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Javed A, Oedairadjsingh T, Ludwig IS, Wood TM, Martin NI, Broere F, Weingarth MH, Veldhuizen EJA. Antimicrobial and immunomodulatory activities of porcine cathelicidin Protegrin-1. Mol Immunol 2024; 173:100-109. [PMID: 39094445 DOI: 10.1016/j.molimm.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/11/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Antimicrobial peptides (AMPs) are a promising alternative to antibiotics in the fight against multi-drug resistant and immune system-evading bacterial infections. Protegrins are porcine cathelicidins which have been identified in porcine leukocytes. Protegrin-1 is the best characterized family member and has broad antibacterial activity by interacting and permeabilizing bacterial membranes. Many host defense peptides (HDPs) like LL-37 or chicken cathelicidin 2 (CATH-2) have also been shown to have protective biological functions during infections. In this regard, it is interesting to study if Protegrin-1 has the immune modulating potential to suppress unnecessary immune activation by neutralizing endotoxins or by influencing the macrophage functionality in addition to its direct antimicrobial properties. This study showed that Protegrin-1 neutralized lipopolysaccharide- (LPS) and bacteria-induced activation of RAW macrophages by binding and preventing LPS from cell surface attachment. Furthermore, the peptide treatment not only inhibited bacterial phagocytosis by murine and porcine macrophages but also interfered with cell surface and intracellular bacterial survival. Lastly, Protegrin-1 pre-treatment was shown to inhibit the amastigote survival in Leishmania infected macrophages. These experiments describe an extended potential of Protegrin-1's protective role during microbial infections and add to the research towards clinical application of cationic AMPs.
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Affiliation(s)
- Ali Javed
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Immunology, Utrecht University, the Netherlands; NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, the Netherlands
| | - Trishana Oedairadjsingh
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Immunology, Utrecht University, the Netherlands
| | - Irene S Ludwig
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Immunology, Utrecht University, the Netherlands
| | - Thomas M Wood
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, the Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, the Netherlands
| | - Femke Broere
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Immunology, Utrecht University, the Netherlands
| | - Markus H Weingarth
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, the Netherlands
| | - Edwin J A Veldhuizen
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Immunology, Utrecht University, the Netherlands.
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2
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Tang Y, Zhang Y, Zhang D, Liu Y, Nussinov R, Zheng J. Exploring pathological link between antimicrobial and amyloid peptides. Chem Soc Rev 2024; 53:8713-8763. [PMID: 39041297 DOI: 10.1039/d3cs00878a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Amyloid peptides (AMYs) and antimicrobial peptides (AMPs) are considered as the two distinct families of peptides, characterized by their unique sequences, structures, biological functions, and specific pathological targets. However, accumulating evidence has revealed intriguing pathological connections between these peptide families in the context of microbial infection and neurodegenerative diseases. Some AMYs and AMPs share certain structural and functional characteristics, including the ability to self-assemble, the presence of β-sheet-rich structures, and membrane-disrupting mechanisms. These shared features enable AMYs to possess antimicrobial activity and AMPs to acquire amyloidogenic properties. Despite limited studies on AMYs-AMPs systems, the cross-seeding phenomenon between AMYs and AMPs has emerged as a crucial factor in the bidirectional communication between the pathogenesis of neurodegenerative diseases and host defense against microbial infections. In this review, we examine recent developments in the potential interplay between AMYs and AMPs, as well as their pathological implications for both infectious and neurodegenerative diseases. By discussing the current progress and challenges in this emerging field, this account aims to inspire further research and investments to enhance our understanding of the intricate molecular crosstalk between AMYs and AMPs. This knowledge holds great promise for the development of innovative therapies to combat both microbial infections and neurodegenerative disorders.
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio 44325, USA.
| | - Yanxian Zhang
- Division of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Dong Zhang
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
- Department of Human Molecular Genetics and Biochemistry Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio 44325, USA.
