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Bairagya HR, Tasneem A, Sarmadhikari D. Structural and thermodynamic properties of conserved water molecules in Mpro native: A combined approach by MD simulation and Grid Inhomogeneous Solvation Theory. Proteins 2024; 92:735-749. [PMID: 38213131 DOI: 10.1002/prot.26665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/28/2023] [Accepted: 01/01/2024] [Indexed: 01/13/2024]
Abstract
The new viral strains of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are continuously rising, becoming more virulent, and transmissible. Therefore, the development of new antiviral drugs is essential. Due to its significant role in the viral life cycle of SARS-CoV-2, the main protease (Mpro) enzyme is a leading target for antiviral drug design. The Mpro monomer consists of domain DI, DII, and DI-DII interface. Twenty-one conserved water molecules (W4-W24) are occupied at these domains according to multiple crystal structure analyses. The crystal and MD structures reveal the presence of eight conserved water sites in domain DI, DII and remaining in the DI-DII interface. Grid-based inhomogeneous fluid solvation theory (GIST) was employed on MD structures of Mpro native to predict structural and thermodynamic properties of each conserved water site for focusing to identify the specific conserved water molecules that can easily be displaced by proposed ligands. Finally, MD water W13 is emerged as a promising candidate for water mimic drug design due to its low mean interaction energy, loose binding character with the protein, and its involvement in a water-mediated H-bond with catalytic His41 via the interaction Thr25(OG)---W13---W---His41(NE2). In this context, water occupancy, relative interaction energy, entropy, and topologies of W13 are thermodynamically acceptable for the water displacement method. Therefore, the strategic use of W13's geometrical position in the DI domain may be implemented for drug discovery against COVID disease by designing new ligands with appropriately oriented chemical groups to mimic its structural, electronic, and thermodynamic properties.
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Affiliation(s)
- Hridoy R Bairagya
- Computational Drug Design and Bio-molecular Simulation Lab, Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
| | - Alvea Tasneem
- Mathematical and Computational Biology Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Debapriyo Sarmadhikari
- Computational Drug Design and Bio-molecular Simulation Lab, Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
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2
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Andrä J, Aisenbrey C, Sudheendra US, Prudhon M, Brezesinski G, Zschech C, Willumeit-Römer R, Leippe M, Gutsmann T, Bechinger B. Structural analysis of the NK-lysin-derived peptide NK-2 upon interaction with bacterial membrane mimetics consisting of phosphatidylethanolamine and phosphatidylglycerol. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184267. [PMID: 38159877 DOI: 10.1016/j.bbamem.2023.184267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
NK-2 is an antimicrobial peptide derived from helices 3 and 4 of the pore-forming protein of natural killer cells, NK-lysin. It has potent activities against Gram-negative and Gram-positive bacteria, fungi and protozoan parasites without being toxic to healthy human cells. In biophysical assays its membrane activities were found to require phosphatidylglycerol (PG) and phosphatidylethanolamine (PE), lipids which dominate the composition of bacterial membranes. Here the structure and activities of NK-2 in binary mixtures of different PE/PG composition were investigated. CD spectroscopy reveals that a threshold concentration of 50 % PG is needed for efficient membrane association of NK-2 concomitant with a random coil - helix transition. Association with PE occurs but is qualitatively different when compared to PG membranes. Oriented solid-state NMR spectroscopy of NK-2 specifically labelled with 15N indicates that the NK-2 helices are oriented parallel to the PG bilayer surface. Upon reduction of the PG content to 20 mol% interactions are weaker and/or an in average more tilted orientation is observed. Fluorescence spectroscopy of differently labelled lipids is in agreement of an interfacial localisation of both helices where the C-terminal end is in a less hydrophobic environment. By inserting into the membrane interface and interacting differently with PE and PG the peptides probably induce high curvature strain which result in membrane openings and rupture.
