1
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Schnitzer T, Trapp N, Fischer LM, Wennemers H. Crystal structure analysis of N-acetylated proline and ring size analogs. J Pept Sci 2022; 29:e3473. [PMID: 36579722 DOI: 10.1002/psc.3473] [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: 10/23/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022]
Abstract
Crystal structures of N-acetylated proline and homologs with four- and six-membered rings (azetidine carboxylic acid and piperidine carboxylic acid) were obtained and compared. The distinctly different conformations of the four-, five-, and six-membered rings reflect Bayer strain, n → π* interaction, and allylic strain, and result in crystal lattices with a zigzag structure.
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Affiliation(s)
- Tobias Schnitzer
- Laboratory of Organic Chemistry, ETH Zürich, D-CHAB, Zurich, Switzerland
| | - Nils Trapp
- Laboratory of Organic Chemistry, ETH Zürich, D-CHAB, Zurich, Switzerland
| | - Lisa-Marie Fischer
- Laboratory of Organic Chemistry, ETH Zürich, D-CHAB, Zurich, Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zürich, D-CHAB, Zurich, Switzerland
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2
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Bhat AA, Tandon N, Tandon R. Pyrrolidine derivatives as antibacterial agents, current status and future prospects: a patent review. Pharm Pat Anal 2022; 11:187-198. [PMID: 36366974 DOI: 10.4155/ppa-2022-0015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Bacterial infections are increasingly epitomizing major global health concerns, with rising death rates. Since the most complete assessment of the worldwide impact of antimicrobial resistance to date, with over 1.2 million people dead in 2019 as a direct result of antibiotic-resistant bacterial infections. The majority of antimicrobial drugs have been associated with a multitude of adverse effects including financial costs as well. Pyrrolidine derivatives have sparked the interest of researchers to create novel synthetic molecules with minimal side effect and drawbacks. To close the research gap, the current review discusses the synthetic compounds with active pyrrolidine scaffolds, critical findings and most crucially the structure-activity relationship that affects the activity of the ring over the last one and half decade.
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Affiliation(s)
- Aeyaz A Bhat
- School of Chemical Engineering & Physical Science, Lovely Professional University, Phagwara, 144402, Punjab
| | - Nitin Tandon
- School of Chemical Engineering & Physical Science, Lovely Professional University, Phagwara, 144402, Punjab
| | - Runjhun Tandon
- School of Chemical Engineering & Physical Science, Lovely Professional University, Phagwara, 144402, Punjab
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3
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Al-Momani L, Lataifeh A. Asymmetric Aldol “Reaction in Water” Using Ferrocene-Amino Acid Conjugates. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.1c04725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lo’ay Al-Momani
- Department of Chemistry, Faculty of Science, Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Anas Lataifeh
- Department of Chemistry, Faculty of Science, Tafila Technical University, P.O. Box 179, Tafila 66110, Jordan
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4
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Li Petri G, Raimondi MV, Spanò V, Holl R, Barraja P, Montalbano A. Pyrrolidine in Drug Discovery: A Versatile Scaffold for Novel Biologically Active Compounds. Top Curr Chem (Cham) 2021; 379:34. [PMID: 34373963 PMCID: PMC8352847 DOI: 10.1007/s41061-021-00347-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/25/2021] [Indexed: 01/24/2023]
Abstract
The five-membered pyrrolidine ring is one of the nitrogen heterocycles used widely by medicinal chemists to obtain compounds for the treatment of human diseases. The great interest in this saturated scaffold is enhanced by (1) the possibility to efficiently explore the pharmacophore space due to sp3-hybridization, (2) the contribution to the stereochemistry of the molecule, (3) and the increased three-dimensional (3D) coverage due to the non-planarity of the ring-a phenomenon called "pseudorotation". In this review, we report bioactive molecules with target selectivity characterized by the pyrrolidine ring and its derivatives, including pyrrolizines, pyrrolidine-2-one, pyrrolidine-2,5-diones and prolinol described in the literature from 2015 to date. After a comparison of the physicochemical parameters of pyrrolidine with the parent aromatic pyrrole and cyclopentane, we investigate the influence of steric factors on biological activity, also describing the structure-activity relationship (SAR) of the studied compounds. To aid the reader's approach to reading the manuscript, we have planned the review on the basis of the synthetic strategies used: (1) ring construction from different cyclic or acyclic precursors, reporting the synthesis and the reaction conditions, or (2) functionalization of preformed pyrrolidine rings, e.g., proline derivatives. Since one of the most significant features of the pyrrolidine ring is the stereogenicity of carbons, we highlight how the different stereoisomers and the spatial orientation of substituents can lead to a different biological profile of drug candidates, due to the different binding mode to enantioselective proteins. We believe that this work can guide medicinal chemists to the best approach in the design of new pyrrolidine compounds with different biological profiles.
