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Manna S, Chowdhury T, M. Mandal S, Choudhury SM. Short Amphiphiles or Micelle Peptides May Help to Fight Against
COVID-19. Curr Protein Pept Sci 2022; 23:33-43. [DOI: 10.2174/1389203723666220127154159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/29/2021] [Accepted: 11/26/2021] [Indexed: 11/22/2022]
Abstract
Background:
COVID-19 is a worldwide threat because of the incessant spread of SARS-CoV-2 which urges the development of suitable antiviral drug to secure our society. Already, a group of peptides have been recommended for SARS-CoV-2, but not yet established. SARS-CoV-2 is an enveloped virus with hydrophobic fusion protein and spike glycoproteins.
Methods:
Here, we have summarized several reported amphiphilic peptides and their in-silico docking analysis with spike glycoprotein of SARS-CoV-2.
Result:
The result revealed the complex formation of spike protein and amphiphilic peptides with higher binding affinity. It was also observed that PalL1 (ARLPRTMVHPKPAQP), 10AN1 (FWFTLIKTQAKQPARYRRFC), THETA defensin (RCICGRGICRLL) and mucroporin M1 (LFRLIKSLIKRLVSAFK) showed the binding free energy more than -1000 kcal/mol. Molecular pI and hydrophobicity are also important factors of peptides to enhance the binding affinity with spike protein of SARS-CoV-2
Conclusion:
In the light of these findings, it is necessary to check the real efficacy of amphiphilic peptides in-vitro to in-vivo experimental set up to develop an effective anti-SARS-CoV-2 peptide drug, which might help to control the current pandemic situation.
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Affiliation(s)
- Sounik Manna
- Department of Human Physiology, Vidyasagar University, Midnapore 721 102, West Bengal, India
- Department of Microbiology, Midnapore College (Autonomous), Paschim Medinipur 721101, India
| | - Trinath Chowdhury
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Santi M. Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sujata Maiti Choudhury
- Department of Human Physiology, Vidyasagar University, Midnapore 721 102, West Bengal, India
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Hocking HG, Zangger K, Madl T. Studying the structure and dynamics of biomolecules by using soluble paramagnetic probes. Chemphyschem 2013; 14:3082-94. [PMID: 23836693 PMCID: PMC4171756 DOI: 10.1002/cphc.201300219] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Indexed: 12/20/2022]
Abstract
Characterisation of the structure and dynamics of large biomolecules and biomolecular complexes by NMR spectroscopy is hampered by increasing overlap and severe broadening of NMR signals. As a consequence, the number of available NMR spectroscopy data is often sparse and new approaches to provide complementary NMR spectroscopy data are needed. Paramagnetic relaxation enhancements (PREs) obtained from inert and soluble paramagnetic probes (solvent PREs) provide detailed quantitative information about the solvent accessibility of NMR-active nuclei. Solvent PREs can be easily measured without modification of the biomolecule; are sensitive to molecular structure and dynamics; and are therefore becoming increasingly powerful for the study of biomolecules, such as proteins, nucleic acids, ligands and their complexes in solution. In this Minireview, we give an overview of the available solvent PRE probes and discuss their applications for structural and dynamic characterisation of biomolecules and biomolecular complexes.
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Affiliation(s)
- Henry G Hocking
- Chair of Biomolecular NMR, Department Chemie, Technische Universität München, 85747 Garching (Germany); Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg (Germany)
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Solution NMR studies on the orientation of membrane-bound peptides and proteins by paramagnetic probes. Molecules 2013; 18:7407-35. [PMID: 23799448 PMCID: PMC6269851 DOI: 10.3390/molecules18077407] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/13/2013] [Accepted: 06/20/2013] [Indexed: 12/24/2022] Open
Abstract
Many peptides and proteins are attached to or immersed in a biological membrane. In order to understand their function not only the structure but also their topology in the membrane is important. Solution NMR spectroscopy is one of the most often used approaches to determine the orientation and localization of membrane-bound peptides and proteins. Here we give an application-oriented overview on the use of paramagnetic probes for the investigation of membrane-bound peptides and proteins. The examples discussed range from the large pool of antimicrobial peptides, bacterial toxins, cell penetrating peptides to domains of larger proteins or the calcium regulating protein phospholamban. Topological information is obtained in all these examples by the use of either attached or freely mobile paramagnetic tags. For some examples information obtained from the paramagnetic probes was included in the structure determination.
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Fröhlich RF, Schrank E, Zangger K. 2,2,2-Trifluoroethyl 6-thio-β-D-glucopyranoside as a selective tag for cysteines in proteins. Carbohydr Res 2012; 361:100-4. [PMID: 23000216 PMCID: PMC4067056 DOI: 10.1016/j.carres.2012.08.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/16/2012] [Accepted: 08/17/2012] [Indexed: 11/30/2022]
Abstract
A synthetic route to a trifluoromethyl and thiol containing glucose derivative (2,2,2-trifluoroethyl 6-thio-β-d-glucopyranoside) is presented, which is based on microwave-assisted Fischer glycosylation under increased pressure. This water-soluble, neutral thiol-compound can be used to selectively introduce a fluorine probe for 19F NMR spectroscopy on cysteines in proteins. It can be attached under mild conditions in an aqueous environment without the risk of denaturing the protein. This tag has been applied to determine the redox-state of two cysteine residues in a bacterial transcription activator. Qualitative information about the solvent accessibility can be obtained from F-19 solvent PREs.