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Affiliation(s)
- Jörg Andrä
- Department of Biotechnology, Faculty of Life Sciences, Hamburg University of Applied Sciences, Hamburg, Germany.
| | | | - U S Sudheendra
- University of Strasbourg / CNRS, UMR7177, Chemistry Institute, Strasbourg, France
| | - Marc Prudhon
- University of Strasbourg / CNRS, UMR7177, Chemistry Institute, Strasbourg, France
| | - Gerald Brezesinski
- Department of Physics, TU Darmstadt, Darmstadt, Germany; Department of Interfaces, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Claudia Zschech
- Department of Interfaces, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | | | - Matthias Leippe
- Comparative Immunobiology, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Thomas Gutsmann
- Research Center Borstel, Leibniz Lung Center, Borstel, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Burkhard Bechinger
- University of Strasbourg / CNRS, UMR7177, Chemistry Institute, Strasbourg, France; Institut Universitaire de France, 75005 Paris, France.
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Bairagya HR, Tasneem A, Rai GP, Reyaz S. New biochemical insights into the dynamics of water molecules at the GMP or IMP binding site of human GMPR enzyme: A molecular dynamics study. Proteins 2022; 90:200-217. [PMID: 34368983 DOI: 10.1002/prot.26207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/24/2021] [Accepted: 07/22/2021] [Indexed: 12/31/2022]
Abstract
Human GMP reductase (hGMPR) enzyme is involved in a cellular metabolic pathway, converting GMP into IMP, and also it is an important target for anti-leukemic agents. Present computational investigations explain dynamical behavior of water molecules during the conformational transition process from GMP to IMP using molecular dynamics simulations. Residues at substrate-binding site of cancerous protein (PDB Id. 2C6Q) are mostly more dynamic in nature than the normal protein (PDB Id. 2BLE). Nineteen conserved water molecules are identified at the GMP/IMP binding site and are classified as (i) conserved stable dynamic and (ii) infrequent dynamic. Water molecules W11, W14, and W16 are classified as conserved stable dynamic due to their immobile character, whereas remaining water molecules (W1, W2, W3, W4, W5, W7, W8, W9, W10, W12, W13, W15, W17, W18, and W19) are infrequent with dynamic nature. Entrance or displacement of these infrequent water molecules at GMP/IMP sites may occur due to forward and backward movement of reference residues involving ligands. Four water molecules of hGMPR-I and nine water molecules of hGMPR-II are observed in repetitive transitions from GMP to IMP pathway, which indicates discrimination between two isoforms of hGMPRs. Water molecules in cancerous protein are more dynamic and unstable compared to normal protein. These water molecules execute rare dynamical events at GMP binding site and could assist in detailed understanding of conformational transitions that influence the hGMPR's biological functionality. The present study should be of interest to the experimental community engaged in leukemia research and drug discovery for CML cancer.
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Affiliation(s)
| | - Alvea Tasneem
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Gyan Prakash Rai
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Saima Reyaz
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
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Reyaz S, Tasneem A, Rai GP, Bairagya HR. Investigation of structural analogs of hydroxychloroquine for SARS-CoV-2 main protease (Mpro): A computational drug discovery study. J Mol Graph Model 2021; 109:108021. [PMID: 34537554 PMCID: PMC8426616 DOI: 10.1016/j.jmgm.2021.108021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/18/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022]
Abstract
The main protease (Mpro) is the key enzyme of nCOVID-19 and plays a decisive role that makes it an attractive drug target. Multiple analysis of crystal structures reveals the presence of W1, W2, and W3 water locations in the active site pocket of Mpro; W1 and W2 are unstable and are weakly bonded with protein in comparison to W3 of Mpro-native. So, we adopt the water displacement method to occupy W1 or W2 sites by triggering HCQ or its analogs to inactivate the enzyme. Virtual screening is employed to find out best analogs of HCQ, molecular docking is used for water displacement from catalytic region of Mpro, and finally, MD simulations are conducted for validation of these findings. The docking study reveals that W1 and W2 are occupied by respective atoms of ZINC28706440 whereas W2 by HCQ and indacaterol. Finally, MD results demonstrate (i) HCQ occupies W1 and W2 positions, but its analogs (indacaterol and ZINC28706440) are inadequate to retain either W1 or W2 (ii) His41 and Asp187 are stabilized by W3 in Mpro-native and His41, Cys145 and HCQ by W7 in ZINC28706440, and W4, W5, and W6 make water mediated bridge between indacaterol with His41. The structural, dynamical, and thermodynamic (WFP and J value) profiling parameters suggest that W3, W4, and W7 are prominent in their corresponding positions in comparison with W5 and W6. The final results conclude that ZINC28706440 may act as a best analog of HCQ with acceptable physico-chemical and toxicological scores and may further be synthesized for experimental validation.
