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Cao X, Liu T, Wang T, Wang X, Xu Z, Zhou L, Tian C, Sun D. De Novo Screening and Mirror Image Isomerization of Linear Peptides Targeting α7 Nicotinic Acetylcholine Receptor. ACS Chem Biol 2024; 19:592-598. [PMID: 38380973 DOI: 10.1021/acschembio.3c00674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
As ligand-gated ion channels, nicotinic acetylcholine receptors (nAChRs) are widely distributed in the central and peripheral nervous systems and are associated with the pathogenesis of various degenerative neurological diseases. Here, we report the results of phage display-based de novo screening of an 11-residue linear peptide (named LKP1794) that targets the α7 nAChR, which is among the most abundant nAChR subtypes in the brain. Moreover, two d-peptides were generated through mirror image and/or primary sequence inverso isomerization (termed DRKP1794 and DKP1794) and displayed improved inhibitory effects (IC50 = 0.86 and 0.35 μM, respectively) on α7 nAChR compared with the parent l-peptide LKP1794 (IC50 = 2.48 μM), which markedly enhanced serum stability. A peptide-based fluorescence probe was developed using proteolytically resistant DKP1794 to specifically image the α7 nAChR in living cells. This work provides a new peptide tool to achieve inhibitory modulation and specifically image the α7 nAChR.
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Affiliation(s)
- Xiuxiu Cao
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, P. R. China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Tianqi Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Tao Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Xudong Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Ziyan Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Li Zhou
- Anhui Provincial Peptide Drug Laboratory, Hefei 230026, P. R. China
| | - Changlin Tian
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, P. R. China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
- Anhui Provincial Peptide Drug Laboratory, Hefei 230026, P. R. China
- School of Biomedical Engineering, Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, P. R. China
- Beijing Life Science Academy, Beijing 102200, P. R. China
| | - Demeng Sun
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
- Anhui Provincial Peptide Drug Laboratory, Hefei 230026, P. R. China
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Errante F, Pallecchi M, Bartolucci G, Frediani E, Margheri F, Giovannelli L, Papini AM, Rovero P. Retro-Inverso Collagen Modulator Peptide Derived from Serpin A1 with Enhanced Stability and Activity In Vitro. J Med Chem 2024. [PMID: 38470817 DOI: 10.1021/acs.jmedchem.4c00137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The rising demand for novel cosmeceutical ingredients has highlighted peptides as a significant category. Based on the collagen turnover modulation properties of SA1-III, a decapeptide derived from a serine protease inhibitor (serpin A1), this study focused on designing shorter, second-generation peptides endowed with improved properties. A tetrapeptide candidate was further modified employing the retro-inverso approach that uses d-amino acids aiming to enhance peptide stability against dermal enzymes. Surprisingly, the modified peptide AAT11RI displayed notably high activity in vitro, as compared to its precursors, and suggested a mode of action based on the inhibition of collagen degradation. It is worth noting that AAT11RI showcases stability against dermal enzymes contained in human skin homogenates due to its rationally designed structure that hampers recognition by most proteases. The rational approach we embraced in this study underscored the added value of substantiated claims in the design of new cosmeceutical ingredients, representing a rarity in the field.
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Affiliation(s)
- Fosca Errante
- Department of Neurosciences, Psychology, Drug Research and Child Health, University of Florence, Sesto Fiorentino, FI 50019, Italy
- Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
- Espikem s.r.l., Prato, PO 59100, Italy
| | - Marco Pallecchi
- Department of Neurosciences, Psychology, Drug Research and Child Health, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Gianluca Bartolucci
- Department of Neurosciences, Psychology, Drug Research and Child Health, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Elena Frediani
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Firenze, FI 50139, Italy
| | - Francesca Margheri
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Firenze, FI 50139, Italy
| | - Lisa Giovannelli
- Department of Neurosciences, Psychology, Drug Research and Child Health, University of Florence, Firenze, FI 50139, Italy
| | - Anna M Papini
- Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Paolo Rovero
- Department of Neurosciences, Psychology, Drug Research and Child Health, University of Florence, Sesto Fiorentino, FI 50019, Italy
- Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
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HIV-1 gp120-CXCR4 recognition probed with synthetic nanomolar affinity D-peptides containing fragments of gp120 V3 loop. Eur J Med Chem 2022; 244:114797. [PMID: 36270088 PMCID: PMC10150781 DOI: 10.1016/j.ejmech.2022.114797] [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: 05/18/2022] [Revised: 09/18/2022] [Accepted: 09/23/2022] [Indexed: 11/22/2022]
Abstract
The human immunodeficiency virus type 1 (HIV-1) recognizes one of its principal coreceptors, the CXC chemokine receptor 4 (CXCR4) on the host cell via the third variable loop (V3 loop) of HIV-1 envelope glycoprotein gp120 during the viral entry process. Here, we investigated the stereochemical mechanism of the molecular recognition of HIV-1 gp120 V3 loop with coreceptor CXCR4 by using peptide probes containing important fragments of the V3 loop. The tip and base/stem fragments of the V3 loop critical for V3 loop function were linked individually with the fragment derived from another CXCR4's chemokine ligand, vMIP-II to generate nanomolar affinity peptide probes of the interactions of CXCR4-V3 loop fragments. When the amino acid residues of the V3 loop fragments in these combinational peptides were changed from L-to D-configurations, the resulting peptides remarkably retained or had even enhanced recognition by CXCR4 as shown by competitive ligand-receptor binding. The ability of these peptides, regardless of the different l- or d-amino acids used, in binding CXCR4 and antagonizing CXCR4 functions was demonstrated by their blockade of calcium influx, cell migration, and CXCR4 internalization triggered by the activation of CXCR4 signaling by its endogenous ligand SDF-1α. The structural mechanisms of CXCR4 interactions with these peptides were examined with site-directed mutagenesis and molecular modeling. These results indicate that CXCR4's interface with key segments of HIV-1 gp120 V3 loop is flexible in terms of stereospecificity of ligand-receptor interaction which may have implication on understanding the viral entry mechanism and how the virus evades immune detection with V3 loop mutations and retains effective recognition of the host cell's coreceptor.
