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Gori A, Gagni P, Rinaldi S. Disulfide Bond Mimetics: Strategies and Challenges. Chemistry 2017; 23:14987-14995. [PMID: 28749012 DOI: 10.1002/chem.201703199] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Indexed: 12/25/2022]
Abstract
The activity profile of many biologically relevant proteins and peptides often relies on a precise 3D structural organization. In this context, disulfide bonds are natural covalent constraints that play a key role in driving and stabilizing the folding pattern of these molecules. Despite its prominent significance as structural motif, the disulfide bond itself is inherently unstable under physiological conditions, posing a major limit to the use and development of disulfide-rich peptides and proteins as molecular tools and drug lead compounds. To tackle this restriction, disulfide engineering with stable functional analogues has arisen a considerable interest. Here, the most popular approaches to disulfide replacement are reviewed and discussed with particular emphasis on advantages and limitations under both functional and synthetic perspectives.
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Affiliation(s)
- Alessandro Gori
- Istituto di Chimica del Riconoscimento Molecolare (ICRM), National Research Council of, Italy) (CNR, via Mario Bianco 9, 20131, Milano, Italy
| | - Paola Gagni
- Istituto di Chimica del Riconoscimento Molecolare (ICRM), National Research Council of, Italy) (CNR, via Mario Bianco 9, 20131, Milano, Italy
| | - Silvia Rinaldi
- Istituto di Chimica del Riconoscimento Molecolare (ICRM), National Research Council of, Italy) (CNR, via Mario Bianco 9, 20131, Milano, Italy
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2
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Bruno PA, Morriss-Andrews A, Henderson AR, Brooks CL, Mapp AK. A Synthetic Loop Replacement Peptide That Blocks Canonical NF-κB Signaling. Angew Chem Int Ed Engl 2016; 55:14997-15001. [PMID: 27791341 PMCID: PMC5587901 DOI: 10.1002/anie.201607990] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Indexed: 11/06/2022]
Abstract
Aberrant canonical NF-κB signaling is implicated in diseases from autoimmune disorders to cancer. A major therapeutic challenge is the need for selective inhibition of the canonical pathway without impacting the many non-canonical NF-κB functions. Here we show that a selective peptide-based inhibitor of canonical NF-κB signaling, in which a hydrogen bond in the NBD peptide is synthetically replaced by a non-labile bond, shows an about 10-fold increased potency relative to the original inhibitor. Not only is this molecule, NBD2, a powerful tool for dissection of canonical NF-κB signaling in disease models and healthy tissues, the success of the synthetic loop replacement suggests that the general strategy could be useful for discovering modulators of the many protein-protein interactions mediated by such structures.
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Affiliation(s)
- Paul A Bruno
- Department of Chemistry, University of Michigan, Ann Arbor, USA
- Life Sciences Institute, Program in Chemical Biology, University of Michigan, Ann Arbor, USA
| | | | - Andrew R Henderson
- Department of Chemistry, University of Michigan, Ann Arbor, USA
- Life Sciences Institute, Program in Chemical Biology, University of Michigan, Ann Arbor, USA
| | | | - Anna K Mapp
- Department of Chemistry, University of Michigan, Ann Arbor, USA
- Life Sciences Institute, Program in Chemical Biology, University of Michigan, Ann Arbor, USA
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Gleeson EC, Wang ZJ, Robinson SD, Chhabra S, MacRaild CA, Jackson WR, Norton RS, Robinson AJ. Stereoselective synthesis and structural elucidation of dicarba peptides. Chem Commun (Camb) 2016; 52:4446-9. [PMID: 26892179 DOI: 10.1039/c5cc10540d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A facile stereoselective synthesis of cis and trans unsaturated dicarba peptides has been established using preformed diaminosuberic acid derivatives as bridging units. In addition, characteristic spectral differences in the (13)C-NMR spectra of the cis- and trans-isomers show that the chemical shift of carbons in the Δ4,5-diaminosuberic acid residue can be used to assign stereochemistry in unsaturated dicarba peptides formed from ring closing metathesis of linear peptide sequences.
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Affiliation(s)
- Ellen C Gleeson
- School of Chemistry, Monash University, Clayton 3800, Victoria, Australia.
| | - Zhen J Wang
- School of Chemistry, Monash University, Clayton 3800, Victoria, Australia.
| | - Samuel D Robinson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria, Australia
| | - Sandeep Chhabra
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria, Australia
| | - Christopher A MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria, Australia
| | - W Roy Jackson
- School of Chemistry, Monash University, Clayton 3800, Victoria, Australia.
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria, Australia
| | - Andrea J Robinson
- School of Chemistry, Monash University, Clayton 3800, Victoria, Australia.
