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Sreelakshmi KP, Madhuri M, Swetha R, Rangarajan V, Roy U. Microbial lipopeptides: their pharmaceutical and biotechnological potential, applications, and way forward. World J Microbiol Biotechnol 2024; 40:135. [PMID: 38489053 DOI: 10.1007/s11274-024-03908-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/24/2024] [Indexed: 03/17/2024]
Abstract
As lead molecules, cyclic lipopeptides with antibacterial, antifungal, and antiviral properties have garnered a lot of attention in recent years. Because of their potential, cyclic lipopeptides have earned recognition as a significant class of antimicrobial compounds with applications in pharmacology and biotechnology. These lipopeptides, often with biosurfactant properties, are amphiphilic, consisting of a hydrophilic moiety, like a carboxyl group, peptide backbone, or carbohydrates, and a hydrophobic moiety, mostly a fatty acid. Besides, several lipopeptides also have cationic groups that play an important role in biological activities. Antimicrobial lipopeptides can be considered as possible substitutes for antibiotics that are conventional to address the current drug-resistant issues as pharmaceutical industries modify the parent antibiotic molecules to render them more effective against antibiotic-resistant bacteria and fungi, leading to the development of more resistant microbial strains. Bacillus species produce lipopeptides, which are secondary metabolites that are amphiphilic and are typically synthesized by non-ribosomal peptide synthetases (NRPSs). They have been identified as potential biocontrol agents as they exhibit a broad spectrum of antimicrobial activity. A further benefit of lipopeptides is that they can be produced and purified biotechnologically or biochemically in a sustainable manner using readily available, affordable, renewable sources without harming the environment. In this review, we discuss the biochemical and functional characterization of antifungal lipopeptides, as well as their various modes of action, method of production and purification (in brief), and potential applications as novel antibiotic agents.
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Affiliation(s)
- K P Sreelakshmi
- Department of Biological Sciences, Birla Institute of Technology and Science-KK Birla Goa Campus Goa, NH 17 B Bypass Rd., Goa, 403726, India
| | - M Madhuri
- Department of Biological Sciences, Birla Institute of Technology and Science-KK Birla Goa Campus Goa, NH 17 B Bypass Rd., Goa, 403726, India
| | - R Swetha
- Department of Biological Sciences, Birla Institute of Technology and Science-KK Birla Goa Campus Goa, NH 17 B Bypass Rd., Goa, 403726, India
| | - Vivek Rangarajan
- Department of Chemical Engineering, Birla Institute of Technology and Science-KK Birla Goa Campus Goa, NH 17 B Bypass Rd., Goa, 403726, India
| | - Utpal Roy
- Department of Biological Sciences, Birla Institute of Technology and Science-KK Birla Goa Campus Goa, NH 17 B Bypass Rd., Goa, 403726, India.
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Golonka I, Pucułek JE, Greber KE, Dryś A, Sawicki W, Musiał W. Evaluation of the Effect of Antibacterial Peptides on Model Monolayers. Int J Mol Sci 2023; 24:14861. [PMID: 37834308 PMCID: PMC10573695 DOI: 10.3390/ijms241914861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/19/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
The aim of the study was to assess the effect of the synthesized antibacterial peptides: P2 (WKWK)2-KWKWK-NH2, P4 (C12)2-KKKK-NH2, P5 (KWK)2-KWWW-NH2, and P6 (KK)2-KWWW-NH2 on the physicochemical properties of a model biological membrane made of azolectin or lecithin. The Langmuir Wilhelmy method was used for the experiments. Based on the compressibility factor, it was determined that the monolayers formed of azolectin and peptides in the aqueous subphase are in the condensed liquid phase. At the boundary between the condensed and expanded liquid phases, there was a monolayer made of lecithin and P4, P5 or P6 in the aqueous subphase. In turn, the film consisting of lecithin alone (37.7 mN/m) and lecithin and P2 (42.6 mN/m) in the water subphase was in the expanded liquid phase. All peptides change, to varying degrees, the organization and packing of molecules in the monolayer, both those made of azolectin and of lecithin. The test results can be used for further research to design a system with the expected properties for specific organisms.
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Affiliation(s)
- Iwona Golonka
- Department of Physical Chemistry and Biophysics, Wroclaw Medical University, Borowska 211A, 50–556 Wrocław, Poland; (I.G.); (J.E.P.); (A.D.)
| | - Jakub E. Pucułek
- Department of Physical Chemistry and Biophysics, Wroclaw Medical University, Borowska 211A, 50–556 Wrocław, Poland; (I.G.); (J.E.P.); (A.D.)
| | - Katarzyna E. Greber
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (K.E.G.); (W.S.)
| | - Andrzej Dryś
- Department of Physical Chemistry and Biophysics, Wroclaw Medical University, Borowska 211A, 50–556 Wrocław, Poland; (I.G.); (J.E.P.); (A.D.)
| | - Wiesław Sawicki
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (K.E.G.); (W.S.)
| | - Witold Musiał
- Department of Physical Chemistry and Biophysics, Wroclaw Medical University, Borowska 211A, 50–556 Wrocław, Poland; (I.G.); (J.E.P.); (A.D.)