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Affiliation(s)
- Giovanna Li Petri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Maria Valeria Raimondi
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123, Palermo, Italy.
| | - Virginia Spanò
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Ralph Holl
- Department of Chemistry, Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Paola Barraja
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Alessandra Montalbano
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123, Palermo, Italy
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5
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Kumar P, Kumar R, Banerjee P. Accessing Dihydro-1,2-oxazine via Cloke–Wilson-Type Annulation of Cyclopropyl Carbonyls: Application toward the Diastereoselective Synthesis of Pyrrolo[1,2-b][1,2]oxazine. J Org Chem 2020; 85:6535-6550. [DOI: 10.1021/acs.joc.0c00531] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Pankaj Kumar
- Department of Chemistry, Indian Institute of Technology Ropar, Nangal Road, Rupnagar, Punjab 140001, India
| | - Rakesh Kumar
- Department of Chemistry, Indian Institute of Technology Ropar, Nangal Road, Rupnagar, Punjab 140001, India
| | - Prabal Banerjee
- Department of Chemistry, Indian Institute of Technology Ropar, Nangal Road, Rupnagar, Punjab 140001, India
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6
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Irwin LC, Allen MA, Vriesen MR, Kerr MA. Annulation of Oxime‐Ether Tethered Donor–Acceptor Cyclopropanes. Chemistry 2019; 26:171-175. [DOI: 10.1002/chem.201904521] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/07/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Lauren C. Irwin
- Department of Chemistry The University of Western Ontario 1151 Richmond St London ON N6A 3K7 Canada
| | - Meredith A. Allen
- Department of Chemistry The University of Western Ontario 1151 Richmond St London ON N6A 3K7 Canada
| | - Matthew R. Vriesen
- Department of Chemistry The University of Western Ontario 1151 Richmond St London ON N6A 3K7 Canada
| | - Michael A. Kerr
- Department of Chemistry The University of Western Ontario 1151 Richmond St London ON N6A 3K7 Canada
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7
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Kubyshkin V. Stabilization of the triple helix in collagen mimicking peptides. Org Biomol Chem 2019; 17:8031-8047. [PMID: 31464337 DOI: 10.1039/c9ob01646e] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Collagen mimics are peptides designed to reproduce structural features of natural collagen. A triple helix is the first element in the hierarchy of collagen folding. It is an assembly of three parallel peptide chains stabilized by packing and interchain hydrogen bonds. In this review we summarize the existing chemical approaches towards stabilization of this structure including the most recent developments. Currently proposed methods include manipulation of the amino acid composition, application of unnatural amino acid analogues, stimuli-responsive modifications, chain tethering approaches, peptide amphiphiles, modifications that target interchain interactions and more. This ability to manipulate the triple helix as a supramolecular self-assembly contributes to our understanding of the collagen folding. It also provides essential information needed to design collagen-based biomaterials of the future.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry, University of Manitoba, Dysart Rd. 144, R3T 2N2, Winnipeg, Manitoba, Canada.
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8
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Sampaio-Dias IE, Silva-Reis SC, Pinto da Silva L, García-Mera X, Maestro MA, Rodríguez-Borges JE. Mechanistic insights for the transprotection of tertiary amines with Boc2O via charged carbamates: access to both enantiomers of 2-azanorbornane-3-exo-carboxylic acids. Org Chem Front 2019. [DOI: 10.1039/c9qo00957d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Development of a synthetic methodology for the selective transprotection in hindered tertiary amines using Boc2O under N–C hydrogenolysis catalyzed by Pd/C: access to both enantiomers of 2-azanorbornane-3-exo-carboxylates.