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3
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Zhang X, Malle MG, Thomsen RP, Sørensen RS, Sørensen EW, Hatzakis NS, Kjems J. Deconvoluting the Effect of Cell-Penetrating Peptides for Enhanced and Controlled Insertion of Large-Scale DNA Nanopores. ACS APPLIED MATERIALS & INTERFACES 2024; 16:18422-18433. [PMID: 38573069 DOI: 10.1021/acsami.3c18636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
DNA nanopores have emerged as powerful tools for molecular sensing, but the efficient insertion of large DNA nanopores into lipid membranes remains challenging. In this study, we investigate the potential of cell-penetrating peptides (CPPs), specifically SynB1 and GALA, to enhance the insertion efficiency of large DNA nanopores. We constructed SynB1- or GALA-functionalized DNA nanopores with an 11 nm inner diameter and visualized and quantified their membrane insertion using a TIRF microscopy-based single-liposome assay. The results demonstrated that incorporating an increasing number of SynB1 or GALA peptides into the DNA nanopore significantly enhanced the membrane perforation. Kinetic analysis revealed that the DNA nanopore scaffold played a role in prearranging the CPPs, which facilitated membrane interaction and pore formation. Notably, the use of pH-responsive GALA peptides allowed highly efficient and pH-controlled insertion of large DNA pores. Furthermore, single-channel recording elucidated that the insertion process of single GALA-modified nanopores into planar lipid bilayers was dynamic, likely forming transient large toroidal pores. Overall, our study highlights the potential of CPPs as insertion enhancers for DNA nanopores, which opens avenues for improved molecule sensing and the controlled release of cargo molecules.
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Affiliation(s)
- Xialin Zhang
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | - Rasmus P Thomsen
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | | | - Nikos S Hatzakis
- Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark
- Novonordisk Center for Protein Research, University of Copenhagen, Copenhagen 2100, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
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4
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Tang Z, Feng J, Challa M, Rowthu SR, Xiong S, Zou C, Li J, Verma CS, Peng H, He X, Huang C, He Y. Discovery of novel Thymol-TPP antibiotics that eradicate MRSA persisters. Eur J Med Chem 2024; 270:116381. [PMID: 38604097 DOI: 10.1016/j.ejmech.2024.116381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/13/2024]
Abstract
The high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) strains and the formation of non-growing, dormant "persisters" subsets help bacteria evade antibiotic treatment and enhance bacterial resistance, which poses a serious threat to human life and health. It is urgent to discover novel antibacterial therapies effective against MRSA persisters. Thymol is a common nutraceutical with weak antibacterial and antitumor activities. A series of Thymol triphenylphosphine (TPP) conjugates (TPP-Thy3) was designed and synthesized. These compounds showed significantly improved inhibitory activity against Gram-positive bacteria compared with Thymol. Among them, Thy3d displayed a low probability of resistance selection and showed excellent biocompatibility. Interestingly, Thy3d elicited a rapid killing effect of MRSA persisters (99.999%) at high concentration. Fluorescence experiments, electron microscopy, molecular dynamics simulation and bilayer experiment confirmed that Thy3d conjugates exerted potent antimicrobial activity by disrupting the integrity of the membrane of bacterial even the persister. Furthermore, Thy3d exhibited considerable efficacy in a mouse model of subcutaneous murine MRSA infection. In summary, TPP-Thy3 conjugates are a series of novel antibacterial agents and could serve as a new therapeutic strategy for combating antibiotic resistance.
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Affiliation(s)
- Ziyi Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Jizhou Feng
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Mahesh Challa
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Sankara Rao Rowthu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Shuxin Xiong
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Cheng Zou
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Jianguo Li
- Singapore Eye Research Institute, Singapore, 169856, Singapore; Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix, 138671, Singapore
| | - Chandra Shekhar Verma
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix, 138671, Singapore; Department of Biological Sciences, National University of Singapore, 117543, Singapore; School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Haibo Peng
- Chongqing Academy of Science and Technology, Chongqing, 401123, China
| | - Xiaoli He
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Chao Huang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China.