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Melcrová A, Maity S, Melcr J, de Kok NAW, Gabler M, van der Eyden J, Stensen W, Svendsen JSM, Driessen AJM, Marrink SJ, Roos WH. Lateral membrane organization as target of an antimicrobial peptidomimetic compound. Nat Commun 2023; 14:4038. [PMID: 37419980 PMCID: PMC10328936 DOI: 10.1038/s41467-023-39726-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 06/20/2023] [Indexed: 07/09/2023] Open
Abstract
Antimicrobial resistance is one of the leading concerns in medical care. Here we study the mechanism of action of an antimicrobial cationic tripeptide, AMC-109, by combining high speed-atomic force microscopy, molecular dynamics, fluorescence assays, and lipidomic analysis. We show that AMC-109 activity on negatively charged membranes derived from Staphylococcus aureus consists of two crucial steps. First, AMC-109 self-assembles into stable aggregates consisting of a hydrophobic core and a cationic surface, with specificity for negatively charged membranes. Second, upon incorporation into the membrane, individual peptides insert into the outer monolayer, affecting lateral membrane organization and dissolving membrane nanodomains, without forming pores. We propose that membrane domain dissolution triggered by AMC-109 may affect crucial functions such as protein sorting and cell wall synthesis. Our results indicate that the AMC-109 mode of action resembles that of the disinfectant benzalkonium chloride (BAK), but with enhanced selectivity for bacterial membranes.
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Affiliation(s)
- Adéla Melcrová
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Sourav Maity
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Josef Melcr
- Molecular Dynamics, Groningen Biomolecular Sciences & Biotechnology Institute, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Niels A W de Kok
- Molecular Microbiology, Groningen Biomolecular Sciences & Biotechnology Institute, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Mariella Gabler
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Jonne van der Eyden
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Wenche Stensen
- Department of Chemistry, UiT Arctic University of Norway, Tromsø, Norway
| | - John S M Svendsen
- Department of Chemistry, UiT Arctic University of Norway, Tromsø, Norway
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences & Biotechnology Institute, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Siewert J Marrink
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
- Molecular Dynamics, Groningen Biomolecular Sciences & Biotechnology Institute, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Wouter H Roos
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands.
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Puelles JS, Ghorbani M, Tuck B, Machuca LL, Ackland ML, Chen F, Somers AE, Forsyth M. Effect of cetrimonium carrier micelles on bacterial membranes and extracellular DNA, an in silico study. Sci Rep 2023; 13:8041. [PMID: 37198168 DOI: 10.1038/s41598-023-32475-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/28/2023] [Indexed: 05/19/2023] Open
Abstract
Microorganisms do not live as dispersed single cells but rather they form aggregates with extracellular polymeric substances at interfaces. Biofilms are considered efficient life forms because they shield bacteria from biocides and collect dilute nutrients. This is a big concern in industry since the microorganisms can colonize a wide range of surfaces, accelerating material deterioration, colonizing medical devices, contaminating ultrapure drinking water, increasing energy costs and creating focus of infection. Conventional biocides that target a specific component of the bacteria are not effective in the presence of biofilms. Efficient biofilm inhibitors are based on a multitarget approach interacting with the bacteria and the biofilm matrix. Their rationale design requires a thorough understanding of inhibitory mechanisms that are still largely lacking today. Herein we uncover via molecular modelling the inhibition mechanism of cetrimonium 4-OH cinnamate (CTA-4OHcinn). Simulations show that CTA-4OH micelles can disrupt symmetric and asymmetric bilayers, representative of inner and outer bacterial membranes, following three stages: adsorption, assimilation, and defect formation. The main driving force for micellar attack is electrostatic interactions. In addition to disrupting the bilayers, the micelles work as carriers facilitating the trapping of 4OH cinnamate anions within the bilayer upper leaflet and overcoming electrostatic repulsion. The micelles also interact with extracellular DNA (e-DNA), which is one of the main components of biofilms. It is observed that CTA-4OHcinn forms spherical micelles on the DNA backbone; which hinders their ability to pack. This is demonstrated by modelling the DNA along the hbb histone-like protein, showing that in the presence of CTA-4OHcinn, DNA does not pack properly around hbb. The abilities of CTA-4OHcinn to cause cell death through membrane disruption and to disperse a mature, multi-species biofilm are also confirmed experimentally.
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Affiliation(s)
| | - Mahdi Ghorbani
- Institute for Frontier Materials, Deakin University, Geelong, VIC, 3217, Australia
| | - Benjamin Tuck
- Curtin Corrosion Centre, WA School of Mines: Minerals, Energy and Chemical Engineering, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - Laura L Machuca
- Curtin Corrosion Centre, WA School of Mines: Minerals, Energy and Chemical Engineering, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - M Leigh Ackland
- ARC Centre of Excellence for Electromaterials Science (ACES), Deakin University, Burwood, 3125, Australia
- School of Life and Environmental Sciences, Deakin University, Burwood, Victoria, 3125, Australia
| | - Fangfang Chen
- Institute for Frontier Materials, Deakin University, Geelong, VIC, 3217, Australia.
- ARC Centre of Excellence for Electromaterials Science (ACES), Deakin University, Burwood, 3125, Australia.
| | - Anthony E Somers
- Institute for Frontier Materials, Deakin University, Geelong, VIC, 3217, Australia.
| | - Maria Forsyth
- Institute for Frontier Materials, Deakin University, Geelong, VIC, 3217, Australia.
- ARC Centre of Excellence for Electromaterials Science (ACES), Deakin University, Burwood, 3125, Australia.