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Affiliation(s)
- Saima Reyaz
- Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025, India
| | - Alvea Tasneem
- Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025, India
| | - Gyan Prakash Rai
- Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025, India
| | - Hridoy R Bairagya
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India.
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Bairagya HR, Tasneem A, Rai GP, Reyaz S. Structural and Dynamical Impact of Water Molecules at Substrate- or Product-Binding Sites in Human GMPR Enzyme: A Study by Molecular Dynamics Simulations. J Phys Chem B 2021; 125:1351-1362. [PMID: 33369428 DOI: 10.1021/acs.jpcb.0c08818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human guanosine monophosphate reductase (hGMPR) enzyme maintains the intracellular balance between adenine and guanine nucleotide pools, and it is an excellent target for the design of isoform-specific antileukemic agents. In the present study, we have investigated solvation properties of substrate GMP or product inosine-5'-monophosphate (IMP)-binding pocket of hGMPR by employing molecular dynamics simulations on conformations A (substrate GMP), B [substrate GMP with cofactor nicotinamide adenine dinucleotide phosphate (NDP)], C (product IMP with cofactor NDP), and D (product IMP). Nineteen water sites are identified precisely; they are responsible for the catalytic activity of this site, control structural and dynamical integrity, and electronic consequences of GMP or IMP in the binding site of hGMPR. The water sites of category-1 (W1, W4, W5, W6, W13, and W15) in normal protein and category-2 (W2, W3, W7, W8, W10, W17, and W18) in cancerous protein are unique and stabilize the guanosine or inosine group of GMP or IMP for participation in the enzymatic reaction, whereas the remaining water centers either stabilize pentose sugar ribose or the phosphate group of GMP or IMP. Furthermore, water sites of category-4 (W11, W14, and W16) appear to be conserved in all conformations during the entire simulation. The GMP-binding site in cancerous protein 2C6Q is significantly expanded, and its dynamics are very different from normal protein 2BLE. Furthermore, unique interactions of GMP(N1)···W2···Asp129/Asn158, IMP(N1)···W3···Glu289, and IMP(O6)···W10···Ser270 might be used in a water mimic drug design for hGMPR-II. In this context, water finding probability, relative interaction energy (J) associated with water site W, entropy, and topologies of these three water sites are thermodynamically acceptable for the water displacement method by the modified ligand. Hence, their positions in the catalytic pocket may also facilitate future drug discovery for chronic myelogenous leukemia by the design of appropriately oriented chemical groups that may displace these water molecules to mimic their structural, electronic, and thermodynamic properties.
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Affiliation(s)
- Hridoy R Bairagya
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Alvea Tasneem
- Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi 110025, India
| | - Gyan Prakash Rai
- Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi 110025, India
| | - Saima Reyaz
- Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi 110025, India
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Edwards-Gayle CC, Castelletto V, Hamley IW, Barrett G, Greco F, Hermida-Merino D, Rambo RP, Seitsonen J, Ruokolainen J. Self-Assembly, Antimicrobial Activity, and Membrane Interactions of Arginine-Capped Peptide Bola-Amphiphiles. ACS APPLIED BIO MATERIALS 2019; 2:2208-2218. [PMID: 31157325 PMCID: PMC6537463 DOI: 10.1021/acsabm.9b00172] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/16/2019] [Indexed: 12/27/2022]
Abstract
The self-assembly and antimicrobial activity of two novel arginine-capped bola-amphiphile peptides, namely RA6R and RA9R (R, arginine; A, alanine) are investigated. RA6R does not self-assemble in water due to its high solubility, but RA9R self-assembles above a critical aggregation concentration into ordered nanofibers due to the high hydrophobicity of the A9block. The structure of the RA9R nanofibers is studied by cryogenic transmission electron microscopy (cryo-TEM) and small-angle X-ray scattering (SAXS). Circular dichroism spectroscopy shows that both RA6R and RA9R adopt coil conformations in water at low concentration, but only RA9R adopts a β-sheet conformation at high concentration. SAXS and differential scanning calorimetry are used to study RA6R and RA9R interactions with a mixed lipid membrane that models a bacterial cell wall, consisting of multilamellar 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol/1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine vesicles. Cytotoxicity studies show that RA6R is more cytocompatible than RA9R. RA6R has enhanced activity against the Gram-negative pathogen P. aeruginosa at a concentration where viability of mammalian cells is retained. RA9R has little antimicrobial activity, independently of concentration. Our results highlight the influence of the interplay between relative charge and hydrophobicity on the self-assembly, cytocompatibility, and bioactivity of peptide bola-amphiphiles.
