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Incorporation of Non-Canonical Amino Acids into Antimicrobial Peptides: Advances, Challenges, and Perspectives. Appl Environ Microbiol 2022; 88:e0161722. [PMID: 36416555 PMCID: PMC9746297 DOI: 10.1128/aem.01617-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The emergence of antimicrobial resistance is a global health concern and calls for the development of novel antibiotic agents. Antimicrobial peptides seem to be promising candidates due to their diverse sources, mechanisms of action, and physicochemical characteristics, as well as the relatively low emergence of resistance. The incorporation of noncanonical amino acids into antimicrobial peptides could effectively improve their physicochemical and pharmacological diversity. Recently, various antimicrobial peptides variants with improved or novel properties have been produced by the incorporation of single and multiple distinct noncanonical amino acids. In this review, we summarize strategies for the incorporation of noncanonical amino acids into antimicrobial peptides, as well as their features and suitabilities. Recent applications of noncanonical amino acid incorporation into antimicrobial peptides are also presented. Finally, we discuss the related challenges and prospects.
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Differentiating interactions of antimicrobials with Gram-negative and Gram-positive bacterial cell walls using molecular dynamics simulations. Biointerphases 2022; 17:061008. [PMID: 36511523 DOI: 10.1116/6.0002087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Developing molecular models to capture the complex physicochemical architecture of the bacterial cell wall and to study the interaction with antibacterial molecules is an important aspect of assessing and developing novel antimicrobial molecules. We carried out molecular dynamics simulations using an atomistic model of peptidoglycan to represent the architecture for Gram-positive S. aureus. The model is developed to capture various structural features of the Staphylococcal cell wall, such as the peptide orientation, area per disaccharide, glycan length distribution, cross-linking, and pore size. A comparison of the cell wall density and electrostatic potentials is made with a previously developed cell wall model of Gram-negative bacteria, E. coli, and properties for both single and multilayered structures of the Staphylococcal cell wall are studied. We investigated the interactions of the antimicrobial peptide melittin with peptidoglycan structures. The depth of melittin binding to peptidoglycan is more pronounced in E. coli than in S. aureus, and consequently, melittin has greater contacts with glycan units of E. coli. Contacts of melittin with the amino acids of peptidoglycan are comparable across both the strains, and the D-Ala residues, which are sites for transpeptidation, show enhanced interactions with melittin. A low energetic barrier is observed for translocation of a naturally occurring antimicrobial thymol with the four-layered peptidoglycan model. The molecular model developed for Gram-positive peptidoglycan allows us to compare and contrast the cell wall penetrating properties with Gram-negative strains and assess for the first time binding and translocation of antimicrobial molecules for Gram-positive cell walls.
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Sharma P, Ayappa KG. A Molecular Dynamics Study of Antimicrobial Peptide Interactions with the Lipopolysaccharides of the Outer Bacterial Membrane. J Membr Biol 2022; 255:665-675. [PMID: 35960325 DOI: 10.1007/s00232-022-00258-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/15/2022] [Indexed: 12/29/2022]
Abstract
With rising bacterial resistance, antimicrobial peptides (AMPs) have been widely investigated as potential antibacterial molecules to replace conventional antibiotics. Our understanding of the molecular mechanisms for membrane disruption are largely based on AMP interactions with the inner phospholipid bilayers of both Gram-negative and Gram-positive bacteria. Mechanisms for AMP translocation across the outer membrane of Gram-negative bacteria composed of lipopolysaccharides and the asymmetric lipid bilayer are complicated by the secondary structure adopted by the peptide in the different membrane environments. We have employed atomistic molecular dynamics and umbrella-sampling simulations with an aggregate duration of [Formula: see text] 6 microseconds to obtain the free energy landscape of CM15 peptide translocating through the lipopolysaccharide region of Gram-negative bacteria, E. coli. The peptide has a favorable binding-free energy (- 130 kJ mol[Formula: see text]) in the O-antigen region with a large barrier (150 kJ mol[Formula: see text]) at the interface between the anionic core saccharides and upper bilayer leaflet made up of lipid-A molecules. Restraint-free molecular dynamics simulations show that the random coil structure is favored over the helix in both the extracellular aqueous region and the cation-rich core-saccharide regions of the outer membrane. The peptide and membrane properties are analyzed at each of the 100 ns duration of the umbrella-sampling windows to illustrate changes in peptide length, orientation, and hydration. Our study provides insights into the free energy landscape for the insertion of the AMP CM15 in the outer membrane of Gram-negative bacteria, and we discuss the implications of our findings with the broader question of how AMPs overcome this barrier during antimicrobial activity.
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Affiliation(s)
- Pradyumn Sharma
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, 560012, India.,Eli Lilly Services India Private Limited, Bengaluru, 560103, India
| | - K Ganapathy Ayappa
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, 560012, India.