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Effects of Cholesterol on the mechanism of fengycin, a biofungicide. Biophys J 2022; 121:1963-1974. [DOI: 10.1016/j.bpj.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/15/2021] [Accepted: 04/05/2022] [Indexed: 11/21/2022] Open
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Jiang X, Yang K, Yuan B, Han M, Zhu Y, Roberts KD, Patil NA, Li J, Gong B, Hancock REW, Velkov T, Schreiber F, Wang L, Li J. Molecular dynamics simulations informed by membrane lipidomics reveal the structure-interaction relationship of polymyxins with the lipid A-based outer membrane of Acinetobacter baumannii. J Antimicrob Chemother 2021; 75:3534-3543. [PMID: 32911540 DOI: 10.1093/jac/dkaa376] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 08/04/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND MDR bacteria represent an urgent threat to human health globally. Polymyxins are a last-line therapy against life-threatening Gram-negative 'superbugs', including Acinetobacter baumannii. Polymyxins exert antimicrobial activity primarily via permeabilizing the bacterial outer membrane (OM); however, the mechanism of interaction between polymyxins and the OM remains unclear at the atomic level. METHODS We constructed a lipid A-based OM model of A. baumannii using quantitative membrane lipidomics data and employed all-atom molecular dynamics simulations with umbrella sampling techniques to elucidate the structure-interaction relationship and thermodynamics governing the penetration of polymyxins [B1 and E1 (i.e. colistin A) representing the two clinically used polymyxins] into the OM. RESULTS Polymyxin B1 and colistin A bound to the A. baumannii OM by the initial electrostatic interactions between the Dab residues of polymyxins and the phosphates of lipid A, competitively displacing the cations from the headgroup region of the OM. Both polymyxin B1 and colistin A formed a unique folded conformation upon approaching the hydrophobic centre of the OM, consistent with previous experimental observations. Polymyxin penetration induced reorientation of the headgroups of the OM lipids near the penetration site and caused local membrane disorganization, thereby significantly increasing membrane permeability and promoting the subsequent penetration of polymyxin molecules into the OM and periplasmic space. CONCLUSIONS The thermodynamics governing the penetration of polymyxins through the outer leaflet of the A. baumannii OM were examined and novel structure-interaction relationship information was obtained at the atomic and membrane level. Our findings will facilitate the discovery of novel polymyxins against MDR Gram-negative pathogens.
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Affiliation(s)
- Xukai Jiang
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Kai Yang
- Centre for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Bing Yuan
- Centre for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Meiling Han
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Yan Zhu
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Kade D Roberts
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Nitin A Patil
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Jingliang Li
- Institute for Frontier Materials, Deakin University, Geelong, Victoria, Australia
| | - Bin Gong
- School of Computer Science and Technology, Shandong University, Jinan, China
| | - Robert E W Hancock
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, University of Melbourne, Melbourne, Australia
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian Li
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
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Wei C, Pohorille A. Fast bilayer-micelle fusion mediated by hydrophobic dipeptides. Biophys J 2021; 120:2330-2342. [PMID: 33887225 DOI: 10.1016/j.bpj.2021.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/15/2021] [Accepted: 04/02/2021] [Indexed: 11/30/2022] Open
Abstract
To understand the transition from inanimate matter to life, we studied a process that directly couples simple metabolism to evolution via natural selection, demonstrated experimentally by Adamala and Szostak. In this process, dipeptides synthesized inside precursors of cells promote absorption of fatty acid micelles to vesicles, inducing their preferential growth and division at the expense of other vesicles. The process is explained on the basis of coarse-grained molecular dynamics simulations, each extending for tens of microseconds, carried out to model fusion between a micelle and a membrane, both made of fatty acids in the absence and presence of hydrophobic dipeptides. In all systems with dipeptides, but not in their absence, fusion events were observed. They involve the formation of a stalk made by hydrophobic chains from the micelle and the membrane, similar to that postulated for vesicle-vesicle fusion. The emergence of a stalk is facilitated by transient clusters of dipeptides, side chains of which form hydrophobic patches at the membrane surface. Committor probability calculations indicate that the size of a patch is a suitable reaction coordinate and allows for identifying the transition state for fusion. Free-energy barrier to fusion is greatly reduced in the presence of dipeptides to only 4-5 kcal/mol, depending on the hydrophobicity of side chains. The mechanism of mediated fusion, which is expected to apply to other small peptides and hydrophobic molecules, provides a robust means by which a nascent metabolism can confer evolutionary advantage to precursors of cells.
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Affiliation(s)
- Chenyu Wei
- NASA Ames Research Center, Moffett Field, California; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Andrew Pohorille
- NASA Ames Research Center, Moffett Field, California; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California.