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Affiliation(s)
- Charlotte
J. C. Edwards-Gayle
- School
of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
- Diamond
Light Source, Harwell Science and Innovation
Campus, Didcot, Oxfordshire OX11 0DE, U.K.
| | - Valeria Castelletto
- School
of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
| | - Ian W. Hamley
- School
of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
| | - Glyn Barrett
- School
of Biological Sciences, University of Reading, Reading RG6 6UR, U.K.
| | - Francesca Greco
- School
of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
| | | | - Robert P. Rambo
- Diamond
Light Source, Harwell Science and Innovation
Campus, Didcot, Oxfordshire OX11 0DE, U.K.
| | - Jani Seitsonen
- Department
of Applied Physics, Aalto School of Science, P.O. Box 15100, FI-00076 Aalto, Finland
| | - Janne Ruokolainen
- Department
of Applied Physics, Aalto School of Science, P.O. Box 15100, FI-00076 Aalto, Finland
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Avci FG, Akbulut BS, Ozkirimli E. Membrane Active Peptides and Their Biophysical Characterization. Biomolecules 2018; 8:biom8030077. [PMID: 30135402 PMCID: PMC6164437 DOI: 10.3390/biom8030077] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/08/2018] [Accepted: 08/13/2018] [Indexed: 12/12/2022] Open
Abstract
In the last 20 years, an increasing number of studies have been reported on membrane active peptides. These peptides exert their biological activity by interacting with the cell membrane, either to disrupt it and lead to cell lysis or to translocate through it to deliver cargos into the cell and reach their target. Membrane active peptides are attractive alternatives to currently used pharmaceuticals and the number of antimicrobial peptides (AMPs) and peptides designed for drug and gene delivery in the drug pipeline is increasing. Here, we focus on two most prominent classes of membrane active peptides; AMPs and cell-penetrating peptides (CPPs). Antimicrobial peptides are a group of membrane active peptides that disrupt the membrane integrity or inhibit the cellular functions of bacteria, virus, and fungi. Cell penetrating peptides are another group of membrane active peptides that mainly function as cargo-carriers even though they may also show antimicrobial activity. Biophysical techniques shed light on peptide–membrane interactions at higher resolution due to the advances in optics, image processing, and computational resources. Structural investigation of membrane active peptides in the presence of the membrane provides important clues on the effect of the membrane environment on peptide conformations. Live imaging techniques allow examination of peptide action at a single cell or single molecule level. In addition to these experimental biophysical techniques, molecular dynamics simulations provide clues on the peptide–lipid interactions and dynamics of the cell entry process at atomic detail. In this review, we summarize the recent advances in experimental and computational investigation of membrane active peptides with particular emphasis on two amphipathic membrane active peptides, the AMP melittin and the CPP pVEC.
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Affiliation(s)
- Fatma Gizem Avci
- Bioengineering Department, Marmara University, Kadikoy, 34722 Istanbul, Turkey.
| | | | - Elif Ozkirimli
- Chemical Engineering Department, Bogazici University, Bebek, 34342 Istanbul, Turkey.
