoring of the coupling step in solid-phase peptide synthesis. The control scheme relies on a feed-forward artificial neural network algorithm which can predict the final yield of the reaction within its initial 5 min by analyzing the conductivity signal profile. The yield values predicted by the artificial neural network algorithm result in good accordance with the data obtained by the commonly used ninhydrin test.
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Affiliation(s)
- A Bagno
- Department of Chemical Processes Engineering, Faculty of Engineering, University of Padova, Italy
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Fox JE, Newton R, Stroud CH. A new detector for fully automatic peptide synthesis. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1991; 38:62-5. [PMID: 1938106 DOI: 10.1111/j.1399-3011.1991.tb01410.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A new method of monitoring the rate of reactions in solid phase peptide synthesis is described. A conductivity detector in the reaction cell enables the deprotection, washing, and subsequent coupling stages to be examined in detail. The half lives of the reactions can be calculated and hence the optimum reaction times predicted. The aggregation of peptide chains and subsequent collapse of the resin is observed. Difficult sequences are sensed and appropriate action taken completely automatically.
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Affiliation(s)
- J E Fox
- Alta Bioscience, School of Biochemistry, University of Birmingham, U.K
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