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Recent Applications of Retro-Inverso Peptides. Int J Mol Sci 2021; 22:ijms22168677. [PMID: 34445382 PMCID: PMC8395423 DOI: 10.3390/ijms22168677] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 12/14/2022] Open
Abstract
Natural and de novo designed peptides are gaining an ever-growing interest as drugs against several diseases. Their use is however limited by the intrinsic low bioavailability and poor stability. To overcome these issues retro-inverso analogues have been investigated for decades as more stable surrogates of peptides composed of natural amino acids. Retro-inverso peptides possess reversed sequences and chirality compared to the parent molecules maintaining at the same time an identical array of side chains and in some cases similar structure. The inverted chirality renders them less prone to degradation by endogenous proteases conferring enhanced half-lives and an increased potential as new drugs. However, given their general incapability to adopt the 3D structure of the parent peptides their application should be careful evaluated and investigated case by case. Here, we review the application of retro-inverso peptides in anticancer therapies, in immunology, in neurodegenerative diseases, and as antimicrobials, analyzing pros and cons of this interesting subclass of molecules.
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Chen J, Meng Q, Zhang Y, Dong M, Zhao L, Zhang Y, Chen L, Chai Y, Meng Z, Wang C, Jia X, Li C. Complexation of an Antimicrobial Peptide by Large‐Sized Macrocycles for Decreasing Hemolysis and Improving Stability. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Junyi Chen
- College of Environmental and Chemical Engineering Shanghai University Shanghai 200444 P. R. China
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Qingbin Meng
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Yadan Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Ming Dong
- Key Laboratory of Inorganic-Organic Hybrid Functional Material Chemistry Ministry of Education Tianjin Key Laboratory of Structure and Performance for Functional Molecules College of Chemistry Tianjin Normal University Tianjin 300387 China
| | - Liang Zhao
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Yahan Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Longming Chen
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Yao Chai
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Zhao Meng
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Chenhong Wang
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Xueshun Jia
- College of Environmental and Chemical Engineering Shanghai University Shanghai 200444 P. R. China
| | - Chunju Li
- College of Environmental and Chemical Engineering Shanghai University Shanghai 200444 P. R. China
- Key Laboratory of Inorganic-Organic Hybrid Functional Material Chemistry Ministry of Education Tianjin Key Laboratory of Structure and Performance for Functional Molecules College of Chemistry Tianjin Normal University Tianjin 300387 China
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Chen J, Meng Q, Zhang Y, Dong M, Zhao L, Zhang Y, Chen L, Chai Y, Meng Z, Wang C, Jia X, Li C. Complexation of an Antimicrobial Peptide by Large‐Sized Macrocycles for Decreasing Hemolysis and Improving Stability. Angew Chem Int Ed Engl 2021; 60:11288-11293. [DOI: 10.1002/anie.202102706] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Indexed: 12/18/2022]
Affiliation(s)
- Junyi Chen
- College of Environmental and Chemical Engineering Shanghai University Shanghai 200444 P. R. China
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Qingbin Meng
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Yadan Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Ming Dong
- Key Laboratory of Inorganic-Organic Hybrid Functional Material Chemistry Ministry of Education Tianjin Key Laboratory of Structure and Performance for Functional Molecules College of Chemistry Tianjin Normal University Tianjin 300387 China
| | - Liang Zhao
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Yahan Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Longming Chen
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Yao Chai
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Zhao Meng
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Chenhong Wang
- State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and Toxicology Beijing 100850 P. R. China
| | - Xueshun Jia
- College of Environmental and Chemical Engineering Shanghai University Shanghai 200444 P. R. China
| | - Chunju Li
- College of Environmental and Chemical Engineering Shanghai University Shanghai 200444 P. R. China
- Key Laboratory of Inorganic-Organic Hybrid Functional Material Chemistry Ministry of Education Tianjin Key Laboratory of Structure and Performance for Functional Molecules College of Chemistry Tianjin Normal University Tianjin 300387 China
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Djillani A, Pietri M, Mazella J, Heurteaux C, Borsotto M. Fighting against depression with TREK-1 blockers: Past and future. A focus on spadin. Pharmacol Ther 2018; 194:185-198. [PMID: 30291907 DOI: 10.1016/j.pharmthera.2018.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Depression is a devastating mood disorder and a leading cause of disability worldwide. Depression affects approximately one in five individuals in the world and represents heavy economic and social burdens. The neurobiological mechanisms of depression are not fully understood, but evidence highlights the role of monoamine neurotransmitter balance. Several antidepressants (ADs) are marketed to treat depression and related mood disorders. However, despite their efficacy, they remain nonspecific and unsafe because they trigger serious adverse effects. Therefore, developing new molecules for new targets in depression has become a real necessity. Eight years ago, spadin was described as a natural peptide with AD properties. This 17-amino acid peptide blocks TREK-1 channels, an original target in depression. Compared to the classical AD drugs such as fluoxetine, which requires 3-4 weeks for the AD effect to manifest, spadin acts rapidly within only 4 days of treatment. The AD properties are associated with increased neurogenesis and synaptogenesis in the brain. Despite the advantages of this fast-acting AD, the in vivo stability is weak and does not last for >7 h. The present review summarizes different strategies such as retro-inverso strategy, cyclization, and shortening the spadin sequence that has led to the development and optimization of spadin as an AD. Shortened spadin analogs present increased inhibition potency for TREK-1, an improved AD activity, and prolonged in vivo bioavailability. Finally, we also discuss about other inhibitors of TREK-1 channels with a proven efficacy in treating depression in the clinic, such as fluoxetine.
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Affiliation(s)
- Alaeddine Djillani
- Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, UMR7275, Université Côte d'Azur, Valbonne, France; Université Côte d'Azur, CNRS, IPMC, France
| | - Mariel Pietri
- Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, UMR7275, Université Côte d'Azur, Valbonne, France; Université Côte d'Azur, CNRS, IPMC, France
| | - Jean Mazella
- Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, UMR7275, Université Côte d'Azur, Valbonne, France; Université Côte d'Azur, CNRS, IPMC, France
| | - Catherine Heurteaux
- Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, UMR7275, Université Côte d'Azur, Valbonne, France; Université Côte d'Azur, CNRS, IPMC, France
| | - Marc Borsotto
- Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, UMR7275, Université Côte d'Azur, Valbonne, France; Université Côte d'Azur, CNRS, IPMC, France.