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Neubauer D, Jaśkiewicz M, Bauer M, Olejniczak-Kęder A, Sikorska E, Sikora K, Kamysz W. Biological and Physico-Chemical Characteristics of Arginine-Rich Peptide Gemini Surfactants with Lysine and Cystine Spacers. Int J Mol Sci 2021; 22:3299. [PMID: 33804887 PMCID: PMC8036666 DOI: 10.3390/ijms22073299] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 12/11/2022] Open
Abstract
Ultrashort cationic lipopeptides (USCLs) and gemini cationic surfactants are classes of potent antimicrobials. Our recent study has shown that the branching and shortening of the fatty acids chains with the simultaneous addition of a hydrophobic N-terminal amino acid in USCLs result in compounds with enhanced selectivity. Here, this approach was introduced into arginine-rich gemini cationic surfactants. l-cystine diamide and l-lysine amide linkers were used as spacers. Antimicrobial activity against planktonic and biofilm cultures of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) strains and Candida sp. as well as hemolytic and cytotoxic activities were examined. Moreover, antimicrobial activity in the presence of human serum and the ability to form micelles were evaluated. Membrane permeabilization study, serum stability assay, and molecular dynamics were performed. Generally, critical aggregation concentration was linearly correlated with hydrophobicity. Gemini surfactants were more active than the parent USCLs, and they turned out to be selective antimicrobial agents with relatively low hemolytic and cytotoxic activities. Geminis with the l-cystine diamide spacer seem to be less cytotoxic than their l-lysine amide counterparts, but they exhibited lower antibiofilm and antimicrobial activities in serum. In some cases, geminis with branched fatty acid chains and N-terminal hydrophobic amino acid resides exhibited enhanced selectivity to pathogens over human cells.
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Affiliation(s)
- Damian Neubauer
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (M.B.); (K.S.); (W.K.)
| | - Maciej Jaśkiewicz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (M.B.); (K.S.); (W.K.)
| | - Marta Bauer
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (M.B.); (K.S.); (W.K.)
| | - Agata Olejniczak-Kęder
- Department of Histology, Faculty of Medicine, Medical University of Gdańsk, 80-211 Gdańsk, Poland;
| | - Emilia Sikorska
- Department of Organic Chemistry, Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland;
| | - Karol Sikora
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (M.B.); (K.S.); (W.K.)
| | - Wojciech Kamysz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (M.B.); (K.S.); (W.K.)
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Siwy CM, Delfing BM, Lockhart C, Smith AK, Klimov DK. Partitioning of Aβ Peptide Fragments into Blood-Brain Barrier Mimetic Bilayer. J Phys Chem B 2021; 125:2658-2676. [PMID: 33656350 DOI: 10.1021/acs.jpcb.0c11253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We used all-atom replica-exchange umbrella sampling molecular dynamics simulations to investigate the partitioning of the charged tetrapeptide KLVF and its neutral apolar counterpart VVIA into the blood-brain barrier (BBB)-mimetic bilayer. Our findings allowed us to reconstruct the partitioning mechanism for these two Aβ peptide fragments. Despite dissimilar sequences, their permeation shares significant common features. Computations of free energies and permeabilities show that partitioning of both peptides is highly unfavorable, ruling out passive transport. The peptides experience multiple rotational transitions within the bilayer and typically cause considerable lipid disorder and bilayer thinning. Near the bilayer midplane, they lose almost entirely their solvation shell and the interactions with the lipid headgroups. The peptides cause complex reorganization within the proximal bilayer region. Upon insertion, they induce striking cholesterol influx reversed by its depletion and the influx of DMPC when the peptides reach the midplane. The differences in partitioning mechanisms are due to the much higher polarity of KLVF peptide, the permeation of which is more unfavorable and which exclusively assumes vertical orientations within the bilayer. In contrast, VVIA positions itself flat between the leaflets, causing minor disorder and even thickening of the BBB-mimetic bilayer. Due to the high density of the cholesterol-rich BBB bilayer, the unfavorable work associated with the peptide insertion provides a significant, but not dominant, contribution to the partition free energy, which is still governed by dehydration and loss of peptide-headgroup interactions. Comparison with experiments indicates that KLVF and VVIA permeation is similar to that of proline tetrapeptide, mannitol, or cimetidine, all of which exhibit no passive transport.
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Affiliation(s)
- Christopher M Siwy
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Bryan M Delfing
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Christopher Lockhart
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Amy K Smith
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Dmitri K Klimov
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
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In Silico Prediction of the Binding, Folding, Insertion, and Overall Stability of Membrane-Active Peptides. Methods Mol Biol 2021; 2315:161-182. [PMID: 34302676 DOI: 10.1007/978-1-0716-1468-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Membrane-active peptides (MAPs) are short-length peptides used for potential biomedical applications in diagnostic imaging of tissues, targeted drug delivery, gene delivery, and antimicrobials and antibiotics. The broad appeal of MAPs is that they are infinitely variable, relatively low cost, and biocompatible. However, experimentally characterizing the specific properties of a MAP or its many variants is a low-resolution and potentially time-consuming endeavor; molecular dynamics (MD) simulations have emerged as an invaluable tool in identifying the biophysical interactions that are fundamental to the function of MAPs. In this chapter, a step-by-step approach to discreetly model the binding, folding, and insertion of a membrane-active peptide to a model lipid bilayer using MD simulations is described. Detailed discussion is devoted to the critical aspects of running these types of simulations: prior knowledge of the system, understanding the strengths and weaknesses of molecular mechanics force fields, proper construction and equilibration of the system, realistically estimating both experimental and computational timescales, and leveraging analysis to make direct comparisons to experimental results as often as possible.