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China; BayRay Innovation Center, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
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5
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Numaguchi Y, Tsukakoshi K, Takeuchi N, Suzuki Y, Ikebukuro K, Kawano R. Real-time monitoring of the amyloid β 1-42 monomer-to-oligomer channel transition using a lipid bilayer system. PNAS NEXUS 2024; 3:pgad437. [PMID: 38156289 PMCID: PMC10753159 DOI: 10.1093/pnasnexus/pgad437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/06/2023] [Indexed: 12/30/2023]
Abstract
This study describes the observation of the transformation of monomeric amyloid β1-42 (Aβ42) into oligomers in a lipid membrane utilizing a lipid bilayer system for electrophysiological measurement. The relevance of oligomers and protofibrils in Alzheimer's disease (AD) is underscored given their significant neurotoxicity. By closely monitoring the shift of Aβ42 from its monomeric state to forming oligomeric channels in phospholipid membranes, we noted that this transformation transpired within a 2-h frame. We manipulated the lipid membrane's constitution with components such as glycerophospholipid, porcine brain total lipid extract, sphingomyelin (SM), and cholesterol (Chol.) to effectively imitate nerve cell membranes. Interesting findings showcased Chol.'s ability to foster stable oligomeric channel formation in the lipid membrane, with SM and GM1 lipids potentially enhancing channel formation as well. Additionally, the study identified the potential of a catechin derivative, epigallocatechin gallate (EGCG), in obstructing oligomerization. With EGCG present in the outer solution of the Aβ42-infused membrane, a noteworthy reduction in channel current was observed, suggesting the successful inhibition of oligomerization. This conclusion held true in both, prior and subsequent, stages of oligomerization. Our findings shed light on the toxicity of oligomers, promising invaluable information for future advancements in AD treatment strategies.
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Affiliation(s)
- Yuri Numaguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-0011, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-0011, Japan
| | - Nanami Takeuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-0011, Japan
| | - Yuki Suzuki
- Department of Chemistry for Materials, Graduate School of Engineering, Mie University, Mie 514-0102, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-0011, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-0011, Japan
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6
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Tang Z, Jiang W, Li S, Huang X, Yang Y, Chen X, Qiu J, Xiao C, Xie Y, Zhang X, Li J, Verma CS, He Y, Yang A. Design and evaluation of tadpole-like conformational antimicrobial peptides. Commun Biol 2023; 6:1177. [PMID: 37980400 PMCID: PMC10657444 DOI: 10.1038/s42003-023-05560-0] [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: 07/03/2023] [Accepted: 11/08/2023] [Indexed: 11/20/2023] Open
Abstract
Antimicrobial peptides are promising alternatives to conventional antibiotics. Herein, we report a class of "tadpole-like" peptides consisting of an amphipathic α-helical head and an aromatic tail. A structure-activity relationship (SAR) study of "tadpole-like" temporin-SHf and its analogs revealed that increasing the number of aromatic residues in the tail, introducing Arg to the α-helical head and rearranging the peptide topology dramatically increased antimicrobial activity. Through progressive structural optimization, we obtained two peptides, HT2 and RI-HT2, which exhibited potent antimicrobial activity, no hemolytic activity and cytotoxicity, and no propensity to induce resistance. NMR and molecular dynamics simulations revealed that both peptides indeed adopted "tadpole-like" conformations. Fluorescence experiments and electron microscopy confirmed the membrane targeting mechanisms of the peptides. Our studies not only lead to the discovery of a series of ultrashort peptides with potent broad-spectrum antimicrobial activities, but also provide a new strategy for rational design of novel "tadpole-like" antimicrobial peptides.
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Affiliation(s)
- Ziyi Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Wuqiao Jiang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Shuangli Li
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xue Huang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Yi Yang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Xiaorong Chen
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Jingyi Qiu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Chuyu Xiao
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Ying Xie
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Xu Zhang
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jianguo Li
- Bioinformatics Institute, A∗STAR, 30 Biopolis Street, Matrix, Singapore, 138671, Singapore
- Singapore Eye Research Institute, Singapore, 169856, Singapore
| | - Chandra Shekhar Verma
- Bioinformatics Institute, A∗STAR, 30 Biopolis Street, Matrix, Singapore, 138671, Singapore
- Department of Biological Sciences, National University of, Singapore, 117543, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Yun He
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China.