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Retro-inverso Urokinase Receptor Antagonists for the Treatment of Metastatic Sarcomas. Sci Rep 2017; 7:1312. [PMID: 28465589 PMCID: PMC5430962 DOI: 10.1038/s41598-017-01425-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/29/2017] [Indexed: 11/12/2022] Open
Abstract
The development of metastases is a multistep process that requires the activation of physiological and biochemical processes that govern migration, invasion and entry of metastatic cells into blood vessels. The urokinase receptor (uPAR) promotes cell migration by interacting with the Formyl Peptide Receptors (FPRs). Since both uPAR and FPR1 are involved in tumor progression, the uPAR-FPR1 interaction is an attractive therapeutic target. We previously described peptide antagonists of the uPAR-FPR1 interaction that inhibited cell migration and angiogenesis. To develop enzyme-resistant analogues, we applied here the Retro-Inverso (RI) approach, whereby the topology of the side chains is maintained by inverting the sequence of the peptide and the chirality of all residues. Molecular dynamics suggests that peptide RI-3 adopts the turn structure typical of uPAR-FPR1 antagonists. Accordingly, RI-3 is a nanomolar competitor of N-formyl-Met-Leu-Phe for binding to FPR1 and inhibits migration, invasion, trans-endothelial migration of sarcoma cells and VEGF-triggered endothelial tube formation. When sarcoma cells were subcutaneously injected in nude mice, tumor size, intra-tumoral microvessel density, circulating tumor cells and pulmonary metastases were significantly reduced in animals treated daily with 6 mg/Kg RI-3 as compared to animals treated with vehicle only. Thus, RI-3 represents a promising lead for anti-metastatic drugs.
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9
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Synthesis, molecular structure, spectral analysis, and biological activity of new malonamide derivatives as α-glucosidase inhibitors. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.12.093] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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10
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Computational and spectroscopic data correlation study of N,N'-bisarylmalonamides (Part II). J Mol Model 2015; 21:239. [PMID: 26289037 DOI: 10.1007/s00894-015-2777-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 07/28/2015] [Indexed: 10/23/2022]
Abstract
To complement a previous UV study, we present a quantitative evaluation of substituent effects on spectroscopic data ((1)H and (13)C NMR chemical shifts as well as FT-IR absorption frequency) applied to N,N'-bisarylmalonamides, using simple and extended Hammett equations as well as the Swain-Lupton equation. Furthermore, the DFT CAM-B3LYP/6-311+G(d,p) method was applied to study the impact of different solvents on the geometry of the molecules and their spectral data. Additionally, experimental data are correlated with theoretical results; excellent linear dependence was obtained. The overall results presented in this paper show that N,N'-bisarylmalonamides are prominent candidates for model molecules.
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Arsovski VM, Božić BĐ, Mirković JM, Vitnik VD, Vitnik ZJ, Fabian WMF, Petrović SD, Mijin DZ. Spectroscopic and quantum mechanical investigation of N,N'-bisarylmalonamides: solvent and structural effects. J Mol Model 2014; 20:2384. [PMID: 25116150 DOI: 10.1007/s00894-014-2384-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/17/2014] [Indexed: 11/26/2022]
Abstract
The UV absorption spectra of ten N,N'-bisarylmalonamides have been recorded in the range 200-400 nm in a set of selected solvents. The solute-solvent interactions have been analyzed on the basis of the linear solvation energy relationship (LSER) concept proposed by Kamlet and Taft. The effects of substituents on the absorption spectra have been interpreted by correlating absorption frequencies with Hammett substituent constants. Furthermore, the experimental findings have been interpreted using the DFT CAM-B3LYP/6-311+G(d,p) method. Electronic energies have been calculated using the same method in combination with the implicit solvation model (conductor-like polarizable continuum model, CPCM) as well as with the explicit addition of two molecules of solvent.
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Croft NP, Purcell AW. Peptidomimetics: modifying peptides in the pursuit of better vaccines. Expert Rev Vaccines 2014; 10:211-26. [DOI: 10.1586/erv.10.161] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Ruttekolk IR, Witsenburg JJ, Glauner H, Bovee-Geurts PHM, Ferro ES, Verdurmen WPR, Brock R. The intracellular pharmacokinetics of terminally capped peptides. Mol Pharm 2012; 9:1077-86. [PMID: 22497602 DOI: 10.1021/mp200331g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
With significant progress in delivery technologies, peptides and peptidomimetics are receiving increasing attention as potential therapeutics also for intracellular applications. However, analyses of the intracellular behavior of peptides are a challenge; therefore, knowledge on the intracellular pharmacokinetics of peptides is limited. So far, most research has focused on peptide degradation in the context of antigen processing, rather than on peptide stability. Here, we studied the structure-activity relationship of peptides with respect to intracellular residence time and proteolytic breakdown. The peptides comprised a collection of interaction motifs of SH2 and SH3 domains with different charge but that were of similar size and carried an N-terminal fluorescein moiety. First, we show that electroporation is a highly powerful technique to introduce peptides with different charge and hydrophobicity in uniform yields. Remarkably, the peptides differed strongly in retention of intracellular fluorescence with half-lives ranging from only 1 to more than 10 h. Residence times were greatly increased for retro-inverso peptides, demonstrating that rapid loss of fluorescence is a function of peptide degradation rather than the physicochemical characteristics of the peptide. Differences in proteolytic sensitivity were further confirmed using fluorescence correlation spectroscopy as a separation-free analytical technique to follow degradation in crude cell lysates and also in intact cells. The results provide a straightforward analytical access to a better understanding of the principles of peptide stability inside cells and will therefore greatly assist the development of bioactive peptides.
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Affiliation(s)
- Ivo R Ruttekolk
- Department of Biochemistry, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands
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Ruttekolk IR, Chakrabarti A, Richter M, Duchardt F, Glauner H, Verdurmen WPR, Rademann J, Brock R. Coupling to polymeric scaffolds stabilizes biofunctional peptides for intracellular applications. Mol Pharmacol 2011; 79:692-700. [PMID: 21247935 DOI: 10.1124/mol.110.068296] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Here, we demonstrate that coupling to N-hydroxypropyl methacrylamide (HPMA) copolymer greatly enhances the activity of apoptosis-inducing peptides inside cells. Peptides corresponding to the BH3 domain of Bid were coupled to a thioester-activated HPMA (28.5 kDa) via native chemical ligation in a simple one-pot synthesis. Peptides and polymer conjugates were introduced into cells either by electroporation or by conjugation to the cell-penetrating peptide nona-arginine. The molecular basis of the increased activity is elucidated in detail. Loading efficiency and intracellular residence time were assessed by confocal microscopy. Fluorescence correlation spectroscopy was used as a separation-free analytical technique to determine proteolytic degradation in crude cell lysates. HPMA conjugation strongly increased the half-life of the peptides in crude cell lysates and inside cells, revealing proteolytic protection as the basis for higher activity.