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Małuch I, Stachurski O, Kosikowska-Adamus P, Makowska M, Bauer M, Wyrzykowski D, Hać A, Kamysz W, Deptuła M, Pikuła M, Sikorska E. Double-Headed Cationic Lipopeptides: An Emerging Class of Antimicrobials. Int J Mol Sci 2020; 21:ijms21238944. [PMID: 33255674 PMCID: PMC7728077 DOI: 10.3390/ijms21238944] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial peptides (AMPs) constitute a promising tool in the development of novel therapeutic agents useful in a wide range of bacterial and fungal infections. Among the modifications improving pharmacokinetic and pharmacodynamic characteristics of natural AMPs, an important role is played by lipidation. This study focuses on the newly designed and synthesized lipopeptides containing multiple Lys residues or their shorter homologues with palmitic acid (C16) attached to the side chain of a residue located in the center of the peptide sequence. The approach resulted in the development of lipopeptides representing a model of surfactants with two polar headgroups. The aim of this study is to explain how variations in the length of the peptide chain or the hydrocarbon side chain of an amino acid residue modified with C16, affect biological functions of lipopeptides, their self-assembling propensity, and their mode of action.
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Affiliation(s)
- Izabela Małuch
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.M.); (O.S.); (P.K.-A.); (M.M.); (D.W.)
| | - Oktawian Stachurski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.M.); (O.S.); (P.K.-A.); (M.M.); (D.W.)
| | - Paulina Kosikowska-Adamus
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.M.); (O.S.); (P.K.-A.); (M.M.); (D.W.)
| | - Marta Makowska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.M.); (O.S.); (P.K.-A.); (M.M.); (D.W.)
| | - Marta Bauer
- Faculty of Pharmacy, Medicinal University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland; (M.B.); (W.K.)
| | - Dariusz Wyrzykowski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.M.); (O.S.); (P.K.-A.); (M.M.); (D.W.)
| | - Aleksandra Hać
- Faculty of Biology, University of Gdansk, Str. 59, 80-308 Gdansk, Poland;
| | - Wojciech Kamysz
- Faculty of Pharmacy, Medicinal University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland; (M.B.); (W.K.)
| | - Milena Deptuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Dębinki 1, 80-211 Gdańsk, Poland; (M.D.); (M.P.)
| | - Michał Pikuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Dębinki 1, 80-211 Gdańsk, Poland; (M.D.); (M.P.)
| | - Emilia Sikorska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.M.); (O.S.); (P.K.-A.); (M.M.); (D.W.)
- Correspondence:
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12
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Rogers JR, Geissler PL. Breakage of Hydrophobic Contacts Limits the Rate of Passive Lipid Exchange between Membranes. J Phys Chem B 2020; 124:5884-5898. [DOI: 10.1021/acs.jpcb.0c04139] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Julia R. Rogers
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Phillip L. Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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13
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Centi A, Dutta A, Parekh SH, Bereau T. Inserting Small Molecules across Membrane Mixtures: Insight from the Potential of Mean Force. Biophys J 2020; 118:1321-1332. [PMID: 32075746 DOI: 10.1016/j.bpj.2020.01.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/05/2020] [Accepted: 01/27/2020] [Indexed: 11/29/2022] Open
Abstract
Small solutes have been shown to alter the lateral organization of cell membranes and reconstituted phospholipid bilayers; however, the mechanisms by which these changes happen are still largely unknown. Traditionally, both experiment and simulation studies have been restricted to testing only a few compounds at a time, failing to identify general molecular descriptors or chemical properties that would allow extrapolating beyond the subset of considered solutes. In this work, we probe the competing energetics of inserting a solute in different membrane environments by means of the potential of mean force. We show that these calculations can be used as a computationally efficient proxy to establish whether a solute will stabilize or destabilize domain phase separation. Combined with umbrella-sampling simulations and coarse-grained molecular dynamics simulations, we are able to screen solutes across a wide range of chemistries and polarities. Our results indicate that for the system under consideration, preferential partitioning and therefore effectiveness in altering membrane phase separation are strictly linked to the location of insertion in the bilayer (i.e., midplane or interface). Our approach represents a fast and simple tool for obtaining structural and thermodynamic insight into the partitioning of small molecules between lipid domains and its relation to phase separation, ultimately providing a platform for identifying the key determinants of this process.
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Affiliation(s)
- Alessia Centi
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Arghya Dutta
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Sapun H Parekh
- Max Planck Institute for Polymer Research, Mainz, Germany; Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany.
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14
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Vaezi Z, Bortolotti A, Luca V, Perilli G, Mangoni ML, Khosravi-Far R, Bobone S, Stella L. Aggregation determines the selectivity of membrane-active anticancer and antimicrobial peptides: The case of killerFLIP. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183107. [PMID: 31678022 DOI: 10.1016/j.bbamem.2019.183107] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 07/19/2019] [Accepted: 09/19/2019] [Indexed: 01/02/2023]
Abstract
Host defense peptides selectively kill bacterial and cancer cells (including those that are drug-resistant) by perturbing the permeability of their membranes, without being significantly toxic to the host. Coulombic interactions between these cationic and amphipathic peptides and the negatively charged membranes of pathogenic cells contribute to the selective toxicity. However, a positive charge is not sufficient for selectivity, which can be achieved only by a finely tuned balance of electrostatic and hydrophobic driving forces. A common property of amphipathic peptides is the formation of aggregated structures in solution, but the role of this phenomenon in peptide activity and selectivity has received limited attention. Our data on the anticancer peptide killerFLIP demonstrate that aggregation strongly increases peptide selectivity, by reducing the effective peptide hydrophobicity and thus the affinity towards membranes composed of neutral lipids (like the outer layer of healthy eukaryotic cell membranes). Aggregation is therefore a useful tool to modulate the selectivity of membrane active peptides and peptidomimetics.