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Jepson TA, Hall SC, Chung JK. Single-molecule phospholipase A2 becomes processive on melittin-induced membrane deformations. Biophys J 2022; 121:1417-1423. [PMID: 35314142 PMCID: PMC9072580 DOI: 10.1016/j.bpj.2022.03.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/13/2022] [Accepted: 03/15/2022] [Indexed: 11/30/2022] Open
Abstract
While it is established that the topology of lipid membranes plays an important role in biochemical processes, few direct observations exist regarding how the membranes are actively restructured and its consequences on subsequent reactions. In this work, we investigated how the two major components of bee venom, melittin and phospholipase A2 (PLA2), achieve activation by such membrane remodeling. Their membrane-disrupting functions have been reported to increase when both are present, but the mechanism of this synergism had not been established. Using membrane reconstitution, we found that melittin can form large-scale membrane deformities upon which PLA2 activity is 25-fold higher. Tracking of single-molecule PLA2 revealed that its processive behavior on these deformities underlies the enhanced activity. These results show how melittin and PLA2 work synergistically to enhance the lytic effects of the bee venom. More broadly, they also demonstrate how the membrane topology may be actively altered to modulate cellular membrane-bound reactions.
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Affiliation(s)
| | - Sarah C Hall
- Colorado State University, Fort Collins, Colorado
| | - Jean K Chung
- Colorado State University, Fort Collins, Colorado.
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Lv N, Yin X, Yang Z, Ma T, Qin H, Xiong B, Jiang H, Zhu J. Electrostatically Controlled ex Situ and in Situ Polymerization of Diacetylene-Containing Peptide Amphiphiles in Living Cells. ACS Macro Lett 2022; 11:223-229. [PMID: 35574773 DOI: 10.1021/acsmacrolett.1c00735] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Precise control of diacetylene-containing peptide amphiphile (DPA) based supramolecular architectures is important for their in cellulo polymerization behaviors and biomedical applications. Herein, we reported two DPAs (cationic PA-NH2 and zwitterionic PA-OH) with a similar molecular structure, which exhibited completely opposite polymerization behaviors in aqueous solution and living cells. Specifically, PA-NH2 was unpolymerizable in aqueous solution but underwent in cellulo polymerization to respond to the intracellular microenvironment. On the contrary, zwitterionic PA-OH was polymerized in solution, rather than inside living cells. Based on the results of cell viability and total internal reflection fluorescent microscopy measurement, PA-OH exhibited higher affinity with cell membranes and lower cytotoxicity than those of PA-NH2. Therefore, it is suggested that the in cellulo polymerization of PA-NH2 should be responsive for greater cytotoxicity, rather than the membrane affinity. This study provides an in-depth understanding of the role of charge properties in the polymerization behavior of DPAs and seeks their potential biomedical applications.
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Affiliation(s)
- Niannian Lv
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Xiaoyan Yin
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Zhuoran Yang
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Teng Ma
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Huimin Qin
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Bijin Xiong
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Hao Jiang
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Jintao Zhu
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
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Chen Z, Wei W, Peng H, Jiang H, Xiong B, Zhu J. Revealing the dynamic adsorption and diffusion of peptide amphiphile on supported lipid bilayer by single molecule experiment and simulation. Colloids Surf B Biointerfaces 2021; 204:111809. [PMID: 33965750 DOI: 10.1016/j.colsurfb.2021.111809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/21/2021] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
Dynamic adsorption and diffusion of peptide amphiphiles (PAs) with different numbers of alkyl tails on supported lipid bilayers (SLBs) were investigated by single molecule tracking experiment and molecule dynamic simulation. Experimental results show two distinct populations of PAs with different residence time. Residence time of adsorbed PAs increases with the increase of the alkyl tails, whereas diffusion coefficient monotonically decreases with rising the number of alkyl tails and also decreases with increasing the mobility of SLBs. All-atom molecule dynamic simulation results prove that the adsorption and diffusion of PAs on SLB surface are mainly determined by interactions between PAs and SLBs and also the intrinsic mobility of PAs in aqueous solution. The electrostatic interactions and the mobility of PAs are two dominated but contradictory coefficients for the adsorption and diffusion of PAs. By increasing the alkyl tails, the mobility of PAs decreases while the electrostatic property does not change significantly, resulting in the increase of residence time and decrease of diffusivity of PAs. Additionally, for the PAs with large number of alkyl tails (≥ 3 alkyl tails), steric hindrance of alkyl tails leads to the decrease of adsorption probability of PAs on SLB surface. These findings lay the groundwork for guiding the design of PAs with high cell affinity, potentially useful for efficient drug delivery.