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Bruno PA, Morriss-Andrews A, Henderson AR, Brooks CL, Mapp AK. A Synthetic Loop Replacement Peptide That Blocks Canonical NF-κB Signaling. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607990] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Paul A. Bruno
- Department of Chemistry; University of Michigan; Ann Arbor USA
- Life Sciences Institute; Program in Chemical Biology; University of Michigan; Ann Arbor USA
| | | | - Andrew R. Henderson
- Department of Chemistry; University of Michigan; Ann Arbor USA
- Life Sciences Institute; Program in Chemical Biology; University of Michigan; Ann Arbor USA
| | | | - Anna K. Mapp
- Department of Chemistry; University of Michigan; Ann Arbor USA
- Life Sciences Institute; Program in Chemical Biology; University of Michigan; Ann Arbor USA
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6
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Qvit N, Kornfeld OS. Development of a Backbone Cyclic Peptide Library as Potential Antiparasitic Therapeutics Using Microwave Irradiation. J Vis Exp 2016:e53589. [PMID: 26863382 DOI: 10.3791/53589] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Protein-protein interactions (PPIs) are intimately involved in almost all biological processes and are linked to many human diseases. Therefore, there is a major effort to target PPIs in basic research and in the pharmaceutical industry. Protein-protein interfaces are usually large, flat, and often lack pockets, complicating the discovery of small molecules that target such sites. Alternative targeting approaches using antibodies have limitations due to poor oral bioavailability, low cell-permeability, and production inefficiency. Using peptides to target PPI interfaces has several advantages. Peptides have higher conformational flexibility, increased selectivity, and are generally inexpensive. However, peptides have their own limitations including poor stability and inefficiency crossing cell membranes. To overcome such limitations, peptide cyclization can be performed. Cyclization has been demonstrated to improve peptide selectivity, metabolic stability, and bioavailability. However, predicting the bioactive conformation of a cyclic peptide is not trivial. To overcome this challenge, one attractive approach it to screen a focused library to screen in which all backbone cyclic peptides have the same primary sequence, but differ in parameters that influence their conformation, such as ring size and position. We describe a detailed protocol for synthesizing a library of backbone cyclic peptides targeting specific parasite PPIs. Using a rational design approach, we developed peptides derived from the scaffold protein Leishmania receptor for activated C-kinase (LACK). We hypothesized that sequences in LACK that are conserved in parasites, but not in the mammalian host homolog, may represent interaction sites for proteins that are critical for the parasites' viability. The cyclic peptides were synthesized using microwave irradiation to reduce reaction times and increase efficiency. Developing a library of backbone cyclic peptides with different ring sizes facilitates a systematic screen for the most biological active conformation. This method provides a general, fast, and facile way to synthesize cyclic peptides.
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Affiliation(s)
- Nir Qvit
- Department of Chemical and Systems Biology, Stanford University School of Medicine;
| | - Opher S Kornfeld
- Department of Chemical and Systems Biology, Stanford University School of Medicine
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7
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Nolen EG, Fedorka CJ, Blicher B. Synthesis of Orthogonally ProtectedS,S-2,6-Diaminopimelic Acid via Olefin Cross-Metathesis. SYNTHETIC COMMUN 2013. [DOI: 10.1080/00397911.2006.10745071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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van Lierop BJ, Bornschein C, Jackson WR, Robinson AJ. Ring-closing Metathesis in Peptides - the Sting is in the Tail! Aust J Chem 2011. [DOI: 10.1071/ch11090] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Performing ring-closing metathesis on resin-bound peptides provides an expedient route to carbocyclic peptidomimetics of medicinal interest. Some sequences are highly resistant to metathesis and special strategies need to be employed to promote viable ring closure. This paper describes an on-resin, alternating solid-phase peptide synthesis-catalysis method to overcome deleterious aggregation phenomena. It can be used to promote high yielding single-ring closures and regioselective multi-ring construction in peptides.
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Dallinger D, Irfan M, Suljanovic A, Kappe CO. An Investigation of Wall Effects in Microwave-Assisted Ring-Closing Metathesis and Cyclotrimerization Reactions. J Org Chem 2010; 75:5278-88. [DOI: 10.1021/jo1011703] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Doris Dallinger
- Christian Doppler Laboratory for Microwave Chemistry (CDLMC) and Institute of Chemistry, Karl-Franzens-University Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - Muhammed Irfan
- Christian Doppler Laboratory for Microwave Chemistry (CDLMC) and Institute of Chemistry, Karl-Franzens-University Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - Amra Suljanovic
- Christian Doppler Laboratory for Microwave Chemistry (CDLMC) and Institute of Chemistry, Karl-Franzens-University Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - C. Oliver Kappe
- Christian Doppler Laboratory for Microwave Chemistry (CDLMC) and Institute of Chemistry, Karl-Franzens-University Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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Synthesis of chemically modified bioactive peptides: recent advances, challenges and developments for medicinal chemistry. Future Med Chem 2009; 1:1289-310. [DOI: 10.4155/fmc.09.97] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Although not complying with Lipinski’s rule, peptides are to an increasing extent being developed into new active pharmaceutical ingredients. This is mainly due to novel application routes, formulations and chemical modifications, which confer on the peptides improved uptake and increased metabolic stability. A brief survey of currently approved peptide drugs and the present scope of the application of peptides as drugs is provided. Cyclic peptides are emerging as an interesting class of peptides with conformational rigidity and homogeneity, high receptor affinity and selectivity, increased metabolic stability and – in special cases – even oral availability. Challenges and new methodology for the synthesis of cyclic peptides are outlined and an overview of approaches toward the design of peptide conformation and peptide modification by nonproteinogenic building blocks is given.