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Affiliation(s)
- Zahra Vaezi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Annalisa Bortolotti
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Vincenzo Luca
- Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Giulia Perilli
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Maria Luisa Mangoni
- Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Roya Khosravi-Far
- BiomaRx Inc, Cambridge, MA, USA; Department of Pathology, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Sara Bobone
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133 Rome, Italy.
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133 Rome, Italy.
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15
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Stachurski O, Neubauer D, Małuch I, Wyrzykowski D, Bauer M, Bartoszewska S, Kamysz W, Sikorska E. Effect of self-assembly on antimicrobial activity of double-chain short cationic lipopeptides. Bioorg Med Chem 2019; 27:115129. [PMID: 31668583 DOI: 10.1016/j.bmc.2019.115129] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/10/2019] [Accepted: 09/18/2019] [Indexed: 01/03/2023]
Abstract
Short cationic antimicrobial lipopeptides with surfactant-like structure are promising antibiotic candidates that preferentially target microbial membranes. Therefore, we focused our study on double-chain lipopeptides, (C10-16)2Dab-KKK-NH2 and (C10-16)2Dap-KKK-NH2, where Dab and Dap are 2,4-diaminobutyric and 2,3-diaminopropionic acids, respectively. We tried to answer a question how the self-assembly behaviour affects biological activities of the tested compounds. The subject compounds were synthesized by solid-phase method and screened for their antimicrobial and haemolytic activities. Cytotoxicity tests on human keratinocytes were carried out for the most promising lipopeptides. Self-assembly properties were evaluated by both experimental and theoretical methods. Interactions with membrane models were examined using the ITC and FTIR techniques. All the lipopeptides studied showed the tendency to self-assembly in solution, and this behaviour was affected by the length of the hydrocarbon chains. Acyl chain elongation supported the formation of the bilayer structure and deprived the lipopeptides of antimicrobial activity. A multi-step mechanism of interaction with a negatively charged membrane was observed for the short-chain lipopeptides, indicating other processes accompanying the binding process. Short-chain lipopeptides were able to penetrate into the liposome's interior and/or cause the rupture of the liposome, this being compatible with their high antimicrobial activity.
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Affiliation(s)
- Oktawian Stachurski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Damian Neubauer
- Faculty of Pharmacy, Medical University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
| | - Izabela Małuch
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Dariusz Wyrzykowski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Marta Bauer
- Faculty of Pharmacy, Medical University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
| | - Sylwia Bartoszewska
- Faculty of Pharmacy, Medical University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
| | - Wojciech Kamysz
- Faculty of Pharmacy, Medical University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
| | - Emilia Sikorska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
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16
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Abstract
The rise of antibiotic resistant bacteria requires unconventional strategies toward efficient chemotherapeutic agents, preferably with alternative mechanisms of action. The bacterial cell membrane has become an appealing target since its essential and highly conservative structure are key challenges to resistance mechanisms. Inspired by natural antimicrobial peptides, research on membrane-targeting antimicrobials has been growing out of the peptide space. The pursuit of more druggable molecules led to the discovery that the pharmacophore of antimicrobial peptides is smaller than anticipated. Several promising classes of membrane-targeting antimicrobials have been discovered, such as ceragenins, reutericyclines, carbohydrate amphiphiles - among others. This review will discuss the most recent findings on membrane-targeting antibiotics, focusing on small molecules outside the antimicrobial peptide molecular space.
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17
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Selectivity of Antimicrobial Peptides: A Complex Interplay of Multiple Equilibria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1117:175-214. [DOI: 10.1007/978-981-13-3588-4_11] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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18
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Smith LG, Tan Z, Spasic A, Dutta D, Salas-Estrada LA, Grossfield A, Mathews DH. Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations. J Chem Theory Comput 2018; 14:6598-6612. [PMID: 30375860 DOI: 10.1021/acs.jctc.8b00633] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
To benchmark RNA force fields, we compared the folding stabilities of three 12-nucleotide hairpin stem loops estimated by simulation to stabilities determined by experiment. We used umbrella sampling and a reaction coordinate of end-to-end (5' to 3' hydroxyl oxygen) distance to estimate the free energy change of the transition from the native conformation to a fully extended conformation with no hydrogen bonds between non-neighboring bases. Each simulation was performed four times using the AMBER FF99+bsc0+χOL3 force field, and each window, spaced at 1 Å intervals, was sampled for 1 μs, for a total of 552 μs of simulation. We compared differences in the simulated free energy changes to analogous differences in free energies from optical melting experiments using thermodynamic cycles where the free energy change between stretched and random coil sequences is assumed to be sequence-independent. The differences between experimental and simulated ΔΔ G° are, on average, 0.98 ± 0.66 kcal/mol, which is chemically accurate and suggests that analogous simulations could be used predictively. We also report a novel method to identify where replica free energies diverge along a reaction coordinate, thus indicating where additional sampling would most improve convergence. We conclude by discussing methods to more economically perform these simulations.