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Affiliation(s)
- Ivo E. Sampaio-Dias
- LAQV/REQUIMTE
- Department of Chemistry and Biochemistry
- Faculty of Sciences
- University of Porto
- 4169-007 Porto
| | - Sara C. Silva-Reis
- LAQV/REQUIMTE
- Department of Chemistry and Biochemistry
- Faculty of Sciences
- University of Porto
- 4169-007 Porto
| | - Luís Pinto da Silva
- Chemistry Research Unit (CIQUP)
- Department of Chemistry and Biochemistry
- Faculty of Sciences of University of Porto
- 4169-007 Porto
- Portugal
| | - Xerardo García-Mera
- Department of Organic Chemistry
- Faculty of Pharmacy
- University of Santiago de Compostela
- Santiago de Compostela
- Spain
| | - Miguel A. Maestro
- Department of Chemistry-CICA
- Faculty of Sciences
- University of Coruña
- A Coruña
- Spain
| | - José E. Rodríguez-Borges
- LAQV/REQUIMTE
- Department of Chemistry and Biochemistry
- Faculty of Sciences
- University of Porto
- 4169-007 Porto
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9
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Study of the coordination of ortho-tyrosine and trans-4-hydroxyproline with aluminum(III) and iron(III). J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.08.074] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Sun X, Li M, Sun M, Li X, Xi BJ, Wu Y, Yao J, Zhan Z, Bai X, Xi N. Studies on structural requirements for atropisomerism in N -phenyl γ-lactams. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.04.090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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11
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Egli J, Siebler C, Maryasin B, Erdmann RS, Bergande C, Ochsenfeld C, Wennemers H. pH-Responsive Aminoproline-Containing Collagen Triple Helices. Chemistry 2017; 23:7938-7944. [DOI: 10.1002/chem.201701134] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Jasmine Egli
- Laboratory of Organic Chemistry; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Christiane Siebler
- Laboratory of Organic Chemistry; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Boris Maryasin
- Chair of Theoretical Chemistry; Department of Chemistry; University of Munich (LMU); Butenandtstr. 7 81377 Munich Germany
- Center of Integrated Protein Science (CIPSM) at the Department of Chemistry; University of Munich (LMU); Butenandtstr. 5-13 81377 Munich Germany
| | - Roman S. Erdmann
- Laboratory of Organic Chemistry; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Cedric Bergande
- Laboratory of Organic Chemistry; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry; Department of Chemistry; University of Munich (LMU); Butenandtstr. 7 81377 Munich Germany
- Center of Integrated Protein Science (CIPSM) at the Department of Chemistry; University of Munich (LMU); Butenandtstr. 5-13 81377 Munich Germany
| | - Helma Wennemers
- Laboratory of Organic Chemistry; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
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12
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Alonso-Fernández J, Benaiges C, Casas E, Alibés R, Bayón P, Busqué F, Álvarez-Larena Á, Figueredo M. Synthetic studies on Stemona alkaloids. Construction of the sessilifoliamides B and C and 1,12-secostenine skeleton. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.04.077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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Siebler C, Maryasin B, Kuemin M, Erdmann RS, Rigling C, Grünenfelder C, Ochsenfeld C, Wennemers H. Importance of dipole moments and ambient polarity for the conformation of Xaa-Pro moieties - a combined experimental and theoretical study. Chem Sci 2015; 6:6725-6730. [PMID: 30154996 PMCID: PMC6090429 DOI: 10.1039/c5sc02211h] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 07/27/2015] [Indexed: 12/04/2022] Open
Abstract
NMR spectroscopic studies with a series of proline derivatives revealed that the polarity of the environment has a significant effect on the trans : cis isomer ratio of Xaa-Pro bonds. Computational studies showed that this effect is due to differences in the overall dipole moments of trans and cis conformers. Comparisons between the conformational properties of amide and ester derivatives revealed an intricate balance between polarity effects and n → π* interactions of adjacent carbonyl groups. The findings have important implications for protein folding and signaling as well as the performance of proline-based stereoselective catalysts.
