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Sanches K, Wai DCC, Norton RS. Conformational dynamics in peptide toxins: Implications for receptor interactions and molecular design. Toxicon 2021; 201:127-140. [PMID: 34454969 DOI: 10.1016/j.toxicon.2021.08.020] [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: 07/07/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 10/20/2022]
Abstract
Peptide toxins are potent and often exquisitely selective probes of the structure and function of ion channels and receptors, and are therefore of significant interest to the pharmaceutical and biotech industries as both pharmacological tools and therapeutic leads. The three-dimensional structures of peptide toxins are essential as a basis for understanding their structure-activity relationships and their binding to target receptors, as well as in guiding the design of analogues with modified potency and/or selectivity for key targets. NMR spectroscopy has played a key role in elucidating the structures of peptide toxins and probing their structure-function relationships. In this article, we highlight the additional important contribution of NMR to characterising the dynamics of peptide toxins. We also compare the information available from NMR measurements with that afforded by molecular dynamics simulations. We describe several examples of the importance of dynamics measurements over a range of timescales for understanding the structure-function relationships of peptide toxins and their receptor engagement. Peptide toxins that inhibit the voltage-gated potassium channel KV1.3 with pM affinities display different degrees of conformational flexibility, even though they contain multiple disulfide bonds, and this flexibility can affect the relative orientation of residues that have been shown to be critical for channel binding. Information on the dynamic properties of peptide toxins is important in the design of analogues or mimetics where receptor-bound structures are not available.
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Affiliation(s)
- Karoline Sanches
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia; ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria, 3052, Australia
| | - Dorothy C C Wai
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia; ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria, 3052, Australia.
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2
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Kennedy AC, Belgi A, Husselbee BW, Spanswick D, Norton RS, Robinson AJ. α-Conotoxin Peptidomimetics: Probing the Minimal Binding Motif for Effective Analgesia. Toxins (Basel) 2020; 12:E505. [PMID: 32781580 PMCID: PMC7472027 DOI: 10.3390/toxins12080505] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 12/18/2022] Open
Abstract
Several analgesic α-conotoxins have been isolated from marine cone snails. Structural modification of native peptides has provided potent and selective analogues for two of its known biological targets-nicotinic acetylcholine and γ-aminobutyric acid (GABA) G protein-coupled (GABAB) receptors. Both of these molecular targets are implicated in pain pathways. Despite their small size, an incomplete understanding of the structure-activity relationship of α-conotoxins at each of these targets has hampered the development of therapeutic leads. This review scrutinises the N-terminal domain of the α-conotoxin family of peptides, a region defined by an invariant disulfide bridge, a turn-inducing proline residue and multiple polar sidechain residues, and focusses on structural features that provide analgesia through inhibition of high-voltage-activated Ca2+ channels. Elucidating the bioactive conformation of this region of these peptides may hold the key to discovering potent drugs for the unmet management of debilitating chronic pain associated with a wide range of medical conditions.
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Affiliation(s)
- Adam C. Kennedy
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia; (A.C.K.); (A.B.); (B.W.H.)
| | - Alessia Belgi
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia; (A.C.K.); (A.B.); (B.W.H.)
| | - Benjamin W. Husselbee
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia; (A.C.K.); (A.B.); (B.W.H.)
| | - David Spanswick
- Biomedicine Discovery Institute and the Department of Physiology, Monash University, Victoria 3800, Australia;
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
- NeuroSolutions Ltd., Coventry CV4 7AL, UK
| | - Raymond S. Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Science, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia;
- ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria 3052, Australia
| | - Andrea J. Robinson
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia; (A.C.K.); (A.B.); (B.W.H.)
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3
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Wong MSY, Jolliffe KA. A comparison of pseudoproline substitution effects on cyclisation yield in the total syntheses of segetalins B and G. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Michelle S. Y. Wong
- School of ChemistryThe University of SydneySydney New South Wales2006 Australia
| | - Katrina A. Jolliffe
- School of ChemistryThe University of SydneySydney New South Wales2006 Australia
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4
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Tietze D, Leipold E, Heimer P, Böhm M, Winschel W, Imhof D, Heinemann SH, Tietze AA. Molecular interaction of δ-conopeptide EVIA with voltage-gated Na+ channels. Biochim Biophys Acta Gen Subj 2016; 1860:2053-63. [DOI: 10.1016/j.bbagen.2016.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/02/2016] [Accepted: 06/12/2016] [Indexed: 12/19/2022]
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Prabhu G, Narendra N, Basavaprabhu B, Panduranga V, Sureshbabu VV. Amino acid fluorides: viable tools for synthesis of peptides, peptidomimetics and enantiopure heterocycles. RSC Adv 2015. [DOI: 10.1039/c4ra16142d] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This review provides a broad perspective of the uses of amino acid fluorides in the synthesis of peptides and a wide range of other molecules including peptidomimetics, heterocycles and biologically active molecules.