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Affiliation(s)
- Ivo R Ruttekolk
- Department of Biochemistry, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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15
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Lysakova-Devine T, Keogh B, Harrington B, Nagpal K, Halle A, Golenbock DT, Monie T, Bowie AG. Viral Inhibitory Peptide of TLR4, a Peptide Derived from Vaccinia Protein A46, Specifically Inhibits TLR4 by Directly Targeting MyD88 Adaptor-Like and TRIF-Related Adaptor Molecule. THE JOURNAL OF IMMUNOLOGY 2010; 185:4261-71. [DOI: 10.4049/jimmunol.1002013] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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16
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Rai J. Interaction energy analysis of peptide can predict the possibilities of mimetics by its retroinverso isomer. Chem Biol Drug Des 2009; 74:483-7. [PMID: 19811507 DOI: 10.1111/j.1747-0285.2009.00868.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
It has been previously reported that the retroinverso analog of S peptide cannot mimic the S peptide, whereas the retroinverso analog of foot-and-mouth disease virus antigen can mimic the foot-and-mouth disease virus antigen. The structures of S peptide, foot-and-mouth disease virus antigen, and their retroinverso analogs are known. Here, we have attempted to explain the structural basis of mimetics at the level of atomic interactions by elaborating upon the Guptasarma's hypothesis. Using interaction energy analysis of S peptide and foot-and-mouth disease virus antigen, we propose that if the energy of the CO and NH backbone atoms' non-covalent interactions with all other atoms is negligible as compared with the energy of other non-covalent interactions, then the retroinverso isomer can mimic the original peptide/protein. Previous work has established that the structure of the inverso analog of a protein will be the mirror image of the protein, and it will only recognize the respective mirror image substrate/binding partner. The retro peptide conformation that can be superimposed on all side chains in any conformation of the original peptide does not exist in the conformational space of the peptides.
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Affiliation(s)
- Jagdish Rai
- International Centre For Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India.
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17
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Sinisi R, Ghilardi A, Ruiu S, Lazzari P, Malpezzi L, Sani M, Pani L, Zanda M. Synthesis and in vitro Evaluation of Trifluoroethylamine Analogues of Enkephalins. ChemMedChem 2009; 4:1416-20. [DOI: 10.1002/cmdc.200900158] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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DAUBER-OSGUTHORPE PNINA, CAMPBELL MALCOLMM, OSGUTHORPE DAVIDJ. Conformational analysis of peptide surrogates. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1991.tb01516.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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20
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BERMAN JUDDM, GOODMAN MURRAY. Synthesis of cyclic and acyclic partial retro-inverso modified enkephalins. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1984.tb03133.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Fornoni A, Cobianchi L, Sanabria NY, Pileggi A, Molano RD, Ichii H, Rosero S, Inverardi L, Ricordi C, Pastori RL. The l-isoform but not d-isoforms of a JNK inhibitory peptide protects pancreatic β-cells. Biochem Biophys Res Commun 2007; 354:227-33. [PMID: 17222390 DOI: 10.1016/j.bbrc.2006.12.186] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Accepted: 12/23/2006] [Indexed: 10/23/2022]
Abstract
The activation of c-jun N-terminal kinase (JNK) in pancreatic islets is associated with impaired function and viability, and JNK inhibitory peptides (JNKIs) are cytoprotective. In particular, l-isoforms of JNKIs were shown to improve islets viability, while the d-retroinverso isoform of JNKI (RI-JNKI), with a higher therapeutic potential due to longer half-life, has not been studied. We compared the cytoprotective properties of L-JNKI and RI-JNKI. Treatment of murine islets with L-JNKI resulted in preservation of islet equivalents and greater percentage of viable beta-cells in culture. In contrast, RI-JNKI was not protective. We found that L-JNKI but not RI-JNKI prevents endogenous c-jun phosphorylation in insulinoma cells. Moreover, RI-JNKI induced islet cells necrosis and activates the p-38 kinase. In conclusion, L-JNKI directly affects beta-cells and ameliorates islet viability and function, while RI-JNKI has toxic effects, limiting its biological application to islet cell biology.
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Affiliation(s)
- Alessia Fornoni
- Diabetes Research Institute, University of Miami Miller School of Medicine, 1450 NW 10th Avenue, Miami, FL 33136, USA.
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22
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Kinkead B, Selz KA, Owens MJ, Mandell AJ. Algorithmically designed peptides ameliorate behavioral defects in animal model of ADHD by an allosteric mechanism. J Neurosci Methods 2006; 151:68-81. [PMID: 16423408 DOI: 10.1016/j.jneumeth.2005.07.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Revised: 07/22/2005] [Accepted: 07/22/2005] [Indexed: 10/25/2022]
Abstract
This study exemplifies the use of three ADHD-relevant methodological innovations. (1) The use of novel, patented, computational peptide design techniques to generate peptides targeting the extra-cellular and para-transmembrane amino acid loops of the putatively ADHD-involved, D(2) dopamine receptor, D(2)DAR; (2) experimental evidence that these peptides in L-amino acid/ortho ordered or D-amino acid/reverse ordered (retro-inverso), D(2)DAR, hydrophobic eigenmode matched forms, evoked positive allosteric and indirect agonist influences on in vitro stably receptor transfected CHO and LtK cells and on in vivo, brain mediated activity; (3) a representative 15 residue all-D-amino acid, D(2) mode matched peptide, given parenterally, was found to "repair" a key aberrant ADHD behavioral characteristic in a standard animal model of ADHD, the Spontaneously Hypertensive Rat, SHR, relative to its progenitor species control, the Wistar-Kyoto rat, WKY. The representative, retro-inverso peptide, all-D-LLYKNKPRYPKRNRE, reversed SHR's relative deficiency in sensory motor gating (pre-pulse inhibition, PPI) while leaving SHR's nonselective attention (rearings), impulsive behavior (time in center), and activity level (timed total motor behavior) unchanged. Amphetamine also reversed SHRs sensory gating defect, but with significant increases in nonselective attention, impulsivity and hyperactivity. These preliminary results suggest the possibility of a new, "softer" pharmacological approach to ADHD: hydrophobic mode matched peptide allosteric augmentation of the activity of indigenous dopamine with respect to D(2)DAR mediated function, in place of stimulant drug-induced presynaptic dopamine release or impairment of dopamine uptake.
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Affiliation(s)
- Becky Kinkead
- Laboratory of Neuropsychopharmacology, Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322, USA
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23
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Abstract
In the mid-1970s, Dr. Murray Goodman was interested in a reversed peptide bond as a surrogate to understand the functional role of the amide bond in aspartame, a dipeptide sweetener. Very soon, realizing the breath and potential of this modification, Murray expanded this activity into a full program and I was fortunate to be part of it. Together we formulated new concepts such as the partially modified retro-inverso and end-group modified retro-inverso transformations, tested hypotheses, generated novel nomenclature, developed synthetic routes, characterized the preferred conformations of the unique building blocks employed in this modification, the gem-diaminoalkyl and the C2-substituted malonyl residues, and studied the biological activity of retro-inverso isomers of bioactive peptides. In the early 1980s several laboratories initiated extensive research targeted at the retro-inverso modification. The revival of this field led to new applications, new methods of synthesis, and new insights on the conformational and topological properties of the retro-inverso modification. Among the fields that embraced the retro-inverso concept were immunology as pertains to subjects such as synthetic vaccines, immunomodulators, and diagnostic tools, and drug delivery field as pertains to targeted and nontargeted cell permeation vectors loaded with bioactive cargo. Doctor Murray Goodman's sudden death leaves behind not only family, friends, and colleagues, but also an impressive record of scientific achievements among which is the revival of the modern era of the retro-inverso transformation. Murray's numerous contributions, excellent leadership, enthusiastic promotion, and outstanding teachings in this field will carry and illuminate his memory far into the future.
