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Damjanovic J, Miao J, Huang H, Lin YS. Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations. Chem Rev 2021; 121:2292-2324. [PMID: 33426882 DOI: 10.1021/acs.chemrev.0c01087] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein-protein interactions are vital to biological processes, but the shape and size of their interfaces make them hard to target using small molecules. Cyclic peptides have shown promise as protein-protein interaction modulators, as they can bind protein surfaces with high affinity and specificity. Dozens of cyclic peptides are already FDA approved, and many more are in various stages of development as immunosuppressants, antibiotics, antivirals, or anticancer drugs. However, most cyclic peptide drugs so far have been natural products or derivatives thereof, with de novo design having proven challenging. A key obstacle is structural characterization: cyclic peptides frequently adopt multiple conformations in solution, which are difficult to resolve using techniques like NMR spectroscopy. The lack of solution structural information prevents a thorough understanding of cyclic peptides' sequence-structure-function relationship. Here we review recent development and application of molecular dynamics simulations with enhanced sampling to studying the solution structures of cyclic peptides. We describe novel computational methods capable of sampling cyclic peptides' conformational space and provide examples of computational studies that relate peptides' sequence and structure to biological activity. We demonstrate that molecular dynamics simulations have grown from an explanatory technique to a full-fledged tool for systematic studies at the forefront of cyclic peptide therapeutic design.
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Affiliation(s)
- Jovan Damjanovic
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - He Huang
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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2
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Corbett KM, Pouton CW, Chalmers DK. Temperature Replica Exchange Molecular Dynamics Simulations of Cyclic Peptide Conformation. Aust J Chem 2021. [DOI: 10.1071/ch21120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Bennett JA, Mansouri W, Lin Q, Feustel P, Andersen TT. Pharmacodynamic and Pharmacokinetic Properties of AFPep, a Novel Peptide for the Treatment of Breast Cancer. Int J Pept Res Ther 2017. [DOI: 10.1007/s10989-017-9628-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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4
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Wu Z, Lan XB, Jiang WZ. 3D-QSAR research of curcumin derivatives. Med Chem Res 2015. [DOI: 10.1007/s00044-015-1406-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Zhu YP, Liu YR, Huang T, Jiang S, Xu KM, Wen H, Zhang WJ, Huang W. Theoretical Study of the Hydration of Atmospheric Nucleation Precursors with Acetic Acid. J Phys Chem A 2014; 118:7959-74. [DOI: 10.1021/jp506226z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yu-Peng Zhu
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Yi-Rong Liu
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Teng Huang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Shuai Jiang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Kang-Ming Xu
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Hui Wen
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Wei-Jun Zhang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wei Huang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui 230026, China
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6
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Temelso B, Alser KA, Gauthier A, Palmer AK, Shields GC. Structural Analysis of α-Fetoprotein (AFP)-like Peptides with Anti-Breast-Cancer Properties. J Phys Chem B 2014; 118:4514-26. [DOI: 10.1021/jp500017b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Berhane Temelso
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
- Dean’s Office, College of Science and Technology, and Department of Chemistry & Physics, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, Georgia 31419, United States
| | - Katherine A. Alser
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Arianne Gauthier
- Dean’s Office, College of Science and Technology, and Department of Chemistry & Physics, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, Georgia 31419, United States
| | - Amber Kay Palmer
- Dean’s Office, College of Science and Technology, and Department of Chemistry & Physics, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, Georgia 31419, United States
| | - George C. Shields
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
- Dean’s Office, College of Science and Technology, and Department of Chemistry & Physics, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, Georgia 31419, United States
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7
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Development of an Active Site Peptide Analog of α-Fetoprotein That Prevents Breast Cancer. Cancer Prev Res (Phila) 2014; 7:565-73. [DOI: 10.1158/1940-6207.capr-13-0405] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Temelso B, Phan TN, Shields GC. Computational Study of the Hydration of Sulfuric Acid Dimers: Implications for Acid Dissociation and Aerosol Formation. J Phys Chem A 2012; 116:9745-58. [DOI: 10.1021/jp3054394] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Berhane Temelso
- Dean’s Office, College of Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837,
United States
| | - Thuong Ngoc Phan
- Dean’s Office, College of Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837,
United States
