1
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Haque M, Forte N, Baker JR. Site-selective lysine conjugation methods and applications towards antibody-drug conjugates. Chem Commun (Camb) 2021; 57:10689-10702. [PMID: 34570125 PMCID: PMC8516052 DOI: 10.1039/d1cc03976h] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Site-selective protein modification is of significant interest in chemical biology research, with lysine residues representing a particularly challenging target. Whilst lysines are popular for bioconjugation, due to their nucleophilicity, solvent accessibility and the stability of the resultant conjugates, their high abundance means site-selectivity is very difficult to achieve. Antibody-drug conjugates (ADCs) present a powerful therapeutic application of protein modification, and have often relied extensively upon lysine bioconjugation for their synthesis. Here we discuss advances in methodologies for achieving site-selective lysine modification, particularly within the context of antibody conjugate construction, including the cysteine-to-lysine transfer (CLT) protocol which we have recently reported.
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Affiliation(s)
- Muhammed Haque
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
| | - Nafsika Forte
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
| | - James R Baker
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
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2
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Bokhtia RM, Panda SS, Girgis AS, Honkanadavar HH, Ibrahim TS, George RF, Kashef MT, Fayad W, Sakhuja R, Abdel-Aal EH, Al-Mahmoudy AMM. Fluoroquinolone-3-carboxamide Amino Acid Conjugates: Synthesis, Antibacterial Properties And Molecular Modeling Studies. Med Chem 2020; 17:71-84. [DOI: 10.2174/1573406415666190904143852] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 12/14/2022]
Abstract
Background:
Bacterial infections are considered as one of the major global health
threats, so it is very essential to design and develop new antibacterial agents to overcome the
drawbacks of existing antibacterial agents.
Method:
The aim of this work is to synthesize a series of new fluoroquinolone-3-carboxamide
amino acid conjugates by molecular hybridization. We utilized benzotriazole chemistry to synthesize
the desired hybrid conjugates.
Result:
All the conjugates were synthesized in good yields, characterized, evaluated for their antibacterial
activity. The compounds were screened for their antibacterial activity using methods
adapted from the Clinical and Laboratory Standards Institute. Synthesized conjugates were tested
for activity against medically relevant pathogens; Escherichia coli (ATCC 25922), Pseudomonas
aeruginosa (ATCC 27856) Staphylococcus aureus (ATCC 25923) and Enterococcus faecalis
(ATCC 19433).
Conclusion:
The observed antibacterial experimental data indicates the selectivity of our synthesized
conjugates against E.Coli. The protecting group on amino acids decreases the antibacterial
activity. The synthesized conjugates are non-toxic to the normal cell lines. The experimental data
were supported by computational studies.
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Affiliation(s)
- Riham M. Bokhtia
- Department of Chemistry & Physics, Augusta University, Augusta, GA 30912, United States
| | - Siva S. Panda
- Department of Chemistry & Physics, Augusta University, Augusta, GA 30912, United States
| | - Adel S. Girgis
- Department of Pesticide Chemistry, National Research Centre, Dokki, Giza 12622, Egypt
| | | | - Tarek S. Ibrahim
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Egypt
| | - Riham F. George
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Mona T. Kashef
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Walid Fayad
- Drug Bioassay-Cell Culture Laboratory, Pharmacognosy Department, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Rajeev Sakhuja
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333 031, Rajasthan, India
| | - Eatedal H. Abdel-Aal
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Egypt
| | - Amany M. M. Al-Mahmoudy
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Egypt
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3
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Forte N, Benni I, Karu K, Chudasama V, Baker JR. Cysteine-to-lysine transfer antibody fragment conjugation. Chem Sci 2019; 10:10919-10924. [PMID: 32190247 PMCID: PMC7066670 DOI: 10.1039/c9sc03825f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/11/2019] [Indexed: 12/11/2022] Open
Abstract
The modification of lysine residues with acylating agents has represented a ubiquitous approach to the construction of antibody conjugates, with the resulting amide bonds being robustly stable and clinically validated. However, the conjugates are highly heterogeneous, due to the presence of numerous lysines on the surface of the protein, and greater control of the sites of conjugation are keenly sought. Here we present a novel approach to achieve the targeted modification of lysines distal to an antibody fragment's binding site, using a disulfide bond as a temporary 'hook' to deliver the acylating agent. This cysteine-to-lysine transfer (CLT) methodology offers greatly improved homogeneity of lysine conjugates, whilst retaining the advantages offered by the formation of amide linkages.