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Affiliation(s)
- Louis G Smith
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States.,Center for RNA Biology , University of Rochester , Rochester , New York 14642 , United States
| | - Zhen Tan
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States.,Center for RNA Biology , University of Rochester , Rochester , New York 14642 , United States
| | - Aleksandar Spasic
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States.,Center for RNA Biology , University of Rochester , Rochester , New York 14642 , United States
| | - Debapratim Dutta
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States.,Center for RNA Biology , University of Rochester , Rochester , New York 14642 , United States
| | - Leslie A Salas-Estrada
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States
| | - Alan Grossfield
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States
| | - David H Mathews
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States.,Department of Biostatistics and Computational Biology , University of Rochester , Rochester , New York 14642 , United States.,Center for RNA Biology , University of Rochester , Rochester , New York 14642 , United States
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19
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Pokhrel N, Maibaum L. Free Energy Calculations of Membrane Permeation: Challenges Due to Strong Headgroup-Solute Interactions. J Chem Theory Comput 2018; 14:1762-1771. [PMID: 29406707 DOI: 10.1021/acs.jctc.7b01159] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased molecular dynamics computer simulations to calculate and compare the free energy profiles of translocation of several small molecules across 1,2-dioleoyl- sn-glycero-3-phosphocholine (DOPC) lipid bilayers as a first step toward determining the most efficient method for free energy calculations. We study the translocation of arginine, a sodium ion, alanine, and a single water molecule using the metadynamics, umbrella sampling, and replica exchange umbrella sampling techniques. Within the fixed lengths of our simulations, we find that all methods produce similar results for charge-neutral permeants, but not for polar or positively charged molecules. We identify the long relaxation time scale of electrostatic interactions between lipid headgroups and the solute to be the principal cause of this difference and show that this slow process can lead to an erroneous dependence of computed free energy profiles on the initial system configuration. We demonstrate the use of committor analysis to validate the proper sampling of the presumed transition state, which in our simulations is achieved only in replica exchange calculations. On the basis of these results we provide some useful guidance to perform and evaluate free energy calculations of membrane permeation.
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Affiliation(s)
- Nihit Pokhrel
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Lutz Maibaum
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
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20
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Sur S, Romo TD, Grossfield A. Selectivity and Mechanism of Fengycin, an Antimicrobial Lipopeptide, from Molecular Dynamics. J Phys Chem B 2018; 122:2219-2226. [PMID: 29376372 DOI: 10.1021/acs.jpcb.7b11889] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fengycin is a cyclic lipopeptide used as an agricultural fungicide. It is synthesized by Bacillus subtilis as an immune response against fungal infection and functions by damaging the target's cell membrane. Previous molecular dynamics simulations and experiments have led to the hypothesis that the aggregation of fengycins on the membrane surface plays a key role in cell disruption. Here, we used microsecond-scale all-atom molecular dynamics simulations to understand the specificity, selectivity, and structure of fengycin oligomers. Our simulations suggest that fengycin is more likely to form stable oligomers in model fungal membranes (phosphatidylcholine) compared to the model bacterial membranes (phosphatidylethanolamine:phosphatidylglycerol). Furthermore, we characterize the differences in the structure and kinetics of the membrane-bound aggregates and discuss their functional implications.
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Affiliation(s)
- Sreyoshi Sur
- Department of Chemistry, University of Rochester , 404 Hutchison Hall, Box 270216, Rochester, New York 14627, United States
| | - Tod D Romo
- Center for Integrated Research Computing, University of Rochester , 601 Elmwood Avenue, Box 712, Rochester, New York 14642, United States
| | - Alan Grossfield
- Department of Biochemistry and Biophysics, University of Rochester Medical Center , Rochester, 601 Elmwood Avenue, Box 712, New York 14642, United States
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21
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Bonhenry D, Dehez F, Tarek M. Effects of hydration on the protonation state of a lysine analog crossing a phospholipid bilayer – insights from molecular dynamics and free-energy calculations. Phys Chem Chem Phys 2018; 20:9101-9107. [DOI: 10.1039/c8cp00312b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Protonation states of amino acids crossing lipid bilayers from multidimensional free energy surfaces.
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Affiliation(s)
| | | | - Mounir Tarek
- Université de Lorraine
- CNRS
- LPCT
- F-54000 Nancy
- France
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22
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Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations. Biophys J 2017. [PMID: 28636916 DOI: 10.1016/j.bpj.2017.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Microsecond molecular dynamics simulations of harzianin HK VI (HZ) interacting with a dimyristoylphosphatidylcholine bilayer were performed at the condition of low peptide-to-lipid ratio. Two orientations of HZ molecule in the bilayer were found and characterized. In the orientation perpendicular to the bilayer surface, HZ induces a local thinning of the bilayer. When inserted into the bilayer parallel to its surface, HZ is located nearly completely within the hydrophobic region of the bilayer. A combination of solid-state NMR and circular dichroism experiments found the latter orientation to be dominant. An extended sampling simulation provided qualitative results and showed the same orientation to be a global minimum of free energy. The secondary structure of HZ was characterized, and it was found to be located in the 310-helical family. The specific challenges of computer simulation of nonpolar peptides are discussed briefly.