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Affiliation(s)
- Michael Chorev
- Harvard Medical School, Laboratory for Translational Research, One Kendall Square, Building 600, 3rd Floor, Cambridge, MA 02139, USA.
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Santagada V, Frecentese F, Fiorino F, Cirillo D, Perissutti E, Severino B, Terracciano S, Caliendo G. A Valuable Synthesis of Reduced Peptide Bond by Microwave Irradiation. ACTA ACUST UNITED AC 2004. [DOI: 10.1002/qsar.200420037] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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25
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Grassi G, Foti F, Risitano F, Cordaro M, Nicolò F, Bruno G. Synthesis, structural and theoretical studies of new ring-chain adducts of 5(4H)-oxazol-5-ones and aldehyde methylhydrazones. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2004.04.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Alemán C, Bella J. Chain conformation in polyretropeptides: Quantum mechanical and empirical force field calculations on 2,6,8-trioxo-3,5,9-triazadecane, a model compound for poly(retro-glycine). Biopolymers 2004. [DOI: 10.1002/bip.360350302] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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27
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Mandell AJ, Selz KA, Owens MJ, Kinkead B, Shlesinger MF, Gutman DA, Arguragi V. Cellular and behavioral effects of D2 dopamine receptor hydrophobic eigenmode-targeted peptide ligands. Neuropsychopharmacology 2003; 28 Suppl 1:S98-107. [PMID: 12827150 DOI: 10.1038/sj.npp.1300134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Patterns in G-protein-coupled receptors' hydrophobically transformed amino-acid sequences can be computationally characterized as hierarchies of autocorrelation waves, "hydrophobic eigenmodes", using autocovariance matrix decomposition and all poles power spectral and wavelet transformations. L- or D-amino acid (retro-inverso) 12-18 residue peptides targeting these modes can be designed using eigenvector templates derived from these computations. In all, 12 human long-form D(2) dopamine receptor eigenmode-targeted 15 mer peptides were designed, synthesized, and shown to modulate and/or indirectly activate the extracellular acidification response, EAR, in stably receptor-transfected CHO and LtK cells, with an 83% hit rate. Representative L- and D-amino-acid retro-inverso peptides injected bilaterally in the nucleus accumbens demonstrated changes in rat exploratory behavior and prepulse inhibition similar to those observed following parenteral amphetamine. In contrast with geometric models used for ligand design, such as pharmacophores, the hydrophobic eigenmode approach to lead modulatory peptide design targets hydrophobic eigenmode-bearing subsequences, including those not visible from X-ray and NMR studies such as extracellular segments and loops.
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Affiliation(s)
- Arnold J Mandell
- Cielo Institute, 486 Sunset Drive, Asheville, NC 28804-3727, USA.
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28
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Tretiakova AP, Albert RH, Jameson BA. A rational design approach for developing immunomodulators based on CD4 and CD8. Biotechnol Genet Eng Rev 2003; 19:175-203. [PMID: 12520878 DOI: 10.1080/02648725.2002.10648029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Anna P Tretiakova
- Department of Biochemistry, School of Medicine, MCP Hahnemann University, 245 North 15th Street, Philadelphia, PA 19102, USA
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29
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Carotti A, Carrieri A, Cellamare S, Fanizzi FP, Gavuzzo E, Mazza F. Extended form of a retro-inverso peptide stabilized by beta-sheet unidirectional H-bonds: Crystallographic and NMR evidence. Biopolymers 2002; 60:322-32. [PMID: 11774235 DOI: 10.1002/1097-0282(2001)60:4<322::aid-bip9993>3.0.co;2-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The crystallographic investigation of the retro-inverso peptide Bz-S-gAla-R-mAla-NHPh reveals an extended backbone conformation where the NH groups of the gem-diamino alkyl moiety and the CO groups of the malonyl residue face side by side. This extended conformation, presenting all carbonyls on opposite sides of the NH groups, is stabilized by interstrand H-bonds running in a single direction of the parallel beta-sheets that characterize the crystal packing. These sheets differ from the beta-sheets formed by native amino acids only. (1)H-NMR nuclear Overhauser effect spectroscopy (NOESY) experiments suggest that a conformation similar to that found in the crystal also prevails in dimethylsulfoxide solution. Previous potential energy calculations of gem-diamino alkyl (g) and malonyl (m) Ala residues predicted that extended forms were less stable than the helical ones because of strong electrostatic repulsions between the parallel polar groups. Similar arguments were invoked to give more weight to helical forms of the retro-peptide units in the proposal of packing models of some nylons in their crystalline polar regions. The present findings show that both g and m Ala residues can experience the extended conformation in the beta-sheet aggregation. The energy increase occurring in one strand, due to the parallel orientation of consecutive peptide dipoles, is more than compensated by favorable cooperative interactions among head-to-tail aligned peptide dipoles of facing strands, resulting in the formation of two C==O...H==N H-bonds per residue.
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Affiliation(s)
- A Carotti
- Dipartimento Farmaco-Chimico, Universitá degli Studi, V. E. Orabona 4, 70125 Bari, Italy
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30
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Affiliation(s)
- Carlos Alemán
- Departament d'Enginyeria Química, E.T.S.E.I.B, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain
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31
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Affiliation(s)
- Carlos Alemán
- Departament d'Enginyeria Química, E.T.S. d'Enginyers Industrials de Barcelona, Universitat Politécnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain
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32
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Alemán C. A Computational Study of Partially Modified Retro-Inverso Valine Dipeptides: Effect of the Side Chain on the Conformational Preferences of Malonyl and gem-Diamino Residues. J Phys Chem B 2001. [DOI: 10.1021/jp002806r] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carlos Alemán
- Departament d'Enginyeria Química, E.T.S. d'Enginyers Industrials, Universitat Politècnica de Catalunya, Diagona 647, Barcelona E−08028, Spain
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33
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Schiavoni MM, Mack HG, Ulic SE, Della Védova CO. Tautomers and conformers of malonamide, NH2-C(O)-CH2-C(O)-NH2: vibrational analysis, NMR spectra and ab initio calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2000; 56A:1533-1541. [PMID: 10907882 DOI: 10.1016/s1386-1425(99)00276-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The conformational and tautomeric compositions of malonamide, NH2-C(O)-CH2-C(O)-NH2 were determined by vibrational spectroscopy and theoretical calculations (HF/6-31G*, B3PW91/6-31G*). Solid state Fourier transform infrared and Raman spectra were analysed. They reveal the existence of a diketo tautomer. Theoretical calculations predict a diketo structure belonging to the C1 symmetry group. No enol form is present in the molecule in the solid. 13C-NMR studies show only signals of a diketo tautomer.