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Affiliation(s)
- Nafsika Forte
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H 0AJ , UK . ;
| | - Irene Benni
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H 0AJ , UK . ;
| | - Kersti Karu
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H 0AJ , UK . ;
| | - Vijay Chudasama
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H 0AJ , UK . ;
- Research Institute for Medicines (iMed.ULisboa) , Faculty of Pharmacy , Universidade de Lisboa , Lisbon , Portugal
| | - James R Baker
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H 0AJ , UK . ;
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4
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Agouridas V, El Mahdi O, Diemer V, Cargoët M, Monbaliu JCM, Melnyk O. Native Chemical Ligation and Extended Methods: Mechanisms, Catalysis, Scope, and Limitations. Chem Rev 2019; 119:7328-7443. [DOI: 10.1021/acs.chemrev.8b00712] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vangelis Agouridas
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Ouafâa El Mahdi
- Faculté Polydisciplinaire de Taza, University Sidi Mohamed Ben Abdellah, BP 1223 Taza Gare, Morocco
| | - Vincent Diemer
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Marine Cargoët
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Jean-Christophe M. Monbaliu
- Center for Integrated Technology and Organic Synthesis, Department of Chemistry, University of Liège, Building B6a, Room 3/16a, Sart-Tilman, B-4000 Liège, Belgium
| | - Oleg Melnyk
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
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5
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De Bo G, Gall MAY, Kitching MO, Kuschel S, Leigh DA, Tetlow DJ, Ward JW. Sequence-Specific β-Peptide Synthesis by a Rotaxane-Based Molecular Machine. J Am Chem Soc 2017; 139:10875-10879. [DOI: 10.1021/jacs.7b05850] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Guillaume De Bo
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Malcolm A. Y. Gall
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Matthew O. Kitching
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Sonja Kuschel
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - David A. Leigh
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Daniel J. Tetlow
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - John W. Ward
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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6
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Burke HM, McSweeney L, Scanlan EM. Exploring chemoselective S-to-N acyl transfer reactions in synthesis and chemical biology. Nat Commun 2017; 8:15655. [PMID: 28537277 PMCID: PMC5458133 DOI: 10.1038/ncomms15655] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 04/13/2017] [Indexed: 12/16/2022] Open
Abstract
S -to-N acyl transfer is a high-yielding chemoselective process for amide bond formation. It is widely utilized by chemists for synthetic applications, including peptide and protein synthesis, chemical modification of proteins, protein-protein ligation and the development of probes and molecular machines. Recent advances in our understanding of S -to-N acyl transfer processes in biology and innovations in methodology for thioester formation and desulfurization, together with an extension of the size of cyclic transition states, have expanded the boundaries of this process well beyond peptide ligation. As the field develops, this chemistry will play a central role in our molecular understanding of Biology. The conversion of thioesters to amides via acyl transfer has become one of the most important synthetic techniques for the chemical synthesis and modification of proteins. This review discusses this S-to-N acyl transfer process, and highlights some of the key applications across chemistry and biology.
