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Tosi E, Campagne JM, de Figueiredo RM. Amine Activation: "Inverse" Dipeptide Synthesis and Amide Function Formation through Activated Amino Compounds. J Org Chem 2022; 87:12148-12163. [PMID: 36069394 DOI: 10.1021/acs.joc.2c01288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A copper(II)/HOBt-catalyzed procedure for the synthesis of dipeptides and "general" amides has been developed using microwave irradiation to considerably hasten the reaction. As an alternative to using traditional carboxylic acid activation, the method relies on the use of N-acyl imidazoles as activated amino partners. By doing so, a nonconventional way to reach dipeptides and amides has been proposed through the challenging and less studied N → C direction synthesis. A series of dipeptides and "general" amides have been successfully synthesized, and the applicability of the method has been illustrated in gram-scale syntheses. The mild reaction conditions proposed are completely adequate for couplings in the presence of sensitive amino acids, affording the products without detectable racemization. Furthermore, experimental observations prompted us to propose a plausible reaction pathway for the couplings.
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Affiliation(s)
- Eleonora Tosi
- ICGM, Univ Montpellier, CNRS, ENSCM, Montpellier 34293, France
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2
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Chiral secondary amino acids, their importance, and methods of analysis. Amino Acids 2022; 54:687-719. [PMID: 35192062 DOI: 10.1007/s00726-022-03136-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 02/04/2022] [Indexed: 11/01/2022]
Abstract
Naturally occurring secondary amino acids, with proline as the main representative, contain an alpha-imino group in a cycle that is typically four-, five-, and six-membered. The unique ring structure exhibits exceptional properties-conformational rigidity, chemical stability, and specific roles in protein structure and folding. Many proline analogues have been used as valuable compounds for the study of metabolism of both prokaryotic and eukaryotic cells and for the synthesis of compounds with desired biological, pharmaceutical, or industrial properties. The D-forms of secondary amino acids play different roles in living organisms than the L-forms. They have different metabolic pathways, biological, physiological, and pharmacological effects, they can be indicators of changes and also serve as biomarkers of diseases. In the scientific literature, the number of articles examining D-amino acids in biological samples is increasing. The review summarises information on the occurrence and importance of D- and L-secondary amino acids-azetidic acid, proline, hydroxyprolines, pipecolic, nipecotic, hydroxypipecolic acids and related peptides containing these D-AAs, as well as the main analytical methods (mostly chromatographic) used for their enantiomeric determination in different matrices (biological samples, plants, food, water, and soil).
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Cummings AE, Miao J, Slough DP, McHugh SM, Kritzer JA, Lin YS. β-Branched Amino Acids Stabilize Specific Conformations of Cyclic Hexapeptides. Biophys J 2019; 116:433-444. [PMID: 30661666 DOI: 10.1016/j.bpj.2018.12.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/19/2018] [Accepted: 12/13/2018] [Indexed: 01/11/2023] Open
Abstract
Cyclic peptides (CPs) are a promising class of molecules for drug development, particularly as inhibitors of protein-protein interactions. Predicting low-energy structures and global structural ensembles of individual CPs is critical for the design of bioactive molecules, but these are challenging to predict and difficult to verify experimentally. In our previous work, we used explicit-solvent molecular dynamics simulations with enhanced sampling methods to predict the global structural ensembles of cyclic hexapeptides containing different permutations of glycine, alanine, and valine. One peptide, cyclo-(VVGGVG) or P7, was predicted to be unusually well structured. In this work, we synthesized P7, along with a less well-structured control peptide, cyclo-(VVGVGG) or P6, and characterized their global structural ensembles in water using NMR spectroscopy. The NMR data revealed a structural ensemble similar to the prediction for P7 and showed that P6 was indeed much less well-structured than P7. We then simulated and experimentally characterized the global structural ensembles of several P7 analogs and discovered that β-branching at one critical position within P7 is important for overall structural stability. The simulations allowed deconvolution of thermodynamic factors that underlie this structural stabilization. Overall, the excellent correlation between simulation and experimental data indicates that our simulation platform will be a promising approach for designing well-structured CPs and also for understanding the complex interactions that control the conformations of constrained peptides and other macrocycles.
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Affiliation(s)
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, Massachusetts
| | - Diana P Slough
- Department of Chemistry, Tufts University, Medford, Massachusetts
| | - Sean M McHugh
- Department of Chemistry, Tufts University, Medford, Massachusetts
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts.
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts.
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4
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Northfield SE, Wielens J, Headey SJ, Williams-Noonan BJ, Mulcair M, Scanlon MJ, Parker MW, Thompson PE, Chalmers DK. Cyclic Hexapeptide Mimics of the LEDGF Integrase Recognition Loop in Complex with HIV-1 Integrase. ChemMedChem 2018; 13:1555-1565. [PMID: 29862651 DOI: 10.1002/cmdc.201800129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/21/2018] [Indexed: 12/18/2022]
Abstract
The p75 splice variant of lens epithelium-derived growth factor (LEDGF) is a 75 kDa protein, which is recruited by the human immunodeficiency virus (HIV) to tether the pre-integration complex to the host chromatin and promote integration of proviral DNA into the host genome. We designed a series of small cyclic peptides that are structural mimics of the LEDGF binding domain, which interact with integrase as potential binding inhibitors. Herein we present the X-ray crystal structures, NMR studies, SPR analysis, and conformational studies of four cyclic peptides bound to the HIV-1 integrase core domain. Although the X-ray studies show that the peptides closely mimic the LEDGF binding loop, the measured affinities of the peptides are in the low millimolar range. Computational analysis using conformational searching and free energy calculations suggest that the low affinity of the peptides is due to mismatch between the low-energy solution and bound conformations.