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Affiliation(s)
- M M Schiavoni
- LADECOR, Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Argentina
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34
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Lee M, Jin Y, Kim DH. 2-Benzyl-2-methylsuccinic acid as inhibitor for carboxypeptidase A. synthesis and evaluation. Bioorg Med Chem 1999; 7:1755-60. [PMID: 10482467 DOI: 10.1016/s0968-0896(99)00110-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, Asante-Appiah et al. (Asante-Appiah, E.; Seetharaman, J.; Sicheri, F.; Yang, D. S.-C.; Chan, W. W.-C. Biochemistry 1997, 36, 8710 8715) reported that 2-ethyl-2-methylsuccinic acid is a highly potent inhibitor for carboxypeptidase A (CPA), a prototypic zinc protease. The X-ray crystal structure of the complex of the enzyme formed with 2-ethyl-2-methylsuccinic acid revealed that at the active site of CPA there is present a small cavity which accommodates the methyl group of the inhibitor. These investigators postulated that incorporation of a methyl group at the alpha-position to the carboxylate of existing inhibitors of CPA would improve the inhibitory potency. We have synthesized racemic and optically active 2-benzyl-2-methylsuccinic acids and evaluated their inhibitory activities for CPA to find the K(i) values to be 0.28, 0.15, and 17microM for racemic form, (R)-, and (S)-enantiomer, respectively. Contrary to the expectation, the effect on the binding affinity by the incorporation of the methyl group is minimal. The validity of the proposition that the small cavity may be utilized for the improvement of the inhibitory potency appears questionable.
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Affiliation(s)
- M Lee
- Center for Biofunctional Molecules and Department of Chemistry, Pohang University of Science and Technology, South Korea
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35
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Saphire AC, Bark SJ, Gerace L. All four homochiral enantiomers of a nuclear localization sequence derived from c-Myc serve as functional import signals. J Biol Chem 1998; 273:29764-9. [PMID: 9792690 DOI: 10.1074/jbc.273.45.29764] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The information that targets a protein to the nucleus often consists of a short cluster of basic amino acids called a nuclear localization sequence (NLS). Since a wide range of sequences rich in basic amino acid residues function as NLSs, we postulated that an NLS-like sequence composed exclusively of D-amino acids might have biological activity. We synthesized peptides corresponding to the c-Myc NLS composed of either all L or D-amino acids, both in the forward and reverse order. We tested these peptides for nuclear import activity in a digitonin-permeabilized cell assay. All four peptide-bovine serum albumin conjugates localized to the nucleus with similar efficiency, and each conjugate competed for import with an SV40 large T antigen-derived NLS conjugate. Cross-linking experiments with free NLS peptides in HeLa cytosol indicated that each peptide bound to a protein that migrated at the molecular weight of importin alpha. Recombinant importin alpha, importin beta, Ran, and NTF2 alone were sufficient to support the import of both L-form and D-form conjugates in permeabilized cells. This indicates that both D- and L-form NLS peptides use the same import machinery. Although the free D-forms of the NLS were proteolytically resistant in cytosol, the L-forms were rapidly degraded. To our knowledge, this is the first example of an intracellular pathway in which the receptor is insensitive to the chirality of the ligand.
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Affiliation(s)
- A C Saphire
- The Scripps Research Institute, La Jolla, California 92037, USA
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36
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Fletcher MD, Campbell MM. Partially Modified Retro-Inverso Peptides: Development, Synthesis, and Conformational Behavior. Chem Rev 1998; 98:763-796. [PMID: 11848914 DOI: 10.1021/cr970468t] [Citation(s) in RCA: 160] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Puiggalí J, Subirana JA. An experimental Ramachandran plot for retropeptide derivatives: Conformational features of derivatives of GEM-diamino and malonyl amino acids. Biopolymers 1998. [DOI: 10.1002/(sici)1097-0282(199802)45:2<149::aid-bip5>3.0.co;2-s] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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Zhao M, Kleinman HK, Mokotoff M. Synthesis and activity of partial retro-inverso analogs of the antimetastatic laminin-derived peptide, YIGSR-NH2. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1997; 49:240-53. [PMID: 9151257 DOI: 10.1111/j.1399-3011.1997.tb00883.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This paper describes the synthesis and biological evaluation of six partial retro-inverso peptidomimetic analogs of YIGSR-NH2, a synthetic peptide from the beta 1 chain of laminin, which has antimetastatic activity. The intent was to improve the antimetastatic potency of YIGSR-NH2 by limiting the in vivo enzymatic degradation through the incorporation of fraudulent peptide bonds. We have prepared the following retro-inverso peptides, Tyr-Ile-Gly-Ser-gArg-CHO (1), Tyr-gIle-mGly-Ser-Arg-NH2 (2), Tyr-gIle-mGly-Ser-gArg-CHO (3), gTyr-D-rIle-mGly-Ser-Arg-NH2 (4), Tyr-Ile-Gly-gSer-D-rArg-CHO (5) and Tyr-gIle-rGly-D-rSer-D-rArg-CHO (6). In vitro assays for B16F10 melanoma cell adhesion showed no significant activity for these six peptides. Peptides 1-3, 5 and 6 were further tested, in vivo, for their ability to inhibit tumor metastases to the lung in mice injected in the tail vein with B16F10 melanoma cells. All five of the retro-inverso peptides tested showed statistically significant inhibition of metastasis, but the most active peptides were 5 and 6, which showed 57 and 69% inhibition of metastasis, respectively.
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Affiliation(s)
- M Zhao
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pennsylvania, USA
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39
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Abstract
The potential energy surface of the phi [NHCO] delta Ala dipeptide has been computed using ab initio quantum mechanical calculations at different theoretical levels. Three degenerate minima were found and characterized. The most favoured conformation is stabilized by an intramolecular hydrogen bonding interaction. The other two minima correspond to helical and malonamide-like conformations, being 4.6 kcal/mol and 6.9 kcal/mol less stable than the lowest energy conformation, respectively. Influence of solvent effects on the relative stabilities of the different conformations have been accounted using SCRF calculations. Two implicit solvent models have been considered: water and CCl4. The results indicate that in the both cases the conformation with an intramolecular hydrogen bonding interaction retains its lowest energy.