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Affiliation(s)
| | | | - Klaus Zangger
- Corresponding author. Tel.: +43 316 380 8673; fax: +43 316 380 9840.
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Kosol S, Schrank E, Krajačić MB, Wagner GE, Meyer NH, Göbl C, Rechberger GN, Zangger K, Novak P. Probing the Interactions of Macrolide Antibiotics with Membrane-Mimetics by NMR Spectroscopy. J Med Chem 2012; 55:5632-6. [DOI: 10.1021/jm300647f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Simone Kosol
- Institute
of Chemistry/Organic
and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28,
A-8010 Graz, Austria
| | - Evelyne Schrank
- Institute
of Chemistry/Organic
and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28,
A-8010 Graz, Austria
| | | | - Gabriel E. Wagner
- Institute
of Chemistry/Organic
and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28,
A-8010 Graz, Austria
| | - N. Helge Meyer
- Institute
of Chemistry/Organic
and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28,
A-8010 Graz, Austria
| | - Christoph Göbl
- Institute
of Chemistry/Organic
and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28,
A-8010 Graz, Austria
| | - Gerald N. Rechberger
- Institute of Molecular Biosciences,
University of Graz, Humboldtstrasse 50, A-8010 Graz, Austria
| | - Klaus Zangger
- Institute
of Chemistry/Organic
and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28,
A-8010 Graz, Austria
| | - Predrag Novak
- Department of Chemistry, Faculty
of Natural Science, University of Zagreb, Laboratory for Analytical
Chemistry, Horvatovac 102a, HR-10000 Zagreb, Croatia
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Hohlweg W, Kosol S, Zangger K. Determining the orientation and localization of membrane-bound peptides. Curr Protein Pept Sci 2012; 13:267-79. [PMID: 22044140 PMCID: PMC3394173 DOI: 10.2174/138920312800785049] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 10/01/2011] [Accepted: 10/10/2011] [Indexed: 01/06/2023]
Abstract
Many naturally occurring bioactive peptides bind to biological membranes. Studying and elucidating the mode of interaction is often an essential step to understand their molecular and biological functions. To obtain the complete orientation and immersion depth of such compounds in the membrane or a membrane-mimetic system, a number of methods are available, which are separated in this review into four main classes: solution NMR, solid-state NMR, EPR and other methods. Solution NMR methods include the Nuclear Overhauser Effect (NOE) between peptide and membrane signals, residual dipolar couplings and the use of paramagnetic probes, either within the membrane-mimetic or in the solvent. The vast array of solid state NMR methods to study membrane-bound peptide orientation and localization includes the anisotropic chemical shift, PISA wheels, dipolar waves, the GALA, MAOS and REDOR methods and again the use of paramagnetic additives on relaxation rates. Paramagnetic additives, with their effect on spectral linewidths, have also been used in EPR spectroscopy. Additionally, the orientation of a peptide within a membrane can be obtained by the anisotropic hyperfine tensor of a rigidly attached nitroxide label. Besides these magnetic resonance techniques a series of other methods to probe the orientation of peptides in membranes has been developed, consisting of fluorescence-, infrared- and oriented circular dichroism spectroscopy, colorimetry, interface-sensitive X-ray and neutron scattering and Quartz crystal microbalance.
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Affiliation(s)
| | | | - Klaus Zangger
- Institute of Chemistry / Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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Wang Q, Hong G, Johnson GR, Pachter R, Cheung MS. Biophysical properties of membrane-active peptides based on micelle modeling: a case study of cell-penetrating and antimicrobial peptides. J Phys Chem B 2011; 114:13726-35. [PMID: 20939546 DOI: 10.1021/jp1069362] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated the molecular mechanisms of short peptides interacting with membrane-mimetic systems. Three short peptides were selected for this study: penetratin as a cell-penetrating peptide (CPP), and temporin A and KSL as antimicrobial peptides (AMP). We investigated the detailed interactions of the peptides with dodecylphosphocholine (DPC) and sodium dodecyl sulfate (SDS) micelles, and the subsequent peptide insertion based on free energy calculations by using all-atomistic molecular dynamics simulations with the united atom force field and explicit solvent models. First, we found that the free energy barrier to insertion for the three peptides is dependent on the chemical composition of the micelles. Because of the favorable electrostatic interactions between the peptides and the headgroups of lipids, the insertion barrier into an SDS micelle is less than a DPC micelle. Second, the peptides' secondary structures may play a key role in their binding and insertion ability, particularly for amphiphilic peptides such as penetratin and KSL. The secondary structures with a stronger ability to bind with and insert into micelles are the ones that account for a smaller surface area of hydrophobic core, thus offering a possible criterion for peptide design with specific functionalities.