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Taniguchi M, Ochiai A. Characterization and production of multifunctional cationic peptides derived from rice proteins. Biosci Biotechnol Biochem 2017; 81:634-650. [DOI: 10.1080/09168451.2016.1277944] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Abstract
Food proteins have been identified as a source of bioactive peptides. These peptides are inactive within the sequence of the parent protein and must be released during gastrointestinal digestion, fermentation, or food processing. Of bioactive peptides, multifunctional cationic peptides are more useful than other peptides that have specific activity in promotion of health and/or the treatment of diseases. We have identified and characterized cationic peptides from rice enzymes and proteins that possess multiple functions, including antimicrobial, endotoxin-neutralizing, arginine gingipain-inhibitory, and/or angiogenic activities. In particular, we have elucidated the contribution of cationic amino acids (arginine and lysine) in the peptides to their bioactivities. Further, we have discussed the critical parameters, particularly proteinase preparations and fractionation or purification, in the enzymatic hydrolysis process for producing bioactive peptides from food proteins. Using an ampholyte-free isoelectric focusing (autofocusing) technique as a tool for fractionation, we successfully prepared fractions containing cationic peptides with multiple functions.
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Affiliation(s)
- Masayuki Taniguchi
- Department of Materials Science and Technology, Graduate School of Science and Technology, Niigata University, Niigata, Japan
- Center for Transdisciplinary Research, Niigata University, Niigata, Japan
| | - Akihito Ochiai
- Department of Materials Science and Technology, Graduate School of Science and Technology, Niigata University, Niigata, Japan
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Alaybeyoglu B, Akbulut BS, Ozkirimli E. A novel chimeric peptide with antimicrobial activity. J Pept Sci 2015; 21:294-301. [PMID: 25597294 DOI: 10.1002/psc.2739] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 12/05/2014] [Accepted: 12/12/2014] [Indexed: 11/09/2022]
Abstract
Beta-lactamase-mediated bacterial drug resistance exacerbates the prognosis of infectious diseases, which are sometimes treated with co-administration of beta-lactam type antibiotics and beta-lactamase inhibitors. Antimicrobial peptides are promising broad-spectrum alternatives to conventional antibiotics in this era of evolving bacterial resistance. Peptides based on the Ala46-Tyr51 beta-hairpin loop of beta-lactamase inhibitory protein (BLIP) have been previously shown to inhibit beta-lactamase. Here, our goal was to modify this peptide for improved beta-lactamase inhibition and cellular uptake. Motivated by the cell-penetrating pVEC sequence, which includes a hydrophobic stretch at its N-terminus, our approach involved the addition of LLIIL residues to the inhibitory peptide N-terminus to facilitate uptake. Activity measurements of the peptide based on the 45-53 loop of BLIP for enhanced inhibition verified that the peptide was a competitive beta-lactamase inhibitor with a K(i) value of 58 μM. Incubation of beta-lactam-resistant cells with peptide decreased the number of viable cells, while it had no effect on beta-lactamase-free cells, indicating that this peptide had antimicrobial activity via beta-lactamase inhibition. To elucidate the molecular mechanism by which this peptide moves across the membrane, steered molecular dynamics simulations were carried out. We propose that addition of hydrophobic residues to the N-terminus of the peptide affords a promising strategy in the design of novel antimicrobial peptides not only against beta-lactamase but also for other intracellular targets.