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Affiliation(s)
- Christiane Siebler
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Boris Maryasin
- Chair of Theoretical Chemistry , Department of Chemistry , University of Munich (LMU) , Butenandtstr. 7 , D-81377 Munich , Germany
- Center of Integrated Protein Science (CIPSM) at the Department of Chemistry , University of Munich (LMU) , Butenandtstr. 5-13 , D-81377 Munich , Germany
| | - Michael Kuemin
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Roman S Erdmann
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Carla Rigling
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Claudio Grünenfelder
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry , Department of Chemistry , University of Munich (LMU) , Butenandtstr. 7 , D-81377 Munich , Germany
- Center of Integrated Protein Science (CIPSM) at the Department of Chemistry , University of Munich (LMU) , Butenandtstr. 5-13 , D-81377 Munich , Germany
| | - Helma Wennemers
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
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14
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Bartuschat AL, Wicht K, Heinrich MR. Switching and Conformational Fixation of Amides Through Proximate Positive Charges. Angew Chem Int Ed Engl 2015; 54:10294-8. [DOI: 10.1002/anie.201502474] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Indexed: 01/03/2023]
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15
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Bartuschat AL, Wicht K, Heinrich MR. Schaltung und Fixierung der Konformation von Amiden durch nahegelegene positive Ladungen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502474] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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16
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Kaplaneris N, Koutoulogenis G, Raftopoulou M, Kokotos CG. 4-Fluoro and 4-Hydroxy Pyrrolidine-thioxotetrahydropyrimidinones: Organocatalysts for Green Asymmetric Transformations in Brine. J Org Chem 2015; 80:5464-73. [PMID: 25942500 DOI: 10.1021/acs.joc.5b00283] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The synthesis of both trans- and cis-diastereomers of pyrrolidinine-thioxotetrahydropyrimidinone bearing either a fluorine or a hydroxyl group was accomplished. The new compounds were tested for their catalytic properties in a variety of asymmetric organic transformations and compared with the first generation catalyst. It was found that the new catalysts could efficiently catalyze the reactions in brine, without the use of organic solvent, and by employing an almost stoichiometric amount of reagents. Thus, the products were isolated by simple extractions, avoiding the use of chromatography in excellent yields, diastereoselectivities, and enantioselectivities.
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Affiliation(s)
- Nikolaos Kaplaneris
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Giorgos Koutoulogenis
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Marianna Raftopoulou
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Christoforos G Kokotos
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
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17
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Siebler C, Trapp N, Wennemers H. Crystal structure of (4S
)-aminoproline: conformational insight into a pH-responsive proline derivative. J Pept Sci 2015; 21:208-11. [DOI: 10.1002/psc.2734] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/03/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Christiane Siebler
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
| | - Helma Wennemers
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
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18
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Kaur G, Vikas. Exploring the mechanism of isomerisation and water-migration in the water-complexes of amino-acid l-proline: electrostatic potential and vibrational analysis. RSC Adv 2015. [DOI: 10.1039/c5ra06088e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This work reveals interesting pathways for water-migration and neutral ↔ zwitterionic isomerisation in the water complexes of l-proline.
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Affiliation(s)
- Gurpreet Kaur
- Quantum Chemistry Group
- Department of Chemistry & Centre of Advanced Studies in Chemistry
- Panjab University
- Chandigarh – 160014
- India
| | - Vikas
- Quantum Chemistry Group
- Department of Chemistry & Centre of Advanced Studies in Chemistry
- Panjab University
- Chandigarh – 160014
- India
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19
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Neumann LN, Baker MB, Leenders CMA, Voets IK, Lafleur RPM, Palmans ARA, Meijer EW. Supramolecular polymers for organocatalysis in water. Org Biomol Chem 2015; 13:7711-9. [DOI: 10.1039/c5ob00937e] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An l-proline-functionalised benzene-1,3,5-tricarboxamide derivative self-assembles in water into well-defined, one-dimensional, helical, supramolecular polymers that efficiently catalyse aldol reactions.