| | - George C. Shields
- Dean’s Office, College of Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837,
United States
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9
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Husar DE, Temelso B, Ashworth AL, Shields GC. Hydration of the Bisulfate Ion: Atmospheric Implications. J Phys Chem A 2012; 116:5151-63. [DOI: 10.1021/jp300717j] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Devon E. Husar
- Dean’s Office, College of
Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Berhane Temelso
- Dean’s Office, College of
Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Alexa L. Ashworth
- Dean’s Office, College of
Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - George C. Shields
- Dean’s Office, College of
Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
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10
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Bryan A, Joseph L, Bennett JA, Jacobson HI, Andersen TT. Design and synthesis of biologically active peptides: a 'tail' of amino acids can modulate activity of synthetic cyclic peptides. Peptides 2011; 32:2504-10. [PMID: 22015269 PMCID: PMC3230782 DOI: 10.1016/j.peptides.2011.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 10/05/2011] [Accepted: 10/05/2011] [Indexed: 10/16/2022]
Abstract
In earlier work, we synthesized a cyclic 9-amino acid peptide (AFPep, cyclo[EKTOVNOGN]) and showed it to be useful for prevention and therapy of breast cancer. In an effort to explore the structure-function relationships of AFPep, we have designed analogs that bear a short 'tail' (one or two amino acids) attached to the cyclic peptide distal to its pharmacophore. Analogs that bore a tail of either one or two amino acids, either of which had a hydrophilic moiety in the side chain (e.g., cyclo[EKTOVNOGN]FS) exhibited greatly diminished biological activity (inhibition of estrogen-stimulated uterine growth) relative to AFPep. Analogs that bore a tail of either one or two amino acids which had hydrophobic (aliphatic or aromatic) side chains (e.g., cyclo[EKTOVNOGN]FI) retained (or had enhanced) growth inhibition activity. Combining in the same biological assay a hydrophilic-tailed analog with either AFPep or a hydrophobic-tailed analog resulted in decreased activity relative to that for AFPep or for the hydrophobic-tailed analog alone, suggesting that hydrophilic-tailed analogs are binding to a biologically active receptor. An analog with a disrupted pharmacophore (cyclo[EKTOVGOGN]) exhibited little or no growth inhibition activity. An analog with a hydrophilic tail and a disrupted pharmacophore (cyclo[EKTOVGOGN]FS) exhibited no growth inhibition activity of its own and did not affect the activity of a hydrophobic-tailed analog, but enhanced the growth inhibition activity of AFPep. These results are discussed in the context of a two-receptor model for binding of AFPep and ring-and-tail analogs. We suggest that tails on cyclic peptides may comprise a useful method to enhance diversity of peptide design and specificity of ligand-receptor interactions.
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Affiliation(s)
- Alberto Bryan
- Center for Cardiovascular Science Albany Medical College 47 New Scotland Avenue Albany, NY 12208
| | - Leroy Joseph
- Center for Cardiovascular Science Albany Medical College 47 New Scotland Avenue Albany, NY 12208
| | - James A. Bennett
- Center for Immunology and Microbial Diseases Albany Medical College 47 New Scotland Avenue Albany, NY 12208
| | - Herbert I. Jacobson
- Center for Immunology and Microbial Diseases Albany Medical College 47 New Scotland Avenue Albany, NY 12208
| | - Thomas T. Andersen
- Center for Cardiovascular Science Albany Medical College 47 New Scotland Avenue Albany, NY 12208
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11
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Mizejewski GJ. Mechanism of Cancer Growth Suppression of Alpha-Fetoprotein Derived Growth Inhibitory Peptides (GIP): Comparison of GIP-34 versus GIP-8 (AFPep). Updates and Prospects. Cancers (Basel) 2011; 3:2709-33. [PMID: 24212829 PMCID: PMC3757439 DOI: 10.3390/cancers3022709] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 06/02/2011] [Accepted: 06/14/2011] [Indexed: 12/31/2022] Open
Abstract
The Alpha-fetoprotein (AFP) derived Growth Inhibitory Peptide (GIP) is a 34-amino acid segment of the full-length human AFP molecule that inhibits tumor growth and metastasis. The GIP-34 and its carboxy-terminal 8-mer segment, termed GIP-8, were found to be effective as anti-cancer therapeutic peptides against nine different human cancer types. Following the uptake of GIP-34 and GIP-8 into the cell cytoplasm, each follows slightly different signal transduction cascades en route to inhibitory pathways of tumor cell growth and proliferation. The parallel mechanisms of action of GIP-34 versus GIP-8 are demonstrated to involve interference of signaling transduction cascades that ultimately result in: (1) cell cycle S-phase/G2-phase arrest; (2) prevention of cyclin inhibitor degradation; (3) protection of p53 from inactivation by phosphorylation; and (4) blockage of K+ ion channels opened by estradiol and epidermal growth factor (EGF). The overall mechanisms of action of both peptides are discussed in light of their differing modes of cell attachment and uptake fortified by RNA microarray analysis and electrophysiologic measurements of cell membrane conductance and resistance. As a chemotherapeutic adjunct, the GIPs could potentially aid in alleviating the negative side effects of: (1) tamoxifen resistance, uterine hyperplasia/cancer, and blood clotting; (2) Herceptin antibody resistance and cardiac (arrest) arrhythmias; and (3) doxorubicin's bystander cell toxicity.
