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Laurencin M, Simon M, Fleury Y, Baudy-Floc'h M, Bondon A, Legrand B. Selectivity Modulation and Structure of α/aza-β3
Cyclic Antimicrobial Peptides. Chemistry 2018; 24:6191-6201. [DOI: 10.1002/chem.201800152] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Indexed: 12/26/2022]
Affiliation(s)
| | - Matthieu Simon
- Institut des Biomolécules Max Mousseron (IBMM); Univ Montpellier, CNRS, UM, ENSCM; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
- Université de Rennes, CNRS; ISCR-UMR 6226; 35000 Rennes France
| | - Yannick Fleury
- Chimie Marines, IUEM; Université de Brest, EA 3884; 6 rue de l'Université 29000 Quimper France
| | | | - Arnaud Bondon
- Université de Rennes, CNRS; ISCR-UMR 6226; 35000 Rennes France
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron (IBMM); Univ Montpellier, CNRS, UM, ENSCM; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
- Université de Rennes, CNRS; ISCR-UMR 6226; 35000 Rennes France
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Rončević T, Vukičević D, Ilić N, Krce L, Gajski G, Tonkić M, Goić-Barišić I, Zoranić L, Sonavane Y, Benincasa M, Juretić D, Maravić A, Tossi A. Antibacterial Activity Affected by the Conformational Flexibility in Glycine–Lysine Based α-Helical Antimicrobial Peptides. J Med Chem 2018; 61:2924-2936. [DOI: 10.1021/acs.jmedchem.7b01831] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tomislav Rončević
- Department of Physics, Faculty of Science, University of Split, 21000 Split, Croatia
| | - Damir Vukičević
- Department of Mathematics, Faculty of Science, University of Split, 21000 Split, Croatia
| | - Nada Ilić
- Department of Physics, Faculty of Science, University of Split, 21000 Split, Croatia
| | - Lucija Krce
- Department of Physics, Faculty of Science, University of Split, 21000 Split, Croatia
| | - Goran Gajski
- Mutagenesis Unit, Institute for Medical Research and Occupational Health, 10000 Zagreb, Croatia
| | - Marija Tonkić
- Department of Clinical Microbiology, University Hospital of Split, 21000 Split, Croatia
- School of Medicine, University of Split, 21000 Split, Croatia
| | - Ivana Goić-Barišić
- Department of Clinical Microbiology, University Hospital of Split, 21000 Split, Croatia
- School of Medicine, University of Split, 21000 Split, Croatia
| | - Larisa Zoranić
- Department of Physics, Faculty of Science, University of Split, 21000 Split, Croatia
| | - Yogesh Sonavane
- Department of Physics, Faculty of Science, University of Split, 21000 Split, Croatia
| | - Monica Benincasa
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Davor Juretić
- Department of Physics, Faculty of Science, University of Split, 21000 Split, Croatia
- Mediterranean Institute for Life Sciences, 21000 Split, Croatia
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
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Mukherjee S, Kar RK, Nanga RPR, Mroue KH, Ramamoorthy A, Bhunia A. Accelerated molecular dynamics simulation analysis of MSI-594 in a lipid bilayer. Phys Chem Chem Phys 2018; 19:19289-19299. [PMID: 28702543 DOI: 10.1039/c7cp01941f] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multidrug resistance against the existing antibiotics is one of the most challenging threats across the globe. Antimicrobial peptides (AMPs), in this regard, are considered to be one of the effective alternatives that can overcome bacterial resistance. MSI-594, a 24-residue linear alpha-helical cationic AMP, has been shown to function via the carpet mechanism to disrupt bacterial membrane systems. To better understand the role of lipid composition in the function of MSI-594, in the present study, eight different model membrane systems have been studied using accelerated molecular dynamics (aMD) simulations. The simulated results are helpful in discriminating the particular effects of cationic MSI-594 against zwitterionic POPC, anionic POPG and POPS, and neutral POPE lipid moieties. Additionally, the effects of various heterogeneous POPC/POPG (7 : 3), POPC/POPS (7 : 3), and POPG/POPE (1 : 3 and 3 : 1) bilayer systems on the dynamic interaction of MSI-594 have also been investigated. The effect on the lipid bilayer due to the interaction with the peptide is characterized by lipid acyl-chain order, membrane thickness, and acyl-chain dynamics. Our simulation results show that the lipid composition affects the membrane interaction of MSI-594, suggesting that membrane selectivity is crucial to its mechanism of action. The results reported in this study are helpful to obtain accurate atomistic-level information governing MSI-594 and its membrane disruptive antimicrobial mechanism of action, and to design next generation potent antimicrobial peptides.
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Affiliation(s)
- Shruti Mukherjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India.
| | - Rajiv K Kar
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India.
| | - Ravi Prakash Reddy Nanga
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA. and Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kamal H Mroue
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India.
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Pore formation and the key factors in antibacterial activity of aurein 1.2 and LLAA inside lipid bilayers, a molecular dynamics study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:347-356. [DOI: 10.1016/j.bbamem.2017.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 11/20/2022]
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Boags A, Hsu PC, Samsudin F, Bond PJ, Khalid S. Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes. J Phys Chem Lett 2017; 8:2513-2518. [PMID: 28467715 DOI: 10.1021/acs.jpclett.7b00473] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacteria are protected by complex molecular architectures known as the cell envelope. The cell envelope is composed of regions with distinct chemical compositions and physical properties, namely, membranes and a cell wall. To develop novel antibiotics to combat pathogenic bacteria, molecular level knowledge of the structure, dynamics, and interplay between the chemical components of the cell envelope that surrounds bacterial cells is imperative. In addition, conserved molecular patterns associated with the bacterial envelope are recognized by receptors as part of the mammalian defensive response to infection, and an improved understanding of bacteria-host interactions would facilitate the search for novel immunotherapeutics. This Perspective introduces an emerging area of computational biology: multiscale molecular dynamics simulations of chemically complex models of bacterial lipids and membranes. We discuss progress to date, and identify areas for future development that will enable the study of aspects of the membrane components that are as yet unexplored by computational methods.
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Affiliation(s)
- Alister Boags
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
| | - Pin-Chia Hsu
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
| | - Firdaus Samsudin
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , Matrix 07-01, 30 Biopolis Street, 138671 Singapore
- Department of Biological Sciences, National University of Singapore , 14 Science Drive 4, 117543 Singapore
| | - Syma Khalid
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
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