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Affiliation(s)
- Laura N. Neumann
- Laboratory for Macromolecular and Organic Chemistry
- Institute for Complex Molecular Sciences
- 5600 MB Eindhoven
- The Netherlands
| | - Matthew B. Baker
- Laboratory for Macromolecular and Organic Chemistry
- Institute for Complex Molecular Sciences
- 5600 MB Eindhoven
- The Netherlands
| | - Christianus M. A. Leenders
- Laboratory for Macromolecular and Organic Chemistry
- Institute for Complex Molecular Sciences
- 5600 MB Eindhoven
- The Netherlands
| | - Ilja K. Voets
- Laboratory for Macromolecular and Organic Chemistry
- Institute for Complex Molecular Sciences
- 5600 MB Eindhoven
- The Netherlands
| | - René P. M. Lafleur
- Laboratory for Macromolecular and Organic Chemistry
- Institute for Complex Molecular Sciences
- 5600 MB Eindhoven
- The Netherlands
| | - Anja R. A. Palmans
- Laboratory for Macromolecular and Organic Chemistry
- Institute for Complex Molecular Sciences
- 5600 MB Eindhoven
- The Netherlands
| | - E. W. Meijer
- Laboratory for Macromolecular and Organic Chemistry
- Institute for Complex Molecular Sciences
- 5600 MB Eindhoven
- The Netherlands
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20
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Siebler C, Erdmann RS, Wennemers H. Switchable Proline Derivatives: Tuning the Conformational Stability of the Collagen Triple Helix by pH Changes. Angew Chem Int Ed Engl 2014; 53:10340-4. [DOI: 10.1002/anie.201404935] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/17/2014] [Indexed: 12/14/2022]
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21
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Switchable Proline Derivatives: Tuning the Conformational Stability of the Collagen Triple Helix by pH Changes. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404935] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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22
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Zhang Z, Ding Q, Liu JJ, Zhang J, Jiang N, Chu XJ, Bartkovitz D, Luk KC, Janson C, Tovar C, Filipovic ZM, Higgins B, Glenn K, Packman K, Vassilev LT, Graves B. Discovery of potent and selective spiroindolinone MDM2 inhibitor, RO8994, for cancer therapy. Bioorg Med Chem 2014; 22:4001-9. [PMID: 24997575 DOI: 10.1016/j.bmc.2014.05.072] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/23/2014] [Accepted: 05/30/2014] [Indexed: 12/19/2022]
Abstract
The field of small-molecule inhibitors of protein-protein interactions is rapidly advancing and the specific area of inhibitors of the p53/MDM2 interaction is a prime example. Several groups have published on this topic and multiple compounds are in various stages of clinical development. Building on the strength of the discovery of RG7112, a Nutlin imidazoline-based compound, and RG7388, a pyrrolidine-based compound, we have developed additional scaffolds that provide opportunities for future development. Here, we report the discovery and optimization of a highly potent and selective series of spiroindolinone small-molecule MDM2 inhibitors, culminating in RO8994.
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Affiliation(s)
- Zhuming Zhang
- Discovery Chemistry, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States.
| | - Qingjie Ding
- Discovery Chemistry, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States
| | - Jin-Jun Liu
- Discovery Chemistry, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States
| | - Jing Zhang
- Discovery Chemistry, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States
| | - Nan Jiang
- Discovery Chemistry, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States
| | - Xin-Jie Chu
- Discovery Chemistry, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States
| | - David Bartkovitz
- Discovery Chemistry, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States
| | - Kin-Chun Luk
- Discovery Chemistry, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States
| | - Cheryl Janson
- Discovery Technologies, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States
| | - Christian Tovar
- Discovery Oncology, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States
| | - Zoran M Filipovic
- Discovery Oncology, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States
| | - Brian Higgins
- Discovery Oncology, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States
| | - Kelli Glenn
- Non-Clinical Development, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States
| | - Kathryn Packman
- Discovery Oncology, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States
| | - Lyubomir T Vassilev
- Discovery Oncology, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States
| | - Bradford Graves
- Discovery Technologies, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States.
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23
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Ding Q, Zhang Z, Liu JJ, Jiang N, Zhang J, Ross TM, Chu XJ, Bartkovitz D, Podlaski F, Janson C, Tovar C, Filipovic ZM, Higgins B, Glenn K, Packman K, Vassilev LT, Graves B. Discovery of RG7388, a potent and selective p53-MDM2 inhibitor in clinical development. J Med Chem 2013; 56:5979-83. [PMID: 23808545 DOI: 10.1021/jm400487c] [Citation(s) in RCA: 412] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Restoration of p53 activity by inhibition of the p53-MDM2 interaction has been considered an attractive approach for cancer treatment. However, the hydrophobic protein-protein interaction surface represents a significant challenge for the development of small-molecule inhibitors with desirable pharmacological profiles. RG7112 was the first small-molecule p53-MDM2 inhibitor in clinical development. Here, we report the discovery and characterization of a second generation clinical MDM2 inhibitor, RG7388, with superior potency and selectivity.