- BayRay Innovation Center, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.
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7
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Somberg NH, Medeiros‐Silva J, Jo H, Wang J, DeGrado WF, Hong M. Hexamethylene amiloride binds the SARS-CoV-2 envelope protein at the protein-lipid interface. Protein Sci 2023; 32:e4755. [PMID: 37632140 PMCID: PMC10503410 DOI: 10.1002/pro.4755] [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: 07/17/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023]
Abstract
The SARS-CoV-2 envelope (E) protein forms a five-helix bundle in lipid bilayers whose cation-conducting activity is associated with the inflammatory response and respiratory distress symptoms of COVID-19. E channel activity is inhibited by the drug 5-(N,N-hexamethylene) amiloride (HMA). However, the binding site of HMA in E has not been determined. Here we use solid-state NMR to measure distances between HMA and the E transmembrane domain (ETM) in lipid bilayers. 13 C, 15 N-labeled HMA is combined with fluorinated or 13 C-labeled ETM. Conversely, fluorinated HMA is combined with 13 C, 15 N-labeled ETM. These orthogonal isotopic labeling patterns allow us to conduct dipolar recoupling NMR experiments to determine the HMA binding stoichiometry to ETM as well as HMA-protein distances. We find that HMA binds ETM with a stoichiometry of one drug per pentamer. Unexpectedly, the bound HMA is not centrally located within the channel pore, but lies on the lipid-facing surface in the middle of the TM domain. This result suggests that HMA may inhibit the E channel activity by interfering with the gating function of an aromatic network. These distance data are obtained under much lower drug concentrations than in previous chemical shift perturbation data, which showed the largest perturbation for N-terminal residues. This difference suggests that HMA has higher affinity for the protein-lipid interface than the channel pore. These results give insight into the inhibition mechanism of HMA for SARS-CoV-2 E.
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Affiliation(s)
- Noah H. Somberg
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - João Medeiros‐Silva
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Hyunil Jo
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgersthe State University of New JerseyPiscatawayNew JerseyUSA
| | - William F. DeGrado
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Mei Hong
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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8
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He C, Li S, Jiang B, Chen F, Hu W, Deng F. Surface Hydrophobicity and Guest Permeability in Polydimethylsiloxane-Coated MIL-53 as Studied by Solid-State Nuclear Magnetic Resonance Spectroscopy. ACS APPLIED MATERIALS & INTERFACES 2023; 15:37936-37945. [PMID: 37503940 DOI: 10.1021/acsami.3c07142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Experimental characterization of the hydrophobic porous materials at the atomic and molecular levels is of great significance, but exploring their hydrophobicity characteristics and interactions with guest molecules with distinct polarity is still challenging. In this work, solid-state NMR is employed to characterize the surface hydrophobicity and explore the guest solvent permeability in polydimethylsiloxane (PDMS)-coated MIL-53. It was found that the PDMS-coated MIL-53 was hydrophobic to water and infiltrated to methanol, acetone, benzene, toluene, and ethylbenzene solvents. In addition, two types of guest solvents (methanol, acetone, benzene, toluene, and ethylbenzene), inside the pore and outside the pore of PDMS-coated MIL-53, were clearly identified using two-dimensional 1H-1H homo-nuclear correlation NMR experiments. Moreover, the membrane thickness of the PDMS-coated MIL-53 could be determined from the analysis of the 1H-1H spin diffusion buildup curves. Furthermore, the permeability of benzene, toluene, and ethylbenzene at different PDMS coating levels was extracted from 1H MAS NMR. The increase of the hydrophobic PDMS layer resulted in a decrease of the penetration of aromatic guests to the internal pore of MIL-53. This work provides deep insights into the understanding of guest solvent permeability of hydrophobic layer-coated MOFs in the application fields of catalysis and separation.