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Affiliation(s)
- Susan E Northfield
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Jerome Wielens
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia.,ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria, 3065, Australia
| | - Stephen J Headey
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Billy J Williams-Noonan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Mark Mulcair
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Michael W Parker
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria, 3065, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
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Akagawa K, Suzuki R, Kudo K. Effect of the Helical Tether of a Resin-Supported Peptide Catalyst for Friedel-Crafts-Type Alkylation in Water. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201100950] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Sharma A, Sharma S, Tripathi RP, Ampapathi RS. Robust Turn Structures in α3β Cyclic Tetrapeptides Induced and Controlled by Carbo-β3 Amino Acid. J Org Chem 2012; 77:2001-7. [DOI: 10.1021/jo2019834] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anindra Sharma
- Divisions
of Medicinal and Process Chemistry and ‡NMR Centre, SAIF, Central Drug Research Institute (CSIR), Lucknow-226001,
India
| | - Shrikant Sharma
- Divisions
of Medicinal and Process Chemistry and ‡NMR Centre, SAIF, Central Drug Research Institute (CSIR), Lucknow-226001,
India
| | - Rama P. Tripathi
- Divisions
of Medicinal and Process Chemistry and ‡NMR Centre, SAIF, Central Drug Research Institute (CSIR), Lucknow-226001,
India
| | - Ravi Sankar Ampapathi
- Divisions
of Medicinal and Process Chemistry and ‡NMR Centre, SAIF, Central Drug Research Institute (CSIR), Lucknow-226001,
India
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Jacobsen Ø, Klaveness J, Rongved P. Structural and pharmacological effects of ring-closing metathesis in peptides. Molecules 2010; 15:6638-77. [PMID: 20877250 PMCID: PMC6257744 DOI: 10.3390/molecules15096638] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 09/13/2010] [Accepted: 09/15/2010] [Indexed: 11/16/2022] Open
Abstract
Applications of ring-closing alkene metathesis (RCM) in acyclic α- and β-peptides and closely related systems are reviewed, with a special emphasis on the structural and pharmacological effects of cyclization by RCM.
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Cluzeau J, Oishi S, Ohno H, Wang Z, Evans B, Peiper SC, Fujii N. Design and synthesis of all diastereomers of cyclic pseudo-dipeptides as mimics of cyclic CXCR4 pentapeptide antagonists. Org Biomol Chem 2007; 5:1915-23. [PMID: 17551641 DOI: 10.1039/b702649h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The four diastereomers of 2,5-bis[(3-guanidino)propyl]-1-[3-(4-hydroxyphenyl)propionyl]-7-(2-naphthylacetyl)-1,4,7-triazacycloundec-9-en-3-one (-) and of 2,5-bis[(3-guanidino)propyl]-1-(4-hydroxyphenylacetyl)-7-(2-naphthylacetyl)-1,4,7-triazacycloundec-9-en-3-one (-) were synthesized by a divergent methodology from l- and D-glutamic acids. The 11-membered ring core was made by ring closing metathesis of linear bis(allylamines), and the guanidyl functions were introduced by a simultaneous double Mitsunobu reaction using bis(Boc)guanidine. These compounds were designed to mimic cyclic pentapeptide FC131 (c[Gly-D-Tyr-Arg-Arg-Nal]).
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Affiliation(s)
- Jérôme Cluzeau
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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Balraju V, Dev RV, Reddy DS, Iqbal J. Synthesis of cyclic peptides using a palladium-catalyzed enyne cycloisomerization. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.03.053] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Synthesis of small cyclic peptides constrained with 3-(3-aminomethylphenyl)propionic acid linkers using free radical-mediated macrocyclization. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.05.115] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Kubasik M, Kotz J, Szabo C, Furlong T, Stace J. Helix-helix interconversion rates of short13C-labeled helical peptides as measured by dynamic NMR spectroscopy. Biopolymers 2005; 78:87-95. [PMID: 15657893 DOI: 10.1002/bip.20235] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The rates at which a peptide hexamer and a peptide octamer interconvert between left- and right-handed helical forms in CD2Cl2 solution have been characterized by 13C dynamic NMR (DNMR) spectroscopy. The peptide esters studied are Fmoc-(Aib)n-OtBu (n = 6 and 8), where Fmoc is 9-fluorenylmethyoxycarbonyl and Aib is the strongly helix-forming residue alpha-aminoisobutyric acid. Because the Aib residue is itself achiral, homooligomers of this residue form a 50/50 mixture of enantiomeric 3(10)-helices in solution. It has been demonstrated (R.-P. Hummel, C. Toniolo, and G. Jung, Angewandte Chemie International Edition, 1987, Vol. 26, pp. 1150-1152) that oligomers of Aib interconvert on the millisecond timescale. We have performed lineshape analysis of 13C-NMR spectra collected for our peptides enriched with 13C at a single residue. Rate constants for the octamer range from 6 s(-1) at 196 K to about 56,500 s(-1) at 320 K. At all temperatures, the hexamer interconverts about three times faster than the octamer. Eyring plots of the data reveal experimentally indistinguishable DeltaH++ values for the hexamer and octamer of 37.8 +/- 0.6 and 37.6 +/- 0.4 kJ mol(-1) respectively. The difference in the rates of interconversion is dictated by entropic factors. The hexamer and octamer exhibit negative DeltaS++ values of -29.0(-1) +/- 2.5 and -37.3 +/- 1.7 J K(-1) mol(-1), respectively. A mechanism for the helix-helix interconversion is proposed. and calculated DeltaG++ values are compared to the estimate for a decamer undergoing a helix-helix interconversion.
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Affiliation(s)
- Matthew Kubasik
- Department of Chemistry, Fairfield University, Fairfield, CT 06824, USA.
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