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Affiliation(s)
- Helen M. Burke
- School of Chemistry, Trinity College Dublin, Dublin D2, Ireland
| | | | - Eoin M. Scanlan
- School of Chemistry, Trinity College Dublin, Dublin D2, Ireland
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8
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Koniev O, Wagner A. Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions for bioconjugation. Chem Soc Rev 2015; 44:5495-551. [PMID: 26000775 DOI: 10.1039/c5cs00048c] [Citation(s) in RCA: 390] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioconjugation methodologies have proven to play a central enabling role in the recent development of biotherapeutics and chemical biology approaches. Recent endeavours in these fields shed light on unprecedented chemical challenges to attain bioselectivity, biocompatibility, and biostability required by modern applications. In this review the current developments in various techniques of selective bond forming reactions of proteins and peptides were highlighted. The utility of each endogenous amino acid-selective conjugation methodology in the fields of biology and protein science has been surveyed with emphasis on the most relevant among reported transformations; selectivity and practical use have been discussed.
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Affiliation(s)
- Oleksandr Koniev
- Laboratory of Functional Chemo-Systems (UMR 7199), Labex Medalis, University of Strasbourg, 74 Route du Rhin, 67401 Illkirch-Graffenstaden, France.
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9
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Panda SS, Jones RA, Hall CD, Katritzky AR. Applications of Chemical Ligation in Peptide Synthesis via Acyl Transfer. Top Curr Chem (Cham) 2015; 362:229-65. [PMID: 25805142 DOI: 10.1007/128_2014_608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The utility of native chemical ligation (NCL) in the solution or solid phase synthesis of peptides, cyclic peptides, glycopeptides, and neoglycoconjugates is reviewed. In addition, the mechanistic details of inter- or intra-molecular NCLs are discussed from experimental and computational points of view.
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Affiliation(s)
- Siva S Panda
- Department of Chemistry, Center for Heterocyclic Compounds, University of Florida, Gainesville, FL, 32611-7200, USA,
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10
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Panda SS, Ibrahim MA, Küçükbay H, Meyers MJ, Sverdrup FM, El-Feky SA, Katritzky AR. Synthesis and antimalarial bioassay of quinine - peptide conjugates. Chem Biol Drug Des 2014; 82:361-6. [PMID: 23497252 DOI: 10.1111/cbdd.12134] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 03/01/2013] [Indexed: 11/28/2022]
Abstract
Amino acid and peptide conjugates of quinine were synthesized using microwave irradiation in 52-95% yields using benzotriazole methodology. The majority of these conjugates retain in vitro antimalarial activity with IC50 values below 100 nm, similar to quinine.
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Affiliation(s)
- Siva S Panda
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL, 32611-7200, USA
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11
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Panda SS, Hall CD, Oliferenko AA, Katritzky AR. Traceless chemical ligation from S-, O-, and N-acyl isopeptides. Acc Chem Res 2014; 47:1076-87. [PMID: 24617996 DOI: 10.1021/ar400242q] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Peptides are ubiquitous in nature where they play crucial roles as catalysts (enzymes), cell membrane ion transporters, and structural elements (proteins) within biological systems. In addition, both linear and cyclic peptides have found use as pharmaceuticals and components of various conjugate molecular systems. Small wonder then that chemists throughout the ages have sought to mimic nature by synthesis of the amide polymers known as peptides and proteins. The fundamental reaction in the formation of a peptide bond is condensation of an amine of one amino acid with the activated carbonyl group of another. This "fragment condensation" has been achieved in many ways both in solution and by solid-phase peptide synthesis (SPSS) on resin. The most successful method for in-solution coupling is known as native chemical ligation (NCL), and the technique dates back to the pioneering work of Wieland (1953) and subsequently Kent (1994) among many others. This Account builds on the established principles of NCL as applied specifically to S-, O-, and N-isopeptides, molecules that are generally more soluble and less prone to aggregation than native peptides. This Account also covers NCL of isopeptides containing terminal and nonterminal S-acylated cysteine units, reactions that enable the synthesis of native peptides from S-acyl peptides without the use of auxiliaries. With C-terminal S-acyl isopeptides, NCL was carried out under microwave irradiation in phosphate buffer (pH 7.3) at 50 °C. Intramolecular acyl migration was observed