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Affiliation(s)
- C Alemán
- Department d'Enginyeria Química, E.T.S.I.I.B., Universitat Politècnica de Catalunya, Barcelona, Spain
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40
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Guichard G, Connan F, Graff R, Ostankovitch M, Muller S, Guillet JG, Choppin J, Briand JP. Partially modified retro-inverso pseudopeptides as non-natural ligands for the human class I histocompatibility molecule HLA-A2. J Med Chem 1996; 39:2030-9. [PMID: 8642561 DOI: 10.1021/jm9509511] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Syntheses of a series of partially modified retro-inverso analogues of the antigenic peptide M58-66 derived from the influenza virus matrix protein are reported. The retro-inverso modification phi(NH-CO) was obtained by replacement of two successive amino acid residues with a 2-substituted malonate derivative and gem-diaminoalkyl residue. The resulting compounds 1-8 were tested for their binding to the human histocompatibility class I molecule HLA-A2 in an assembly assay using lysates of peptide transporter-deficient cells T2. Specific peptide-dependent HLA-A2 assembly was revealed by an enzyme-linked immunosorbent assay. Significant HLA-A2 assembly was detected in the presence of analogues [gGly58-(S)mLeu59]-M58-66 (1a), [gGly61-(R,S)mPhe62]M58-66 (4), [gVal63-(R,S)mPhe64]M58-66 (6), and [gPhe64-(R,S)mAla65]M58-66 (7). The introduction of the retro-inverso modification between P2-P3, P3-P4, P5-P6, and P8-P9 (compounds 2, 3, 5, and 8, respectively) however led to a dramatic reduction in peptide binding to HLA-A2. Interestingly, compound 1a which contains modification between P1-P2 was found to be the most potent analogue, being able to retain the original HLA-A2 binding profile of the parent peptide M58-66. Taken together, these results and recent binding data obtained in the context of murine MHC class I molecule H-2Kd suggest that the incorporation of peptide bond surrogates in MHC class I-restricted epitopes is a useful approach to design molecules having both increased stability and high MHC-binding capacity. Depending on their agonist or antagonist effects at the T-cell receptor, such non-natural MHC ligands are likely to find many applications in the development of peptide-based vaccines or as potential therapeutic agents in the treatment of allergies and autoimmune diseases.
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Affiliation(s)
- G Guichard
- Institut de Biologie Moléculaire et Cellulaire, UPR 9021 CNRS, Strasbourg, France
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41
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Abstract
The X-ray diffraction experiments on peptides and related molecules which have been carried out in Western Europe, except Italy, in the last eight years are reviewed. The crystal structures of some bioactive peptides such as Leu-enkephalin (a neurotransmitter), cyclosporin A (an immunomodulator in both the free and protein-bound state), balhimycin (an antibiotic) and octreotide (a somatostatin analogue) are briefly presented. Crystallized N- and C-protected model peptides have given an insight into the folding tendency and folding modes depending on the peptide sequences. The crystal structures of various pseudopeptide molecules reveal how the three-dimensional structure of peptide analogues can be modulated by substituting non-peptide groups for the peptide bond. A few examples of structural mimetics of the beta- and gamma-turns, and of templates for alpha-helix induction are also presented.
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Affiliation(s)
- M Marraud
- LCPM, CNRS-URA 494, ENSIC-INPL, Nancy, France
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42
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Navarro E, Tereshko V, Subirana JA, Puiggalí J. Incorporation of diacids into the polyglycine II structure: model studies. Biopolymers 1995; 36:711-22. [PMID: 8555419 DOI: 10.1002/bip.360360605] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Aliphatic diacids are often incorporated into polypeptide structures in order to obtain model compounds for hormones, protein turns, etc. They are also fundamental components of many commercial polyamides. On the other hand glycine, the simplest amino acid, shows unique conformational features. In order to better understand the structure of such compounds, we have synthetized and determined the molecular structure of three models represented by the general formula CH3-CH2-CH2-NH-CO-CH2-NH-CO-(CH2)n-2-CO-NH-CH2-CO-NH-CH2-CH2-CH3, with n = 3, 4, or 6. Conformational differences have been found in the dicarboxylic moiety, whereas glycine always has the polyglycine II conformation. The -CO-(CH2)n-2-CO-segment adopts a folded conformation: SS, TGT, and SGTGS for n = 3, 4, and 6, respectively. Molecular packing is always pseudohexagonal and a network of hydrogen bonds oriented in three directions at 120 degrees is formed. The results are of interest in order to provide information about polyamides in which glycine residues are incorporated. Our results confirm the tendency of glycine residues to adopt the polyglycine II conformation in its copolymers with aliphatic compounds.
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Affiliation(s)
- E Navarro
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain
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43
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Byk G, Duchesne M, Parker F, Lelievre Y, Guitton JD, Clerc FF, Becquart J, Tocque B, Scherman D. Local constrained shifty pseudopeptides inhibitors of rasfarnesyl transferase. Bioorg Med Chem Lett 1995. [DOI: 10.1016/0960-894x(95)00482-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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44
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Benedetti E, Pedone EM, Kawahata NH, Goodman M. Conformational studies of retro-inverso peptides: the crystal and molecular structure of the hydantoin from H-Ala-g-Ala-mGly-OBzl. Biopolymers 1995; 36:659-67. [PMID: 7578956 DOI: 10.1002/bip.360360511] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The crystal structure of the hydantoin 1-[(S)-1'-aminoethylmalonyl benzyl ester]-(S)-4-methylimidazolidin-2,5-dione (1) derived from the peptide H-Ala-gAla-mGly-OBzl, having the retro-inverso modification of the Ala-Gly bond, has been determined by x-ray diffraction analysis. The crystals are orthorhombic, space group P2(1)2(1)2(1) with a = 6.539, b = 14.721, c = 17.101 A, z = 4. The structure was solved by direct methods and refined with anisotropic thermal factors to a final R value of 0.067 for the 947 observed reflections. Reversal of the Ala-Gly amide bond perturbs the folding tendency of the backbone shown by the parent peptide t-BuCO-Ala-Gly-NHiPr. The gem-diamino residue, gAla, and the malonyl moieties are found in the helical and the extended conformations, respectively. Intramolecular hydrogen bonding is not observed. The molecules in the crystal are held together by the formation of two intermolecular hydrogen bonds of the N-H ... O=C type with N ... O distances of 2.86 and 3.17 A, respectively.