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12
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Affiliation(s)
- Yoann Coquerel
- Université Paul Cézanne (Aix‐Marseille III), CNRS, UMR 6178, Campus universitaire de St Jérôme, Service 531,13397 Marseille Cedex 20, France
| | - Jean Rodriguez
- Université Paul Cézanne (Aix‐Marseille III), CNRS, UMR 6178, Campus universitaire de St Jérôme, Service 531,13397 Marseille Cedex 20, France
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Brauer ABE, McBride JD, Kelly G, Matthews SJ, Leatherbarrow RJ. Resisting degradation by human elastase: commonality of design features shared by 'canonical' plant and bacterial macrocyclic protease inhibitor scaffolds. Bioorg Med Chem 2007; 15:4618-28. [PMID: 17470393 DOI: 10.1016/j.bmc.2007.03.082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 03/26/2007] [Accepted: 03/30/2007] [Indexed: 10/23/2022]
Abstract
A previously unexplained difference in the resistance to enzymatic hydrolysis of 11-mer Bowman-Birk-type inhibitors of human leukocyte elastase that differ in P1 is found to correlate with the strength of a particular intramolecular hydrogen bond within the inhibitor. This transannular hydrogen bond stabilizes the side chain of the conserved P2 Thr in a 'canonical' +60 degrees -rotamer chi(1) conformation and thereby directs it for a close interaction with the enzyme's catalytic His. As the implications of this NMR analysis are neither limited to this macrocyclic scaffold derived from plant proteins nor to a particular serine protease, we present a unified analysis with inhibitory bacterial depsipeptides of 7-12 residues in length that share key design features for which we propose communal functional explanations.
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Affiliation(s)
- Arnd B E Brauer
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
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Robinson AJ, Elaridi J, Van Lierop BJ, Mujcinovic S, Jackson WR. Microwave-assisted RCM for the synthesis of carbocyclic peptides. J Pept Sci 2007; 13:280-5. [PMID: 17394122 DOI: 10.1002/psc.840] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Microwave irradiation dramatically improves the efficiency of ring closing metathesis (RCM) reactions of resin-attached peptides and the technology is illustrated by the highly selective synthesis of dicarba analogues of alpha-conotoxin IMI.
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Affiliation(s)
- Andrea J Robinson
- School of Chemistry, Monash University, Clayton 3800, Victoria, Australia.
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15
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Herndon JW. The chemistry of the carbon–transition metal double and triple bond: Annual survey covering the year 2004. Coord Chem Rev 2006. [DOI: 10.1016/j.ccr.2005.10.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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16
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Nolen E, Fedorka C, Blicher B. Synthesis of Orthogonally Protected S , S ‐2,6‐Diaminopimelic Acid via Olefin Cross‐Metathesis. SYNTHETIC COMMUN 2006. [DOI: 10.1080/00397910600616701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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18
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Kuznetsov DV, Raev VA, Kuranov GL, Arapov OV, Kostikov RR. Microwave Activation in Organic Synthesis. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2005. [DOI: 10.1007/s11178-006-0030-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Nosse B, Schall A, Jeong W, Reiser O. Optimization of Ring-Closing Metathesis: Inert Gas Sparging and Microwave Irradiation. Adv Synth Catal 2005. [DOI: 10.1002/adsc.200505137] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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20
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Stawikowski M, Stawikowska R, Jaśkiewicz A, Zabłotna E, Rolka K. Examples of peptide-peptoid hybrid serine protease inhibitors based on the trypsin inhibitor SFTI-1 with complete protease resistance at the P1-P1' reactive site. Chembiochem 2005; 6:1057-61. [PMID: 15883970 DOI: 10.1002/cbic.200400412] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Research in the field of protease inhibitors is focused on obtaining potent, specific and protease-resistant inhibitors. To our knowledge, there are no reports in the literature that consider the application of N-substituted glycine residues (peptoid monomers) for the design of peptidomimetic protease inhibitors. We hereby present the chemical synthesis and kinetic properties of two new analogues of the trypsin inhibitor SFTI-1 modified at the P1 position. Substitution of Lys5 in SFTI-1 by N-(4-aminobutyl)-glycine and N-benzylglycine, which mimic Lys and Phe, respectively, made these analogues completely protease-resistant at their P1-P1' reactive sites. The analogues synthesised appeared to be potent inhibitors of bovine beta-trypsin and alpha-chymotrypsin. These noncovalent, competitive and selective peptide-peptoid hybrid (peptomeric) inhibitors might open the way to targeting unwanted proteolysis.