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Affiliation(s)
- Begum Alaybeyoglu
- Chemical Engineering Department, Bogazici University, Bebek, 34342, Istanbul, Turkey
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Takei N, Takahashi N, Takayanagi T, Ikeda A, Hashimoto K, Takagi M, Hamada T, Saitoh E, Ochiai A, Tanaka T, Taniguchi M. Antimicrobial activity and mechanism of action of a novel cationic α-helical dodecapeptide, a partial sequence of cyanate lyase from rice. Peptides 2013; 42:55-62. [PMID: 23270672 DOI: 10.1016/j.peptides.2012.12.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/15/2012] [Accepted: 12/17/2012] [Indexed: 12/26/2022]
Abstract
CL(14-25), a dodecapeptide, that is a partial region near N-terminus of cyanate lyase (CL, EC 4.3.99.1) from rice (Oryza sativa L. japonica), contains three arginine and two lysine residues. It was a novel cationic α-helical antimicrobial peptide. The antimicrobial activity of CL(14-25) against Porphyromonas gingivalis, a periodontal pathogen, was quantitatively evaluated by a chemiluminescence method that measures ATP derived from viable cells. The 50% growth-inhibitory concentration of CL(14-25) against P. gingivalis cells was 145 μM. CL(14-25), even at a concentration of 800 μM, had no hemolytic activity. When giant unilamellar vesicles (GUVs) that mimic the membrane composition of Gram-negative bacteria were used, microscopy image analysis suggested that CL(14-25) disrupted GUVs in a detergent-like manner. Therefore, CL(14-25) appears to exhibit antimicrobial activity through membrane disruption. To investigate the contribution of cationic amino acid residues in CL(14-25) to its antimicrobial activity, we synthesized four truncated CL analogs, in which one or two cationic amino acid residues were deleted from the N- and C- termini of CL(14-25). The degrees of calcein leakage from large unilamellar vesicles (LUVs) and 3,3'-dipropylthiadicarbocyanine iodide (diSC3-5) release from P. gingivalis cells induced by truncated CL analogs were closely related to their antimicrobial activities. CL analogs, which were truncated by removing an arginine residue from the N-terminus and a lysine residue from the C-terminus maintained their antimicrobial activity. However, CL analogs, which were further truncated by removing two arginine residues from the N-terminus, and an arginine and a lysine residue from the C-terminus, rarely exhibited antimicrobial activity.
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Affiliation(s)
- Norihiro Takei
- Center for Fostering Innovative Leadership, Niigata University, Niigata 950-2181, Japan
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Simulation of Volumetric Swelling of Degradable Poly[(Rac-Lactide)-Co-Glycolide] Based Polyesterurethanes Containing Different Urethane-Linkers. J Appl Biomater Funct Mater 2012; 10:293-301. [DOI: 10.5301/jabfm.2012.10432] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2012] [Indexed: 11/20/2022] Open
Abstract
Aim The hydrolytic degradation behavior of degradable aliphatic polyester-based polymers is strongly influenced by the uptake or transport of water into the polymer matrix and also the hydrolysis rate of ester bonds. Methods We examined the volumetric swelling behavior of poly[(rac-lactide)-co-glycolide] (PLGA) and PLGA-based poly-urethanes (PLGA-PU) with water contents of 0 wt%, 2 wt% and 7 wt% water at 310 K using a molecular modeling approach. Polymer systems with a number average molecular weight of Mn = 10,126 g·mol−1 were constructed from PLGA with a lactide content of 67 mol%, whereby PLGA-PU systems were composed of five PLGA segments with Mn = 2052 g·mol−1, which were connected via urethane linkers originated from 2,2,4-trimethyl hexamethylene-1,6-diisocyanate (TMDI), hexamethyl-1,6-diisocyanate (HDI), or L-lysine-1,6-diisocyanate (LDI). Results The calculated densities of the dry PLGA-PU systems were found to be lower than for pure PLGA. The obtained volumetric swelling of the PLGA-PU was depending on the type of urethane linker, whereby all swollen PLGA-PUs contained larger free volume distribution compared to pure PLGA. The mean square displacement curves for dry PLGA and PLGA-PUs showed that urethane linker units reduce the mobility of the polymer chains, while an increase in backbone atoms mobility was found, when water was added to these systems. Consequently, an increased water uptake of PLGA-PU matrices combined with a higher mobility of the chain segments should result in an accelerated hydrolytic chain scission rate in comparison to PLGA. Conclusions It can be anticipated that the incorporation of urethane linkers might be a helpful tool to adjust the degradation behavior of polyesters.