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Affiliation(s)
- E Benedetti
- CNR Department of Chemistry, University of Naples, Federico II, Italy
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Alemán C, Perez JJ. Conformational study of alanine and alpha-aminoisobutyric psi [NHCO]-retroamide peptide analogues. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1994; 43:258-63. [PMID: 8005748 DOI: 10.1111/j.1399-3011.1994.tb00388.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The minimum-energy conformations of N,N'-dimethyl-2-methylmalondiamide (2mMA) and N,N'-dimethyl-2-dimethylmalondiamide (2dmMA) have been computed using the AM1 method. The results show that molecules tend to form an intramolecular six-membered ring hydrogen-bond system. The same trend is observed in crystals of malonamide derivatives substituted in the central carbon atom. The results are also compared with previous molecular-mechanics calculations. The conformational trends of 2mMA and 2dmMA are very similar to those showed by N,N'-dimethylmalondiamide. Details of the computed conformational energy maps for 2mMA and 2dmMA compounds are given.
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Affiliation(s)
- C Alemán
- Department of Chemical Engineering, Technical College for Industrial Engineers, Polytechnic University of Catalunya, Barcelona, Spain
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Alemán C, Pérez JJ. SCF-MO study of the preferred conformation of a symmetric malonamide derivative: N,N' -dimethyl malonamide. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/0166-1280(93)87037-e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Alemán C, Perez JJ. SCF-MO study of the polyhydration of N,N'-dimethylmalonamide. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1993; 41:606-10. [PMID: 8349417 DOI: 10.1111/j.1399-3011.1993.tb00483.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The effect of hydration on the conformation of the N,3 nylons has been studied using AM1 SCF-MO on the model molecule N,N'-dimethylmalonamide (NNMA). The polyhydration model has been used, so that only the water molecules directly bonded to solute molecule are considered. The study reveals that, although hydration induces dramatic changes in the torsional angles of the molecule, the new conformation still remains in the helical region of the Ramachandran map.
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Affiliation(s)
- C Alemán
- Department of Chemical Engineering, U.P.C., Barcelona, Spain
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Nunami K, Yamazaki T, Goodman M. Cyclic retro-inverso dipeptides with two aromatic side chains. I. Synthesis. Biopolymers 1991; 31:1503-12. [PMID: 1814500 DOI: 10.1002/bip.360311307] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A series of cyclic retro-inverso dipeptides--2-[(4-hydroxy)benzyl]-5-benzyl-4,6(1H,2H,3H,5H)-pyrimidinedi one (c[mPhe-gTyr]), 2-benzyl-5-[(4-hydroxy)benzyl]-4,6(1H,2H,3H,5H)-pyrimidinedione (c[mTyr-gPhe]), and 2-benzyl-5-amino-5-[(4-hydroxy)benzyl]-4,6(1H,2H,3H,5H)-pyrimidinedione (c[(alpha-amino)mTyr-gPhe])--were synthesized in order to define the minimum structural requirements for binding affinity with opiate receptors and biological activity. Although the first two compounds lack a free amine proposed to be necessary for receptor recognition, the c[mPhe-gTyr] and c[mTyr-gPhe] analogues serve as model molecules in conformational studies of the target analogue, c[(alpha-amino)mTyr-gPhe]. The cis- and trans-c[(alpha-amino)mTyr-gPhe] contain all the functional groups such as the amine and phenolic groups in the tyrosine, and the aromatic group in the phenylalanine, necessary for opiate activity. In addition, the c[(alpha-amino)mTyr-gPhe] analogues possess similar geometries to the Tyr-Pro part of morphiceptin (Tyr-Pro-Phe-Pro-NH2) whose high mu-receptor activity is attributed to conformations with the Tyr-Pro amide bond in a cis conformation because the peptide bonds assume a cis conformation. However, both analogues are inactive in the guinea pig ileum and the mouse vas deferens assays. This may result from wrong orientation of the benzyl group of the gPhe residue with respect to the (alpha-amino)mTyr residue. Conformational studies of these molecules using 1H-nmr spectroscopy and molecular mechanics calculations will be reported in the following paper. Results of conformational analysis should provide information about backbone-side-chain interactions in the retro-inverso peptide chains since all the fundamental structural elements of the retro-inverso peptides are included in these model systems even though the peptide bonds must assume a cis conformation.
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Affiliation(s)
- K Nunami
- Department of Chemistry, University of California, San Diego, La Jolla 92093-0343
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Wormser U, Laufer R, Chorev M, Gilon C, Selinger Z. Proteolytic resistance and biological activity of N-methylated analogs of [pGlu6] substance P6-11. Neuropeptides 1990; 16:41-9. [PMID: 1701226 DOI: 10.1016/0143-4179(90)90028-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Five synthetic N-methylated analogs (II-V) of the C-terminal hexapeptide analog of substance P (SP), [pGlu6]SP6-11 (I) were evaluated for their metabolic stability and in vitro spasmogenic activity. The metabolic resistance of the analogs was tested by two SP degrading systems with different specificities, namely, the rat parotid and the hypothalamic slice systems. Their biological activity was assessed in the isolated guinea pig ileum. The analog [pGlu6, N-Me Phe7, N-Me Gly9]SP6-11 (III), had relative potency of 65% in the spasmogenic assay as compared to the parent compound. It was found to be more stable than the parent peptide in the hypothalamus, whereas in the parotid system it was susceptible as the parent peptide. However, the analog [pGlu6, N-Me Leu10]SP6-11 (II) (46% relative potency in the spasmogenic assay) was more stable than the parent peptide in the parotid system but did not show any improved stability in the hypothalamus. Identification of degradation products of the [pGlu6, N-Me Leu10]SP6-11 reflected the differences in the specificities of the two preparations. A significant drop in potency (7%) was observed for [pGlu, N-Me Phe7]SP6-11 (IV). This analog was more stable in the hypothalamic system than in the parotid. Introduction of a double methylation, [pGlu6, N-Me Leu10] SP6-11, contributed toward the stabilization in both degrading systems. Its relative spasmogenic activity was comparable to that of analog IV. In light of the above mentioned findings the implications of the N-methylated analogs with respect to putative CNS activity are discussed.
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Affiliation(s)
- U Wormser
- Department of Biological Chemistry, School of Pharmacy, Hebrew University of Jerusalem, Israel
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Goodman M, Rone R, Manesis N, Hassan M, Mammi N. Peptidomimetics: synthesis, spectroscopy, and computer simulations. Biopolymers 1987; 26 Suppl:S25-32. [PMID: 3580499 DOI: 10.1002/bip.360260007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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