through 5-19-membered transition states with relative rates, as assessed by product analysis, in the order, 5 > 10 > 11 > 14, 16, or 17 > 12 > 13, 15, or 19 > 18 ≫ 9 > 8. The rate/pH profile for the 15-membered TS showed a maximum for ligated product versus transacylation at pH 7.0-7.3 presumably associated with the pKa of the N-nucleophile in the hydrogen-bonded TS. Cysteine occurs at low abundance (1.7%) in natural peptides and is rarely available in a terminal position thus limiting the utility of the method. This Account reports, however, NCL at nonterminal acyl cysteine through 5-, 8-, 11-, and 14-membered TSs with relative rates of ligation in the order, 5 ≫ 14 > 11 ≫ 8, thus paralleling the results with acylated terminal cysteine residues. In an obvious sequel to the work with acylated cysteine, we discuss intramolecular O- to N-acyl shift in O-acyl serine and O-acyl tyrosine isopeptides where the story becomes more complex in terms of viable conditions and optimum size of the cyclic TS. N- to N-acyl migration in acyl tryptophan isopeptides is described, and finally, chemical ligation is applied to the synthesis of cyclic peptides. Conformational analysis and quantum chemical calculations are used to rationalize ligation through a range of cyclic transition states. This Account highlights the fact that NCL of acyl isopeptides is an extremely useful strategy for the synthesis of a wide variety of native peptides in good yields and under mild conditions. Mechanistic aspects of the ligations are not fully resolved, but theoretical studies indicate that hydrogen bonding within the various cyclic transition states plays a major role.
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Affiliation(s)
- Siva S. Panda
- Center
for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - C. Dennis Hall
- Center
for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Alexander A. Oliferenko
- Center
for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Alan R. Katritzky
- Center
for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
- Chemistry Department, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
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12
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Panda SS, Oliferenko AA, Marwani HM, Katritzky AR. Effects of preorganization and hydrogen bonding on intramolecular chemical ligation of (N)-and (O)-acyl isopeptides. MENDELEEV COMMUNICATIONS 2014. [DOI: 10.1016/j.mencom.2014.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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13
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Ha K, Lebedyeva I, Li Z, Martin K, Williams B, Faby E, Nasajpour A, Pillai GG, Al-Youbi AO, Katritzky AR. Conformationally Assisted Lactamizations for the Synthesis of Symmetrical and Unsymmetrical Bis-2,5-diketopiperazines. J Org Chem 2013; 78:8510-23. [DOI: 10.1021/jo401235k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Khanh Ha
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Iryna Lebedyeva
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Zhiliang Li
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Kristin Martin
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Byron Williams
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Eric Faby
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Amir Nasajpour
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Girinath G. Pillai
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
- Institute of Chemistry, University of Tartu, Tartu 50411, Estonia
| | - Abdulrahman O. Al-Youbi
- Chemistry Department, Faculty
of Science, King Abdulaziz University,
Jeddah, 21589 Saudi Arabia
| | - Alan R. Katritzky
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
- Chemistry Department, Faculty
of Science, King Abdulaziz University,
Jeddah, 21589 Saudi Arabia
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14
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Popov V, Panda SS, Katritzky AR. Ligations from Tyrosine Isopeptides via 12- to 19-Membered Cyclic Transition States. J Org Chem 2013; 78:7455-61. [DOI: 10.1021/jo4009468] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Vadim Popov
- Center for Heterocyclic
Compounds, University of Florida, Department
of Chemistry, Gainesville,
Florida 32611-7200, United States
| | - Siva S. Panda
- Center for Heterocyclic
Compounds, University of Florida, Department
of Chemistry, Gainesville,
Florida 32611-7200, United States
| | - Alan R. Katritzky
- Center for Heterocyclic
Compounds, University of Florida, Department
of Chemistry, Gainesville,
Florida 32611-7200, United States
- Department of Chemistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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15
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Popov V, Panda SS, Katritzky AR. Ligations of N-acyl tryptophan units to give native peptides via 7-, 10-, 11- and 12-membered cyclic transition states. Org Biomol Chem 2013; 11:1594-7. [DOI: 10.1039/c3ob27421g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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