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Mandal SM, Migliolo L, Franco OL. The use of MALDI-TOF-MS and in silico studies for determination of antimicrobial peptides' affinity to bacterial cells. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1939-1948. [PMID: 22926961 DOI: 10.1007/s13361-012-0453-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 06/28/2012] [Accepted: 07/18/2012] [Indexed: 06/01/2023]
Abstract
Several methods have been proposed for determining the binding affinity of antimicrobial peptides (AMPs) to bacterial cells. Here the utilization of MALDI-TOF-MS was proposed as a reliable and efficient method for high throughput AMP screening. The major advantage of the technique consists of finding AMPs that are selective and specific to a wide range of Gram-negative and -positive bacteria, providing a simple reliable screening tool to determine the potential candidates for broad spectrum antimicrobial drugs. As a prototype, amp-1 and -2 were used, showing highest activity toward Gram-negative and -positive membranes respectively. In addition, in silico molecular docking studies with both peptides were carried out for the membranes. In silico results indicated that both peptides presented affinity for DPPG and DPPE phospholipids, constructed in order to emulate an in vivo membrane bilayer. As a result, amp-1 showed a higher complementary surface for Gram-negative while amp-2 showed higher affinity to Gram-positive membranes, corroborating MS analyses. In summary, results here obtained suggested that in vitro methodology using MALDI-TOF-MS in addition to theoretical studies may be able to improve AMP screening quality.
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Affiliation(s)
- Santi M Mandal
- Mass Spectrometry and Proteomics Laboratory Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur, WB, India
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Antimicrobial selectivity based on zwitterionic lipids and underlying balance of interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2192-201. [DOI: 10.1016/j.bbamem.2012.05.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 04/26/2012] [Accepted: 05/09/2012] [Indexed: 01/03/2023]
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14
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Tsai CW, Ruaan RC, Liu CI. Adsorption of antimicrobial indolicidin-derived peptides on hydrophobic surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:10446-10452. [PMID: 22721449 DOI: 10.1021/la301401v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The hydrophobic interaction between antimicrobial peptides and membrane hydrophobic cores is usually related to their cytotoxicity. In this study, the adsorption mechanism of five plasma membrane-associated peptides, indolicidin (IL) and its four derivatives, with hydrophobic ligands was investigated to understand the relationship between peptide hydrophobicity and bioactivity. The hydrophobic adsorption mechanisms of IL and its derivatives were interpreted thermodynamically and kinetically by reversed-phase chromatography (RPC) analysis and surface plasmon resonance (SPR) measurement, respectively. IL and its derivatives possess a similar random coil structure in both aqueous and organic solvents. Thermodynamic analysis showed that the binding enthalpy of peptides with higher electropositivity was lower than those with lower electropositivity and exhibited unfavorable binding entropy. Higher electropositivity peptides adsorbed to the hydrophobic surface arising from the less bound solvent on the peptide surface. A comparison with the kinetic analysis showed that IL and its derivatives adopt a two-state binding model (i.e., adsorption onto and self-association on the hydrophobic acyl chain) to associate with the hydrophobic surface, and the binding affinity of peptide self-association correlates well with peptide hemolysis. Consequently, this study provided a novel concept for understanding the action of plasma membrane-associated peptides.
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Affiliation(s)
- Ching-Wei Tsai
- Department of Chemical and Materials Engineering, National Central University, Jhong-Li, Taiwan
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von Deuster CIE, Knecht V. Competing interactions for antimicrobial selectivity based on charge complementarity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2867-76. [PMID: 21893025 DOI: 10.1016/j.bbamem.2011.08.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 07/29/2011] [Accepted: 08/01/2011] [Indexed: 11/24/2022]
Abstract
Antimicrobial peptides (AMPs) are an evolutionary conserved component of the innate immune system and possible templates for the development of new antibiotics. An important property of antimicrobial peptides is their ability to discriminate bacterial from eucaryotic cells which is attributed to the difference in lipid composition of the outer leaflet of the plasma membrane between the two types of cells. Whereas eucaryotic cells usually expose zwitterionic lipids, procaryotic cells expose also anionic lipids which bind the cationic antimicrobial peptides electrostatically. An example is the antimicrobial peptide NK-2 which is highly cationic and favors binding to anionic membranes. In the present study, the difference in binding affinity of NK-2 for palmitoyl-oleoyl-phosphatidyl-glycerol (POPG) and palmitoyl-oleoyl-phosphatidyl-choline (POPC) is studied using molecular dynamics simulations in conjunction with a coarse grained model and thermodynamic integration, by computing the change in free energy and its components upon the transfer of NK-2 from POPC to POPG. The transfer is indeed found to be highly favorable. Interestingly, the favorable contribution from the electrostatic interaction between the peptide and the anionic lipids is overcompensated by an unfavorable contribution from the change in lipid-cation interactions due to the release of counterions from the lipids. The increase in entropy due to the release of the cations is compensated by other entropic components. The largest favorable contribution arises from the solvation of the counterions. Overall the interaction between NK-2 and POPG is not determined by a single driving force but a subtle balance of competing interactions.