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Affiliation(s)
- Qingjie Ding
- Discovery Chemistry, ‡Discovery Technologies, §Discovery Oncology, ∥Non-Clinical Development, Roche Research Center, Hoffmann-La Roche, Inc. , 340 Kingsland Street, Nutley, New Jersey 07110, United States
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24
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Rodríguez-Rodríguez JA, Quijada FJ, Brieva R, Rebolledo F, Gotor V. Chemoenzymatic synthesis of orthogonally protected (3R,4R)- and (3S,4S)-trans-3-amino-4-hydroxypyrrolidines. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.04.112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Pandey AK, Naduthambi D, Thomas KM, Zondlo NJ. Proline editing: a general and practical approach to the synthesis of functionally and structurally diverse peptides. Analysis of steric versus stereoelectronic effects of 4-substituted prolines on conformation within peptides. J Am Chem Soc 2013; 135:4333-63. [PMID: 23402492 PMCID: PMC4209921 DOI: 10.1021/ja3109664] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Functionalized proline residues have diverse applications. Herein we describe a practical approach, proline editing, for the synthesis of peptides with stereospecifically modified proline residues. Peptides are synthesized by standard solid-phase peptide synthesis to incorporate Fmoc-hydroxyproline (4R-Hyp). In an automated manner, the Hyp hydroxyl is protected and the remainder of the peptide synthesized. After peptide synthesis, the Hyp protecting group is orthogonally removed and Hyp selectively modified to generate substituted proline amino acids, with the peptide main chain functioning to "protect" the proline amino and carboxyl groups. In a model tetrapeptide (Ac-TYPN-NH2), 4R-Hyp was stereospecifically converted to 122 different 4-substituted prolyl amino acids, with 4R or 4S stereochemistry, via Mitsunobu, oxidation, reduction, acylation, and substitution reactions. 4-Substituted prolines synthesized via proline editing include incorporated structured amino acid mimetics (Cys, Asp/Glu, Phe, Lys, Arg, pSer/pThr), recognition motifs (biotin, RGD), electron-withdrawing groups to induce stereoelectronic effects (fluoro, nitrobenzoate), handles for heteronuclear NMR ((19)F:fluoro; pentafluorophenyl or perfluoro-tert-butyl ether; 4,4-difluoro; (77)SePh) and other spectroscopies (fluorescence, IR: cyanophenyl ether), leaving groups (sulfonate, halide, NHS, bromoacetate), and other reactive handles (amine, thiol, thioester, ketone, hydroxylamine, maleimide, acrylate, azide, alkene, alkyne, aryl halide, tetrazine, 1,2-aminothiol). Proline editing provides access to these proline derivatives with no solution-phase synthesis. All peptides were analyzed by NMR to identify stereoelectronic and steric effects on conformation. Proline derivatives were synthesized to permit bioorthogonal conjugation reactions, including azide-alkyne, tetrazine-trans-cyclooctene, oxime, reductive amination, native chemical ligation, Suzuki, Sonogashira, cross-metathesis, and Diels-Alder reactions. These proline derivatives allowed three parallel bioorthogonal reactions to be conducted in one solution.
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Affiliation(s)
- Anil K. Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - Devan Naduthambi
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - Krista M. Thomas
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
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26
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Krow GR, Edupuganti R, Gandla D, Yu F, Sender M, Sonnet PE, Zdilla MJ, DeBrosse C, Cannon KC, Ross CW, Choudhary A, Shoulders MD, Raines RT. Synthesis of conformationally constrained 5-fluoro- and 5-hydroxymethanopyrrolidines. Ring-puckered mimics of gauche- and anti-3-fluoro- and 3-hydroxypyrrolidines. J Org Chem 2011; 76:3626-34. [PMID: 21500838 PMCID: PMC3304449 DOI: 10.1021/jo200117p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N-acetylmethanopyrrolidine methyl ester and its four 5-syn/anti-fluoro and hydroxy derivatives have been synthesized from 2-azabicyclo[2.2.0]hex-5-ene, a 1,2-dihydropyridine photoproduct. These conformationally constrained mimics of idealized C(β)-gauche and C(β)-anti conformers of pyrrolidines were prepared in order to determine the inherent bridge bias and subsequent heteroatom substituent effects upon trans/cis amide preferences. The bridgehead position and also the presence of gauche(syn)/anti-5-fluoro or 5-hydroxy substituents have minimal influence upon the K(T/C) values of N-acetylamide conformers in both CDCl(3) (43-54% trans) and D(2)O (53-58% trans). O-Benzoylation enhances the trans amide preferences in CDCl(3) (65% for a syn-OBz, 61% for an anti-OBz) but has minimal effect in D(2)O. The synthetic methods developed for N-BOC-methanopyrrolidines should prove useful in the synthesis of more complex derivatives containing α-ester substituents. The K(T/C) results obtained in this study establish baseline amide preferences that will enable determination of contributions of α-ester substituents to trans-amide preferences in methanoprolines.