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Affiliation(s)
- Girish Prabhu
- Room No. 109, Peptide Research Laboratory
- Department of Studies in Chemistry
- Central College Campus
- Dr B. R. Ambedkar Veedhi
- Bangalore University
| | - N. Narendra
- Department of Chemistry
- University College of Science
- Tumkur University
- Tumkur-572 103
- India
| | - Basavaprabhu Basavaprabhu
- Room No. 109, Peptide Research Laboratory
- Department of Studies in Chemistry
- Central College Campus
- Dr B. R. Ambedkar Veedhi
- Bangalore University
| | - V. Panduranga
- Room No. 109, Peptide Research Laboratory
- Department of Studies in Chemistry
- Central College Campus
- Dr B. R. Ambedkar Veedhi
- Bangalore University
| | - Vommina V. Sureshbabu
- Room No. 109, Peptide Research Laboratory
- Department of Studies in Chemistry
- Central College Campus
- Dr B. R. Ambedkar Veedhi
- Bangalore University
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6
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Qian Z, Dougherty PG, Liu T, Oottikkal S, Hogan PG, Hadad CM, Pei D. Structure-based optimization of a peptidyl inhibitor against calcineurin-nuclear factor of activated T cell (NFAT) interaction. J Med Chem 2014; 57:7792-7. [PMID: 25162754 PMCID: PMC4174996 DOI: 10.1021/jm500743t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Calcineurin
inhibitors such as cyclosporine A and FK506 are effective
immunosuppressants but produce severe side effects. Rational modification
of a previously reported peptide inhibitor, GPHPVIVITGPHEE (KD ∼ 500 nM), by replacing the two valine
residues with tert-leucine and the C-terminal proline
with a cis-proline analogue, gave an improved inhibitor
ZIZIT-cisPro, which binds to calcineurin with a KD value of 2.6 nM and is more resistant to proteolysis.
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Affiliation(s)
- Ziqing Qian
- Department of Chemistry and Biochemistry, The Ohio State University , 484 West 12th Avenue, Columbus, Ohio 43210, United States
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7
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Chaume G, Simon J, Caupène C, Lensen N, Miclet E, Brigaud T. Incorporation of CF3–Pseudoprolines into Peptides: A Methodological Study. J Org Chem 2013; 78:10144-53. [DOI: 10.1021/jo401494q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Grégory Chaume
- Laboratoire SOSCO, Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Julien Simon
- Laboratoire SOSCO, Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Caroline Caupène
- Laboratoire SOSCO, Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Nathalie Lensen
- Laboratoire SOSCO, Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Emeric Miclet
- Laboratoire des
BioMolécules, UMR 7203, Ecole Normale Supérieure, UPMC Paris 06, 4 Place Jussieu, 75005 Paris, France
| | - Thierry Brigaud
- Laboratoire SOSCO, Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
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Tischler M, Nasu D, Empting M, Schmelz S, Heinz DW, Rottmann P, Kolmar H, Buntkowsky G, Tietze D, Avrutina O. Peptid in Ketten: Einblicke in die Struktur-Aktivitäts-Beziehungen von Proteaseinhibitormimetika mit fixierten Amidkonformationen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108983] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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9
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Tischler M, Nasu D, Empting M, Schmelz S, Heinz DW, Rottmann P, Kolmar H, Buntkowsky G, Tietze D, Avrutina O. Braces for the peptide backbone: insights into structure-activity relationships of protease inhibitor mimics with locked amide conformations. Angew Chem Int Ed Engl 2012; 51:3708-12. [PMID: 22374650 DOI: 10.1002/anie.201108983] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Indexed: 01/08/2023]
Affiliation(s)
- Marco Tischler
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Petersenstrasse 22, 64287 Darmstadt, Germany
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10
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Monbaliu JCM, Katritzky AR. Recent trends in Cys- and Ser/Thr-based synthetic strategies for the elaboration of peptide constructs. Chem Commun (Camb) 2012; 48:11601-22. [DOI: 10.1039/c2cc34434c] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Xu J, Wang Y, Zhang B, Wang B, Du W. Stereochemistry of 4-hydroxyproline affects the conformation of conopeptides. Chem Commun (Camb) 2010; 46:5467-9. [PMID: 20428585 DOI: 10.1039/c0cc00075b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cis/trans isomerization of 4-hydroxyproline is shown to remarkably affect the conformation of conopeptides with or without disulfide bonds.