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23
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Pumilacidin-Like Lipopeptides Derived from Marine Bacterium Bacillus sp. Strain 176 Suppress the Motility of Vibrio alginolyticus. Appl Environ Microbiol 2017; 83:AEM.00450-17. [PMID: 28389538 DOI: 10.1128/aem.00450-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/03/2017] [Indexed: 01/03/2023] Open
Abstract
Bacterial motility is a crucial factor during the invasion and colonization processes of pathogens, which makes it an attractive therapeutic drug target. Here, we isolated a marine bacterium (Vibrio alginolyticus strain 178) from a seamount in the tropical West Pacific that exhibits vigorous motility on agar plates and severe pathogenicity to zebrafish. We found that V. alginolyticus 178 motility was significantly suppressed by another marine bacterium, Bacillus sp. strain 176, isolated from the same niche. We isolated, purified, and characterized two different cyclic lipopeptides (CLPs) from Bacillus sp. 176 using high-performance liquid chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy. The two related CLPs have a pumilacidin-like structure and were both effective inhibitors of V. alginolyticus 178 motility. The CLPs differ by only one methylene group in their fatty acid chains. In addition to motility suppression, the CLPs also induced cell aggregation in the medium and reduced adherence of V. alginolyticus 178 to glass substrates. Notably, upon CLP treatment, the expression levels of two V. alginolyticus flagellar assembly genes (flgA and flgP) dropped dramatically. Moreover, the CLPs inhibited biofilm formation in several other strains of pathogenic bacteria without inducing cell death. This study indicates that CLPs from Bacillus sp. 176 show promise as antimicrobial lead compounds targeting bacterial motility and biofilm formation with a low potential for eliciting antibiotic resistance.IMPORTANCE Pathogenic bacteria often require motility to establish infections and subsequently spread within host organisms. Thus, motility is an attractive therapeutic target for the development of novel antibiotics. We found that cyclic lipopeptides (CLPs) produced by marine bacterium Bacillus sp. strain 176 dramatically suppress the motility of the pathogenic bacterium Vibrio alginolyticus strain 178, reduce biofilm formation, and promote cellular aggregation without inducing cell death. These findings suggest that CLPs hold great promise as potential drug candidates targeting bacterial motility and biofilm formation with a low overall potential for triggering antibiotic resistance.
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24
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Van Oosten B, Marquardt D, Harroun TA. Testing High Concentrations of Membrane Active Antibiotic Chlorhexidine Via Computational Titration and Calorimetry. J Phys Chem B 2017; 121:4657-4668. [DOI: 10.1021/acs.jpcb.6b12510] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brad Van Oosten
- Department
of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Drew Marquardt
- Institute
of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Thad A. Harroun
- Department
of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada
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25
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Parikh N, Klimov DK. Inclusion of lipopeptides into the DMPC lipid bilayers prevents Aβ peptide insertion. Phys Chem Chem Phys 2017; 19:10087-10098. [DOI: 10.1039/c7cp01003f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lipopeptides prevent penetration of Alzheimer's Aβ peptides into lipid bilayers.
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Affiliation(s)
- Niyati Parikh
- School of Systems Biology
- George Mason University
- Manassas
- USA
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26
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Schikora A, Schenk ST, Hartmann A. Beneficial effects of bacteria-plant communication based on quorum sensing molecules of the N-acyl homoserine lactone group. PLANT MOLECULAR BIOLOGY 2016; 90:605-12. [PMID: 26898296 DOI: 10.1007/s11103-016-0457-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 02/18/2016] [Indexed: 05/08/2023]
Abstract
Bacterial quorum sensing (QS) mechanisms play a crucial role in the proper performance and ecological fitness of bacterial populations. Many key physiological processes are regulated in a QS-dependent manner by auto-inducers, like the N-acyl homoserine lactones (AHLs) in numerous Gram-negative bacteria. In addition, also the interaction between bacteria and eukaryotic hosts can be regulated by AHLs. Those mechanisms gained much attention, because of the positive effects of different AHL molecules on plants. This positive impact ranges from growth promotion to induced resistance and is quite contrasting to the rather negative effects observed in the interactions between bacterial AHL molecules and animals. Only very recently, we began to understand the molecular mechanisms underpinning plant responses to AHL molecules. In this review, we gathered the latest information in this research field. The first part gives an overview of the bacterial aspects of quorum sensing. Later we focus on the impact of AHLs on plant growth and AHL-priming, as one of the most understood phenomena in respect to the inter-kingdom interactions based on AHL-quorum sensing molecules. Finally, we discuss the potential benefits of the understanding of bacteria-plant interaction for the future agricultural applications.
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Affiliation(s)
- Adam Schikora
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Brunswick, Germany.
| | - Sebastian T Schenk
- Institute of Plant Sciences - Paris-Saclay, INRA/CNRS, 630 rue de Noetzlin, Plateau du Moulon, 91405, Orsay, France
| | - Anton Hartmann
- Research Unit Microbe-Plant Interactions, Department for Environmental Sciences, German Research Center for Environmental Health (GmbH), Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
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27
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Neale C, Pomès R. Sampling errors in free energy simulations of small molecules in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2539-2548. [PMID: 26952019 DOI: 10.1016/j.bbamem.2016.03.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 12/14/2022]
Abstract
Free energy simulations are a powerful tool for evaluating the interactions of molecular solutes with lipid bilayers as mimetics of cellular membranes. However, these simulations are frequently hindered by systematic sampling errors. This review highlights recent progress in computing free energy profiles for inserting molecular solutes into lipid bilayers. Particular emphasis is placed on a systematic analysis of the free energy profiles, identifying the sources of sampling errors that reduce computational efficiency, and highlighting methodological advances that may alleviate sampling deficiencies. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Chris Neale
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, 110 8th St, Troy, New York 12180-3590, USA
| | - Régis Pomès
- Molecular Structure and Function, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada; Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.
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28
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Bereau T. Better Together: Lipopeptide Micelle Formation Enhances Antimicrobial Selectivity. Biophys J 2015; 109:668-9. [PMID: 26287619 DOI: 10.1016/j.bpj.2015.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 07/10/2015] [Accepted: 07/10/2015] [Indexed: 10/23/2022] Open
Affiliation(s)
- Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany.
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