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Affiliation(s)
- Carola I E von Deuster
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
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16
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Nguyen LT, de Boer L, Zaat SAJ, Vogel HJ. Investigating the cationic side chains of the antimicrobial peptide tritrpticin: hydrogen bonding properties govern its membrane-disruptive activities. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2297-303. [PMID: 21641334 DOI: 10.1016/j.bbamem.2011.05.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Revised: 05/15/2011] [Accepted: 05/16/2011] [Indexed: 11/27/2022]
Abstract
The positively charged side chains of cationic antimicrobial peptides are generally thought to provide the initial long-range electrostatic attractive forces that guide them towards the negatively charged bacterial membranes. Peptide analogs were designed to examine the role of the four Arg side chains in the cathelicidin peptide tritrpticin (VRRFPWWWPFLRR). The analogs include several noncoded Arg and Lys derivatives that offer small variations in side chain length and methylation state. The peptides were tested for bactericidal and hemolytic activities, and their membrane insertion and permeabilization properties were characterized by leakage assays and fluorescence spectroscopy. A net charge of +5 for most of the analogs maintains their high antimicrobial activity and directs them towards preferential insertion into model bacterial membrane systems with a similar extent of burial of the Trp side chains. However the peptides exhibit significant functional differences. Analogs with methylated cationic side chains cause lower levels of membrane leakage and are associated with lower hemolytic activities, making them potentially attractive pharmaceutical candidates. Analogs containing the Arg guanidinium groups cause more membrane disruption than those containing the Lys amino groups. Peptides in the latter group with shorter side chains have increased membrane activity and conversely, elongating the Arg residue causes slightly higher membrane activity. Altogether, the potential for strong hydrogen bonding between the four positive Arg side chains with the phospholipid head groups seems to be a determinant for the membrane disruptive properties of tritrpticin and many related cationic antimicrobial peptides.
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Affiliation(s)
- Leonard T Nguyen
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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17
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Garcia-Manyes S, Redondo-Morata L, Oncins G, Sanz F. Nanomechanics of Lipid Bilayers: Heads or Tails? J Am Chem Soc 2010; 132:12874-86. [DOI: 10.1021/ja1002185] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sergi Garcia-Manyes
- Department of Biological Sciences, Columbia University, New York, 10027, New York, Departament de Química Física, Universitat de Barcelona, 08028, Spain, Institut de Bioenginyeria de Catalunya, Barcelona, 08028, Spain, Serveis Cientificotècnics, Universitat de Barcelona, 08028, Spain, and CIBER-BBN, Zaragoza 50018, Spain
| | - Lorena Redondo-Morata
- Department of Biological Sciences, Columbia University, New York, 10027, New York, Departament de Química Física, Universitat de Barcelona, 08028, Spain, Institut de Bioenginyeria de Catalunya, Barcelona, 08028, Spain, Serveis Cientificotècnics, Universitat de Barcelona, 08028, Spain, and CIBER-BBN, Zaragoza 50018, Spain
| | - Gerard Oncins
- Department of Biological Sciences, Columbia University, New York, 10027, New York, Departament de Química Física, Universitat de Barcelona, 08028, Spain, Institut de Bioenginyeria de Catalunya, Barcelona, 08028, Spain, Serveis Cientificotècnics, Universitat de Barcelona, 08028, Spain, and CIBER-BBN, Zaragoza 50018, Spain
| | - Fausto Sanz
- Department of Biological Sciences, Columbia University, New York, 10027, New York, Departament de Química Física, Universitat de Barcelona, 08028, Spain, Institut de Bioenginyeria de Catalunya, Barcelona, 08028, Spain, Serveis Cientificotècnics, Universitat de Barcelona, 08028, Spain, and CIBER-BBN, Zaragoza 50018, Spain
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