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Affiliation(s)
- Jia Xu
- Department of Chemistry, Renmin University of China, Beijing, 100872, China
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12
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Tietze D, Tischler M, Voigt S, Imhof D, Ohlenschläger O, Görlach M, Buntkowsky G. Development of a functional cis-prolyl bond biomimetic and mechanistic implications for nickel superoxide dismutase. Chemistry 2010; 16:7572-8. [PMID: 20461826 DOI: 10.1002/chem.200903306] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
During recent years several peptide-based Ni superoxide dismutase (NiSOD) models have been developed. These NiSOD models show an important structural difference compared to the native NiSOD enzyme, which could cause a completely different mechanism of superoxide dismutation. In the native enzyme the peptide bond between Leu4 and Pro5 is cis-configured, while the NiSOD models exhibit a trans-configured peptide bond between these two residues. To shed light on how the configuration of this single peptide bond influences the activity of the NiSOD model peptides, a new cis-prolyl bond surrogate was developed. As surrogate we chose a leucine/alanine-based disubstituted 1,2,3-triazole, which was incorporated into the NiSOD model peptide replacing residues Leu4 and Pro5. The yielded 1,5-disubstituted triazole nickel peptide exhibited high SOD activity, which was approximately the same activity as its parent trans-configured analogue. Hence, the conformation of the prolyl peptide bond apparently has of minor importance for the catalytic activity of the metallopeptides as postulated in literature. Furthermore, it is shown that the triazole metallopeptide is forming a stable cyanide adduct as a substrate analogue model complex.
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Affiliation(s)
- Daniel Tietze
- Technische Universität Darmstadt, Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Petersenstr. 22, 64287 Darmstadt, Germany
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13
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14
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Wong MSY, Jolliffe KA. Synthesis of Cyclogossine B Using a Traceless Pseudoproline Turn-Inducer. Aust J Chem 2010. [DOI: 10.1071/ch09643] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The first synthesis of the cyclic octapeptide, cyclogossine B, has been achieved, confirming the reported structure of this natural product. Cyclization of a linear precursor containing a cysteine-derived thiazolidine as a traceless turn-inducer occurred in significantly higher yields than cyclization of the analogous alanine-containing precursor under identical conditions. Deprotection of the thiazolidine followed by desulfurization provided cyclogossine B in good overall yield, indicating that cysteine-derived pseudoprolines can be effectively used as traceless turn-inducers to facilitate the cyclization of small peptides.
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15
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Haddad V, Lupi O, Lonza JP, Tyring SK. Tropical dermatology: Marine and aquatic dermatology. J Am Acad Dermatol 2009; 61:733-50; quiz 751-2. [DOI: 10.1016/j.jaad.2009.01.046] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Revised: 01/05/2009] [Accepted: 01/11/2009] [Indexed: 02/06/2023]
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16
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Kantharaju, Raghothama S, Raghavender US, Aravinda S, Shamala N, Balaram P. Conformations of heterochiral and homochiral proline-pseudoproline segments in peptides: Context dependentcis-transpeptide bond isomerization. Biopolymers 2009; 92:405-16. [DOI: 10.1002/bip.21207] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Jamet H, Jourdan M, Dumy P. NMR and Theoretical Calculations: A Unified View of the Cis/Trans Isomerization of 2-Substituted Thiazolidines Containing Peptides. J Phys Chem B 2008; 112:9975-81. [DOI: 10.1021/jp7118982] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Helene Jamet
- Département de Chimie Moléculaire, UMR-5250, ICMG FR-2607,CNRS, 301 rue de la Chimie, 38041 Grenoble Cedex 9, France
| | - Muriel Jourdan
- Département de Chimie Moléculaire, UMR-5250, ICMG FR-2607,CNRS, 301 rue de la Chimie, 38041 Grenoble Cedex 9, France
| | - Pascal Dumy
- Département de Chimie Moléculaire, UMR-5250, ICMG FR-2607,CNRS, 301 rue de la Chimie, 38041 Grenoble Cedex 9, France
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18
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Haddad V, de Paula Neto JB, Cobo VJ. Venomous mollusks: the risks of human accidents by conus snails (gastropoda: conidae) in Brazil. Rev Soc Bras Med Trop 2007; 39:498-500. [PMID: 17160331 DOI: 10.1590/s0037-86822006000500015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Accepted: 08/10/2006] [Indexed: 11/22/2022] Open
Abstract
Mollusks of the genus Conus present a venomous apparatus composed of radulae, a chitin structure linked to glands, which injects potent neurotoxic peptides, causing serious human envenomation and even death, associated with the blockage of certain receptors and muscular paralysis. No reported envenomation has occurred in Brazil, but certain populations are at risk of accidents.