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Affiliation(s)
- Grant R Krow
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States.
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27
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Kang YK, Byun BJ, Park HS. Conformational preference and cis-trans isomerization of 4-methylproline residues. Biopolymers 2011; 95:51-61. [PMID: 20725948 DOI: 10.1002/bip.21534] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Conformational preferences and prolyl cis-trans isomerizations of the (2S,4S)-4-methylproline (4S-MePro) and (2S,4R)-4-methylproline (4R-MePro) residues are explored at the M06-2X/cc-pVTZ//M06-2X/6-31+G(d) level of theory in the gas phase and in water, where solvation free energies were calculated using the implicit SMD model. In the gas phase, the down-puckered γ-turn structure with the trans prolyl peptide bond is most preferred for both Ac-4S-MePro-NHMe and Ac-4R-MePro-NHMe, in which the C(7) hydrogen bond between two terminal groups seems to play a role, as found for Ac-Pro-NHMe. Because of the C(7) hydrogen bonds weakened by the favorable direct interactions between the backbone C==O and H--N groups and water molecules, the 4S-MePro residue has a strong preference of the up-puckered polyproline II (PP(II)) structure over the down-puckered PP(II) structure in water, whereas the latter somewhat prevails over the former for the 4R-MePro residue. However, these two structures are nearly equally populated for Ac-Pro-NHMe. The calculated populations for the backbone structures of Ac-4S-MePro-NHMe and Ac-4R-MePro-NHMe in water are reasonably consistent with CD and NMR experiments. In particular, our calculated results on the puckering preference of the 4S-MePro and 4R-MePro residues with the PP(II) structures are in accord with the observed results for the stability of the (X-Y-Gly)(7) triple helix with X = 4R-MePro or Pro and Y = 4S-MePro or Pro. The calculated rotational barriers indicate that the cis-trans isomerization may in common proceed through the anticlockwise rotation for Ac-4S-MePro-NHMe, Ac-4R-MePro-NHMe, and Ac-Pro-NHMe in water. The lowest rotational barriers become higher by 0.24-1.43 kcal/mol for Ac-4S-MePro-NHMe and Ac-4R-MePro-NHMe than those for Ac-Pro-NHMe in water.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea.
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28
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Kuemin M, Nagel YA, Schweizer S, Monnard FW, Ochsenfeld C, Wennemers H. Tuning the cis/trans conformer ratio of Xaa-Pro amide bonds by intramolecular hydrogen bonds: the effect on PPII helix stability. Angew Chem Int Ed Engl 2010; 49:6324-7. [PMID: 20665611 DOI: 10.1002/anie.201001851] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Michael Kuemin
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
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29
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Kuemin M, Nagel Y, Schweizer S, Monnard F, Ochsenfeld C, Wennemers H. Tuning the cis/trans Conformer Ratio of Xaa-Pro Amide Bonds by Intramolecular Hydrogen Bonds: The Effect on PPII Helix Stability. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001851] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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30
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Koivisto JJ, Kumpulainen ETT, Koskinen AMP. Conformational ensembles of flexible beta-turn mimetics in DMSO-d6. Org Biomol Chem 2010; 8:2103-16. [PMID: 20401387 DOI: 10.1039/b921794k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Beta-turns play an important role in peptide and protein chemistry, biophysics, and bioinformatics. The aim of this research was to study short linear peptides that have a high propensity to form beta-turn structures in solution. In particular, we examined conformational ensembles of beta-turn forming peptides with a general sequence CBz-L-Ala-L-Xaa-Gly-L-Ala-OtBu. These tetrapeptides, APGA, A(4R)MePGA, and A(4S)MePGA, incorporate proline, (4R)-methylproline, and (4S)-methylproline, respectively, at the Xaa position. To determine the influence of the 4-methyl substituted prolines on the beta-turn populations, the NAMFIS (NMR analysis of molecular flexibility in solution) deconvolution analysis for these three peptides were performed in DMSO-d(6) solution. The NBO (natural bond orbital) method was employed to gain further insight into the results obtained from the NAMFIS analysis. The emphasis in the NBO analysis was to characterize remote intramolecular interactions that could influence the backbone-backbone interactions contributing to beta-turn stability. NAMFIS results indicate that the enantiospecific incorporation of the methyl substituent at the C(gamma) (C4) position of the proline residue can be used to selectively control the pyrrolidine ring puckering propensities and, consequently, the preferred varphi,psi angles associated with the proline residue in beta-turn forming peptides. The NAMFIS analyses show that the presence of (4S)-methylproline in A(4S)MePGA considerably increased the type II beta-turn population with respect to APGA and A(4R)MePGA. The NBO calculations suggest that this observation can be rationalized based on an n-->pi* interaction between the N-terminus alanine carbonyl oxygen and the proline carbonyl group. Several other interactions between remote orbitals in these peptides provide a more detailed explanation for the observed population distributions.