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Affiliation(s)
- Qian Wang
- Department of Physics, University of Houston, Houston, Texas, USA
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Wieczorek M, Jenssen H, Kindrachuk J, Scott WRP, Elliott M, Hilpert K, Cheng JTJ, Hancock REW, Straus SK. Structural studies of a peptide with immune modulating and direct antimicrobial activity. ACTA ACUST UNITED AC 2011; 17:970-80. [PMID: 20851346 DOI: 10.1016/j.chembiol.2010.07.007] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 07/03/2010] [Accepted: 07/07/2010] [Indexed: 01/17/2023]
Abstract
The structure and function of the synthetic innate defense regulator peptide 1018 was investigated. This 12 residue synthetic peptide derived by substantial modification of the bovine cathelicidin bactenecin has enhanced innate immune regulatory and moderate direct antibacterial activities. The solution state NMR structure of 1018 in zwitterionic dodecyl phosphocholine (DPC) micelles indicated an α-helical conformation, while secondary structures, based on circular dichroism measurements, in anionic sodium dodecyl sulfate (SDS) and phospholipid vesicles (POPC/PG in a 1:1 molar ratio) and simulations revealed that 1018 can adopt a variety of folds, tailored to its different functions. The structural data are discussed in light of the ability of 1018 to potently induce chemokine responses, suppress the LPS-induced TNF-α response, and directly kill both Gram-positive and Gram-negative bacteria.
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Affiliation(s)
- Michal Wieczorek
- Chemistry Department, University of British Columbia, Vancouver, BC, Canada
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Koch K, Afonin S, Ieronimo M, Berditsch M, Ulrich AS. Solid-State 19F-NMR of Peptides in Native Membranes. Top Curr Chem (Cham) 2011; 306:89-118. [DOI: 10.1007/128_2011_162] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Göbl C, Kosol S, Stockner T, Rückert HM, Zangger K. Solution structure and membrane binding of the toxin fst of the par addiction module. Biochemistry 2010; 49:6567-75. [PMID: 20677831 PMCID: PMC2914490 DOI: 10.1021/bi1005128] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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The par toxin−antitoxin system is required for the stable inheritance of the plasmid pAD1 in its native host Enterococcus faecalis. It codes for the toxin Fst and a small antisense RNA which inhibits translation of toxin mRNA, and it is the only known antisense regulated toxin−antitoxin system in Gram-positive bacteria. This study presents the structure of the par toxin Fst, the first atomic resolution structure of a component of an antisense regulated toxin−antitoxin system. The mode of membrane binding was determined by relaxation enhancements in a paramagnetic environment and molecular dynamics simulation. Fst forms a membrane-binding α-helix in the N-terminal part and contains an intrinsically disordered region near the C-terminus. It binds in a transmembrane orientation with the C-terminus likely pointing toward the cytosol. Membrane-bound, α-helical peptides are frequently found in higher organisms as components of the innate immune system. Despite similarities to these antimicrobial peptides, Fst shows neither hemolytic nor antimicrobial activity when applied externally to a series of bacteria, fungal cells, and erythrocytes. Moreover, its charge distribution, orientation in the membrane, and structure distinguish it from antimicrobial peptides.
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Affiliation(s)
- Christoph Göbl
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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Großauer J, Kosol S, Schrank E, Zangger K. The peptide hormone ghrelin binds to membrane-mimetics via its octanoyl chain and an adjacent phenylalanine. Bioorg Med Chem 2010; 18:5483-8. [PMID: 20621491 PMCID: PMC3038380 DOI: 10.1016/j.bmc.2010.06.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 06/15/2010] [Accepted: 06/16/2010] [Indexed: 02/01/2023]
Abstract
The peptide hormone ghrelin, which is the natural ligand of the membrane-bound growth hormone secretagogue receptor (GHS-R), regulates overall body and cell growth, energy homeostasis, carbohydrate, protein and lipid metabolism and water electrolyte balance. It contains an O-acyl linked octanoyl group on Ser3 and is the only peptide known to contain such a modification. Using solution state NMR spectroscopy and ultrafiltration we found that human ghrelin binds to membrane-mimetic environments via its octanoyl group as well as the aromatic moiety of Phe4. Relaxation enhancements in a paramagnetic environment reveal that both the octanoyl group on Ser3 and the aromatic group on Phe4 are inserted deep into the hydrophobic core of phosphocholine assemblies while the remaining peptide is freely mobile in solution. In contrast, no binding was observed for des-octanoyl ghrelin. Thus, the octanoyl chain, together with the Phe4 aromatic group of ghrelin, functions as a membrane anchor. Our results are in parallel with the previous finding that a bulky hydrophobic group on Ser3 and Phe4 of ghrelin are necessary for its function and thus indicate that membrane-binding is essential for ghrelin function.
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Affiliation(s)
| | | | | | - Klaus Zangger
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Graz, Austria
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