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Affiliation(s)
- Vidal Haddad
- Faculdade de Medicina de Botucatu, Universidade Estadual Paulista, Botucatu, SP.
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19
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Suaifan GARY, Arafat T, Threadgill MD. Synthetic approaches to peptides containing the l-Gln-l-Val-D(S)-Dmt motif. Bioorg Med Chem 2007; 15:3474-88. [PMID: 17376694 DOI: 10.1016/j.bmc.2007.03.005] [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: 11/06/2006] [Revised: 02/16/2007] [Accepted: 03/02/2007] [Indexed: 10/23/2022]
Abstract
The pseudoprolines S-Dmo (5,5-dimethyl-4-oxaproline) and R-Dmt (5,5-dimethyl-4-thiaproline) have been used to study the effects of forcing a fully cis conformation in peptides. Synthesis of peptides containing these (which have the same configuration as L-Pro) is straightforward. However, synthesis of peptides containing S-Dmt is difficult, owing to the rapid cyclisation of L-Aaa-S-Dmt amides and esters to form the corresponding diketopiperazines (DKP); thus the intermediacy of L-Aaa-S-Dmt amides and esters must be avoided in the synthetic sequence. Peptides containing the L-Gln-L-Val-D(S)-Dmt motif are particularly difficult, owing to the insolubility of coupling partners containing Gln. Introduction of Gln as N-Boc-pyroglutamate overcame the latter difficulty and the dipeptide active ester BocPygValOC(6)F(5) coupled in good yield with S-DmtOH. BocPygVal-S- DmtNH(CH(2))(2)C(6)H(4)NO(2) was converted quantitatively to BocGlnVal-S-DmtNH(CH(2))(2)C(6)H(4)NO(2) with ammonia, demonstrating the utility of this approach. Two peptide derivatives (CbzSerLysLeuGlnVal-S-DmtNH(CH(2))(2)C(6)H(4)NO(2) and CbzSerSerLysLeuGlnVal-S- DmtNH(CH(2))(2)C(6)H(4)NO(2)) were assembled, using these new methods of coupling a dipeptide acid active ester with S-DmtOH and introduction of Gln as Pyg, followed by conventional peptide couplings. The presence of the Val caused these peptides to be cleaved very slowly by prostate-specific antigen (PSA) at Leu Gln, rather than the expected Gln Val.
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Affiliation(s)
- Ghadeer A R Y Suaifan
- Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
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Chatterjee J, Mierke D, Kessler H. N-methylated cyclic pentaalanine peptides as template structures. J Am Chem Soc 2007; 128:15164-72. [PMID: 17117868 DOI: 10.1021/ja063123d] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The N-methylation of cyclic peptides can be used to modify the activity and/or selectivity of biologically active peptides. As N-methylation introduces different flexibility and lipophilicity, it can also improve the bioavailability (the ADMET profile). To search for conformationally constrained cyclic peptides, a library of 30 different N-methylated peptides with the basic sequence cyclo(-D-Ala-L-Ala4-) was synthesized. Based on the NMR analysis, seven of these peptides exhibited single conformations (>98%). The structural features of these peptides were determined by a combination of NMR and distance geometry and then further refined by molecular dynamics simulations in an explicit DMSO solvent box. The structures provided from these efforts can now serve as templates for the rational design of cyclic pentapeptides with a distinct backbone conformation or for "spatial screening" to explore the bioactive conformation of medically important peptide systems.
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Affiliation(s)
- Jayanta Chatterjee
- Department Chemie, Lehrstuhl II für Organische Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching D-85747, Germany
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