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Affiliation(s)
- Jari J Koivisto
- Aalto University School of Science and Technology, Faculty of Chemistry and Materials Sciences, Department of Chemistry, P.O.Box 16100, FI-00076 Aalto, Finland
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31
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Zhang K, Teklebrhan RB, Schreckenbach G, Wetmore S, Schweizer F. Intramolecular hydrogen bond-controlled prolyl amide isomerization in glucosyl 3'(S)-hydroxy-5'-hydroxymethylproline hybrids: influence of a C-5'-hydroxymethyl substituent on the thermodynamics and kinetics of prolyl amide cis/trans isomerization. J Org Chem 2009; 74:3735-43. [PMID: 19354261 DOI: 10.1021/jo9003458] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptide mimics containing spirocyclic glucosyl-(3'-hydroxy-5'-hydroxymethyl)proline hybrids (Glc3'(S)-5'(CH(2)OH)HypHs) with a polar hydroxymethyl substituent at the C-5' position, such as C-terminal ester Ac-Glc3'(S)-5'(CH(2)OH)Hyp-OMe and C-terminal amide Ac-Glc3'(S)-5'(CH(2)OH)Hyp-N'-CH(3), were synthesized. C-Terminal esters exhibit increased cis population (23-53%) relative to Ac-3(S)HyPro-OMe (17%) or Ac-Pro-OMe (14%) in D(2)O. The prolyl amide cis population is further increased to 38-74% in the C-terminal amide form in D(2)O. Our study shows that the stereochemistry of the hydroxymethyl substituent at the C-5' position of proline permits tuning of the prolyl amide cis/trans isomer ratio. Inversion-magnetization transfer NMR experiments indicate that the stereochemistry of the hydroxymethyl substituent has a dramatic effect on the kinetics of prolyl amide cis/trans isomerization. A 200-fold difference in the trans-to-cis (k(tc)) isomerization and a 90-fold rate difference in the cis-to-trans (k(ct)) isomerization is observed between epimeric C-5' 3 and 4. When compared to reference peptide mimics Ac-Pro-OMe and Ac-3(S)Hyp-OMe, our study demonstrates that a (13-16)-fold decrease in k(tc) and k(ct) is observed for the C-5'(S), while a (5-24)-fold acceleration is observed for the C-5'(R) epimer. DFT calculations indicate that the pyrrolidine ring prefers a C(beta) exo pucker in both Ac-Glc3'(S)-5'(CH(2)OH)Hyp-OMe diastereoisomers. Computational calculations and chemical shift temperature coefficient (Delta delta/Delta T) experiments indicate that the hydroxymethyl group at C-5' in Ac-Glc3'(S)-5'(CH(2)OH)Hyp-OMe forms a stabilizing intramolecular hydrogen bond to the carbonyl of the N-acetyl group in both epimeric cis isomers. However, a competing intramolecular hydrogen bond between the hydroxymethyl groups in the pyrrolidine ring and pyran ring stabilizes the trans isomer in the C-5'(S) diastereoisomer. The dramatic differences in the kinetic properties of the diastereoisomeric peptide mimics are rationalized by the presence or absence of an intramolecular hydrogen bond between the hydroxymethyl substituent located at C-5' and the developing lone pair on the nitrogen atom of the N-acetyl group in the transition state.
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Affiliation(s)
- Kaidong Zhang
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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32
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A new non-natural arginine-like amino acid derivative with a sulfamoyl group in the side-chain. Amino Acids 2009; 38:691-700. [DOI: 10.1007/s00726-009-0267-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Accepted: 02/19/2009] [Indexed: 10/21/2022]
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