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Affiliation(s)
- Caiyan He
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shenhui Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Jiang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
- Optics Valley Laboratory, Wuhan 430074, China
| | - Fang Chen
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Hu
- Songshan Lake Materials Laboratory, Dongguan 523808, China
| | - Feng Deng
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Bolosov IA, Panteleev PV, Sychev SV, Khokhlova VA, Safronova VN, Toropygin IY, Kombarova TI, Korobova OV, Pereskokova ES, Borzilov AI, Ovchinnikova TV, Balandin SV. Design of Protegrin-1 Analogs with Improved Antibacterial Selectivity. Pharmaceutics 2023; 15:2047. [PMID: 37631261 PMCID: PMC10458893 DOI: 10.3390/pharmaceutics15082047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Protegrin-1 (PG-1) is a cationic β-hairpin pore-forming antimicrobial peptide having a membranolytic mechanism of action. It possesses in vitro a potent antimicrobial activity against a panel of clinically relevant MDR ESKAPE pathogens. However, its extremely high hemolytic activity and cytotoxicity toward mammalian cells prevent the further development of the protegrin-based antibiotic for systemic administration. In this study, we rationally modulated the PG-1 charge and hydrophobicity by substituting selected residues in the central β-sheet region of PG-1 to design its analogs, which retain a high antimicrobial activity but have a reduced toxicity toward mammalian cells. In this work, eight PG-1 analogs with single amino acid substitutions and five analogs with double substitutions were obtained. These analogs were produced as thioredoxin fusions in Escherichia coli. It was shown that a significant reduction in hemolytic activity without any loss of antimicrobial activity could be achieved by a single amino acid substitution, V16R in the C-terminal β-strand, which is responsible for the PG-1 oligomerization. As the result, a selective analog with a ≥30-fold improved therapeutic index was obtained. FTIR spectroscopy analysis of analog, [V16R], revealed that the peptide is unable to form oligomeric structures in a membrane-mimicking environment, in contrast to wild-type PG-1. Analog [V16R] showed a reasonable efficacy in septicemia infection mice model as a systemic antibiotic and could be considered as a promising lead for further drug design.
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Affiliation(s)
- Ilia A. Bolosov
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
| | - Pavel V. Panteleev
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
| | - Sergei V. Sychev
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
| | - Veronika A. Khokhlova
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
| | - Victoria N. Safronova
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
| | - Ilia Yu. Toropygin
- V. N. Orekhovich Research Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Tatiana I. Kombarova
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Olga V. Korobova
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Eugenia S. Pereskokova
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Alexander I. Borzilov
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Tatiana V. Ovchinnikova
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
- Department of Biotechnology, I. M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Sergey V. Balandin
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
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10
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Almeida PF. In Search of a Molecular View of Peptide-Lipid Interactions in Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023. [PMID: 37478368 DOI: 10.1021/acs.langmuir.3c00538] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Lipid bilayer membranes are often represented as a continuous nonpolar slab with a certain thickness bounded by two more polar interfaces. Phenomena such as peptide binding to the membrane surface, folding, insertion, translocation, and diffusion are typically interpreted on the basis of this view. In this Perspective, I argue that this membrane representation as a hydrophobic continuum solvent is not adequate to understand peptide-lipid interactions. Lipids are not small compared to membrane-active peptides: their sizes are similar. Therefore, peptide diffusion needs to be understood in terms of free volume, not classical continuum mechanics; peptide solubility or partitioning in membranes cannot be interpreted in terms of hydrophobic mismatch between membrane thickness and peptide length; peptide folding and translocation, often involving cationic peptides, can only be understood if realizing that lipids adapt to the presence of peptides and the membrane may undergo considerable lipid redistribution in the process. In all of those instances, the detailed molecular interactions between the peptide residues and the lipid components are essential to understand the mechanisms involved.