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Affiliation(s)
- Gerald J. Mizejewski
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201, USA; E-Mail: ; Tel.: +1-518-486-5900; Fax: +1-518-402-5002
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12
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Macaluso NJM, Pitkin SL, Maguire JJ, Davenport AP, Glen RC. Discovery of a competitive apelin receptor (APJ) antagonist. ChemMedChem 2011; 6:1017-23. [PMID: 21560248 DOI: 10.1002/cmdc.201100069] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 03/29/2011] [Indexed: 01/27/2023]
Abstract
The apelin receptor (APJ) is a class A G-protein-coupled receptor (GPCR) and is a putative target for the treatment of cardiovascular and metabolic diseases. Apelin-13 (NH₂-QRPRLSHKGPMPF-COOH) is a vasoactive peptide and one of the most potent endogenous inotropic agents identified to date. We report the design and discovery of a novel APJ antagonist. By using a bivalent ligand approach, we have designed compounds with two 'affinity' motifs and a short series of linker groups with different conformational and non-bonded interaction properties. One of these, cyclo(1-6)CRPRLC-KH-cyclo(9-14)CRPRLC is a competitive antagonist at APJ. Radioligand binding in CHO cells transfected with human APJ gave a K(i) value of 82 nM, competition binding in human left ventricle gave a K(D) value of 3.2 μM, and cAMP accumulation assays in CHO-K1-APJ cells gave a K(D) value of 1.32 μM.
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Affiliation(s)
- N J Maximilian Macaluso
- Unilever Centre for Molecular Sciences Informatics, Department of Chemistry, University of Cambridge, Lensfield Road CB2 1EW, Cambridge, UK
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Macaluso NM, Glen R. Exploring the ‘RPRL’ Motif of Apelin-13 through Molecular Simulation and Biological Evaluation of Cyclic Peptide Analogues. ChemMedChem 2010; 5:1247-53. [DOI: 10.1002/cmdc.201000061] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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14
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Xia S, Zhang L, Lu M, Qiu B, Chi Y, Chen G. Enantiomeric separation of chiral dipeptides by CE-ESI-MS employing a partial filling technique with chiral crown ether. Electrophoresis 2010; 30:2837-44. [PMID: 19655329 DOI: 10.1002/elps.200800799] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Enantiomer of chiral dipeptides were separated by CE-ESI-MS in a bare fused-silica capillary using (+)-(18-crown-6)-2,3,11,12-tetracarboxylic acid (18C6H4) as the chiral selector. As 18C6H4 is a kind of nonvolatile chiral selector, in order to prevent from 18C6H4 into the ion-source of CE-ESI-MS, a partial filling technique was employed in this study. Some dipeptides with one chiral center or two chiral centers, such as DL-Leu-DL-Leu, D-Ala-D-Ala and L-Ala-L-Ala, Gly-D-Phe and Gly-L-Phe were used to evaluate this CE-ESI-MS system. Optimized conditions were achivevd with 2.0 mol/L acetic acid (pH 2.15) as the running electrolyte, 5 mM 18C6H4 in 3.0 mol/L acetic acid (pH 2.00) was injected hydrodynamically (50 mbar for 960 s) before sample injection. In total 7.5 mM acetic acid in 80% v/v methanol-water was used as the sheath liquid, and 20 kV applied voltage was used. Under the optimum conditions, these dipeptides were separated and detected. LODs (defined as S/N=3) of this method were 0.20, 0.10, 0.05 and 0.10 micromol/L for D-Ala-D-Ala, L-Ala-L-Ala, DL-Leu-DL-Leu, Gly-L-Phe and Gly-D-Phe, respectively. The RSDs (n=7) of the method were 0.68-2.08% for migration times and 2.32-5.24% for peak areas. The proposed method was also successfully applied to the enantioselective analysis of these dipeptides in the spiked serum samples with satisfactory results.
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Affiliation(s)
- Shifei Xia
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Department of Chemistry, Fuzhou University, Fuzhou, Fujian, P. R. China
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Computational approaches for the design of peptides with anti-breast cancer properties. Future Med Chem 2009; 1:201-12. [DOI: 10.4155/fmc.09.13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background: Breast cancer is the most common cancer among women. Tamoxifen is the preferred drug for estrogen receptor-positive breast cancer treatment, yet many of these cancers are intrinsically resistant to tamoxifen or acquire resistance during treatment. Therefore, scientists are searching for breast cancer drugs that have different molecular targets. Methodology: Recently, a computational approach was used to successfully design peptides that are new lead compounds against breast cancer. We used replica exchange molecular dynamics to predict the structure and dynamics of active peptides, leading to the discovery of smaller bioactive peptides. Conclusions: These analogs inhibit estrogen-dependent cell growth in a mouse uterine growth assay, a test showing reliable correlation with human breast cancer inhibition. We outline the computational methods that were tried and used along with the experimental information that led to the successful completion of this research.
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Joseph LC, Bennett JA, Kirschner KN, Shields GC, Hughes J, Lostritto N, Jacobson HI, Andersen TT. Antiestrogenic and anticancer activities of peptides derived from the active site of alpha-fetoprotein. J Pept Sci 2009; 15:319-25. [DOI: 10.1002/psc.1119] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Gong XY, Dobrunz D, Kümin M, Wiesner M, Revell JD, Wennemers H, Hauser PC. Separating stereoisomers of di-, tri-, and tetrapeptides using capillary electrophoresis with contactless conductivity detection. J Sep Sci 2008; 31:565-73. [DOI: 10.1002/jssc.200700461] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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