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Affiliation(s)
- Zhenxian Chen
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage (HUST) of Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China
| | - Wei Wei
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage (HUST) of Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China
| | - Haiyan Peng
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage (HUST) of Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China
| | - Hao Jiang
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage (HUST) of Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China.
| | - Bijin Xiong
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage (HUST) of Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China.
| | - Jintao Zhu
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage (HUST) of Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China
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Nelson N, Opene B, Ernst RK, Schwartz DK. Antimicrobial peptide activity is anticorrelated with lipid a leaflet affinity. PLoS One 2020; 15:e0242907. [PMID: 33253275 PMCID: PMC7703904 DOI: 10.1371/journal.pone.0242907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/12/2020] [Indexed: 11/18/2022] Open
Abstract
The activity of antimicrobial peptides (AMPs) has significant bacterial species bias, the mechanisms of which are not fully understood. We employed single-molecule tracking to measure the affinity of three different AMPs to hybrid supported bilayers composed of lipid A extracted from four different Gram negative bacteria and observed a strong empirical anticorrelation between the affinity of a particular AMP to a given lipid A layer and the activity of that AMP towards the bacterium from which that lipid A was extracted. This suggested that the species bias of AMP activity is directly related to AMP interactions with bacterial outer membranes, despite the fact that the mechanism of antimicrobial activity occurs at the inner membrane. The trend also suggested that the interactions between AMPs and the outer membrane lipid A (even in the absence of other components, such as lipopolysaccharides) capture effects that are relevant to the minimum inhibitory concentration.
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Affiliation(s)
- Nathaniel Nelson
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Belita Opene
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, Baltimore, Maryland, United States of America
| | - Robert K. Ernst
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, Baltimore, Maryland, United States of America
| | - Daniel K. Schwartz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, United States of America
- * E-mail:
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Yin X, Chen Z, Chen Y, Xie Y, Xiong B, Jiang H, Zhu J. Lipidated gemini peptide amphiphiles with enhanced loading capacity and cell membrane affinity for drug delivery. Colloids Surf B Biointerfaces 2020; 195:111271. [DOI: 10.1016/j.colsurfb.2020.111271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 12/17/2022]
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Deshpande D, Grieshober M, Wondany F, Gerbl F, Noschka R, Michaelis J, Stenger S. Super-Resolution Microscopy Reveals a Direct Interaction of Intracellular Mycobacterium tuberculosis with the Antimicrobial Peptide LL-37. Int J Mol Sci 2020; 21:ijms21186741. [PMID: 32937921 PMCID: PMC7555347 DOI: 10.3390/ijms21186741] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/31/2020] [Accepted: 09/10/2020] [Indexed: 12/26/2022] Open
Abstract
The antimicrobial peptide LL-37 inhibits the growth of the major human pathogen Mycobacterium tuberculosis (Mtb), but the mechanism of the peptide–pathogen interaction inside human macrophages remains unclear. Super-resolution imaging techniques provide a novel opportunity to visualize these interactions on a molecular level. Here, we adapt the super-resolution technique of stimulated emission depletion (STED) microscopy to study the uptake, intracellular localization and interaction of LL-37 with macrophages and virulent Mtb. We demonstrate that LL-37 is internalized by both uninfected and Mtb infected primary human macrophages. The peptide localizes in the membrane of early endosomes and lysosomes, the compartment in which mycobacteria reside. Functionally, LL-37 disrupts the cell wall of intra- and extracellular Mtb, resulting in the killing of the pathogen. In conclusion, we introduce STED microscopy as an innovative and informative tool for studying host–pathogen–peptide interactions, clearly extending the possibilities of conventional confocal microscopy.
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Affiliation(s)
- Dhruva Deshpande
- Institute of Biophysics, Ulm University, 89081 Ulm, Germany; (D.D.); (F.W.)
| | - Mark Grieshober
- Institute of Medical Microbiology and Hygiene, University Hospital Ulm, 89081 Ulm, Germany; (M.G.); (F.G.); (R.N.)
| | - Fanny Wondany
- Institute of Biophysics, Ulm University, 89081 Ulm, Germany; (D.D.); (F.W.)
| | - Fabian Gerbl
- Institute of Medical Microbiology and Hygiene, University Hospital Ulm, 89081 Ulm, Germany; (M.G.); (F.G.); (R.N.)
| | - Reiner Noschka
- Institute of Medical Microbiology and Hygiene, University Hospital Ulm, 89081 Ulm, Germany; (M.G.); (F.G.); (R.N.)
| | - Jens Michaelis
- Institute of Biophysics, Ulm University, 89081 Ulm, Germany; (D.D.); (F.W.)
- Correspondence: (J.M.); (S.S.)
| | - Steffen Stenger
- Institute of Medical Microbiology and Hygiene, University Hospital Ulm, 89081 Ulm, Germany; (M.G.); (F.G.); (R.N.)
- Correspondence: (J.M.); (S.S.)
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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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