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Affiliation(s)
- Maciej Stawikowski
- Department of Bioorganic Chemistry, Faculty of Chemistry, University of Gdansk, Sobieskiego 18 St., 80-523 Gdansk, Poland
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Kazmaier U, Hebach C, Watzke A, Maier S, Mues H, Huch V. A straightforward approach towards cyclic peptides via ring-closing metathesis—scope and limitations. Org Biomol Chem 2005; 3:136-45. [PMID: 15602609 DOI: 10.1039/b411228h] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N- and C-terminal diallylated peptides are obtained by several approaches, such as peptide Claisen rearrangement, N- and O- allylation, and the Ugi reaction of allyl-protected components. These diallylated peptides are suitable substrates for ring-closing metathesis and the success of this cyclisation was investigated with respect to the ring size, the position of the allyl moieties and the reaction parameters. In general, excellent yields are obtained for cyclisation of allyl glycine subunits and N-allylated amides, while allyl esters and allyl carbamates often presented serious problems. However, yields of up to 73% were obtained under optimised conditions, and the new generated double bond is formed with excellent trans-selectivity.
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Affiliation(s)
- Uli Kazmaier
- Institut für Organische Chemie, Universität des Saarlandes, Saarbrücken, D-66123, Germany.
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Kaiser J, Kinderman SS, van Esseveldt BCJ, van Delft FL, Schoemaker HE, Blaauw RH, Rutjes FPJT. Synthetic applications of aliphatic unsaturated α-H-α-amino acids. Org Biomol Chem 2005; 3:3435-67. [PMID: 16172678 DOI: 10.1039/b507973j] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This article provides an overview of the literature concerning synthetic applications of unsaturated aliphatic amino acids in the period May 2000 to December 2004.
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Affiliation(s)
- Jasper Kaiser
- Radboud University Nijmegen, Institute for Molecules and Materials, Toernooiveld 1, NL-6525 ED Nijmegen, The Netherlands
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Abstract
Although fire is now rarely used in synthetic chemistry, it was not until Robert Bunsen invented the burner in 1855 that the energy from this heat source could be applied to a reaction vessel in a focused manner. The Bunsen burner was later superseded by the isomantle, oil bath, or hot plate as a source for applying heat to a chemical reaction. In the past few years, heating and driving chemical reactions by microwave energy has been an increasingly popular theme in the scientific community. This nonclassical heating technique is slowly moving from a laboratory curiosity to an established technique that is heavily used in both academia and industry. The efficiency of "microwave flash heating" in dramatically reducing reaction times (from days and hours to minutes and seconds) is just one of the many advantages. This Review highlights recent applications of controlled microwave heating in modern organic synthesis, and discusses some of the underlying phenomena and issues involved.
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Affiliation(s)
- C Oliver Kappe
- Institute of Chemistry, Organic and Bioorganic Chemistry, Karl-Franzens University Graz, Heinrichstrasse 28, A-8010 Graz, Austria.
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Kappe CO. Kontrolliertes Erhitzen mit Mikrowellen in der modernen organischen Synthese. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200400655] [Citation(s) in RCA: 241] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Declerck V, Ribière P, Martinez J, Lamaty F. Sequential aza-Baylis−Hillman/Ring Closing Metathesis/Aromatization as a Novel Route for the Synthesis of Substituted Pyrroles. J Org Chem 2004; 69:8372-81. [PMID: 15549809 DOI: 10.1021/jo048519r] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new route to diverse 2-substituted-3-methoxycarbonyl pyrroles has been developed. Diverse SES protected alpha-methylene beta-aminoesters were obtained by a 3-component aza-Baylis-Hillman reaction. Diversity arose from the aryl aldehydes which can be used in this reaction. N-Alkylation with allyl bromide under mild conditions provided the corresponding dienes. These substituted dienes were cyclized by ring closing metathesis at room temperature or under microwave-activation with Grubbs-type II catalyst to yield SES-protected pyrroline intermediates. The final pyrroles were obtained by base-promoted dehydrodesulfinylation/aromatization. The scope of each of these reactions was explored.
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Affiliation(s)
- Valérie Declerck
- Laboratoire des Aminoacides, Peptides et Protéines (LAPP), CNRS-Universités Montpellier 1 et 2, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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