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Affiliation(s)
- Paulo F Almeida
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
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11
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Ondevilla JC, Hanashima S, Mukogawa A, Miyazato DG, Umegawa Y, Murata M. Effect of the number of sugar units on the interaction between diosgenyl saponin and membrane lipids. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184145. [PMID: 36914020 DOI: 10.1016/j.bbamem.2023.184145] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 03/15/2023]
Abstract
Saponin is the main bioactive component of the Dioscorea species, which are traditionally used for treating chronic diseases. An understanding of the interaction process of bioactive saponins with biomembranes provides insights into their development as therapeutic agents. The biological effects of saponins have been thought to be associated with membrane cholesterol (Chol). To shed light on the exact mechanisms of their interactions, we investigated the effects of diosgenyl saponins trillin (TRL) and dioscin (DSN) on the dynamic behavior of lipids and membrane properties in palmitoyloleolylphosphatidylcholine (POPC) bilayers using solid-state NMR and fluorescence spectroscopy. The membrane effects of diosgenin, a sapogenin of TRL and DSN, are similar to those of Chol, suggesting that diosgenin plays a major role in membrane binding and POPC chain ordering. The amphiphilicity of TRL and DSN enabled them to interact with POPC bilayers, regardless of Chol. In the presence of Chol, the sugar residues more prominently influenced the membrane-disrupting effects of saponins. The activity of DSN, which bears three sugar units, led to perturbation and further disruption of the membrane in the presence of Chol. However, TRL, which bears one sugar residue, increased the ordering of POPC chains while maintaining the integrity of the bilayer. This effect on the phospholipid bilayers is similar to that of cholesteryl glucoside. The influence of the number of sugars in saponin is discussed in more detail.
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Affiliation(s)
- Joan Candice Ondevilla
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, De La Salle University, 2401 Taft Avenue, Manila 0922, Philippines
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8552, Japan.
| | - Akane Mukogawa
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Darcy Garza Miyazato
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan; Forefront Research Centre for Fundamental Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan; Forefront Research Centre for Fundamental Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
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12
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Lin P, Yan Y, Huang SY. DeepHomo2.0: improved protein-protein contact prediction of homodimers by transformer-enhanced deep learning. Brief Bioinform 2023; 24:6849483. [PMID: 36440949 DOI: 10.1093/bib/bbac499] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/08/2022] [Accepted: 10/21/2022] [Indexed: 11/30/2022] Open
Abstract
Protein-protein interactions play an important role in many biological processes. However, although structure prediction for monomer proteins has achieved great progress with the advent of advanced deep learning algorithms like AlphaFold, the structure prediction for protein-protein complexes remains an open question. Taking advantage of the Transformer model of ESM-MSA, we have developed a deep learning-based model, named DeepHomo2.0, to predict protein-protein interactions of homodimeric complexes by leveraging the direct-coupling analysis (DCA) and Transformer features of sequences and the structure features of monomers. DeepHomo2.0 was extensively evaluated on diverse test sets and compared with eight state-of-the-art methods including protein language model-based, DCA-based and machine learning-based methods. It was shown that DeepHomo2.0 achieved a high precision of >70% with experimental monomer structures and >60% with predicted monomer structures for the top 10 predicted contacts on the test sets and outperformed the other eight methods. Moreover, even the version without using structure information, named DeepHomoSeq, still achieved a good precision of >55% for the top 10 predicted contacts. Integrating the predicted contacts into protein docking significantly improved the structure prediction of realistic Critical Assessment of Protein Structure Prediction homodimeric complexes. DeepHomo2.0 and DeepHomoSeq are available at http://huanglab.phys.hust.edu.cn/DeepHomo2/.
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Affiliation(s)
- Peicong Lin
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Yumeng Yan
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
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13
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Matching amino acids membrane preference profile to improve activity of antimicrobial peptides. Commun Biol 2022; 5:1199. [PMID: 36347951 PMCID: PMC9643456 DOI: 10.1038/s42003-022-04164-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
Antimicrobial peptides (AMPs) are cationic antibiotics that can kill multidrug-resistant bacteria via membrane insertion. However, their weak activity limits their clinical use. Ironically, the cationic charge of AMPs is essential for membrane binding, but it obstructs membrane insertion. In this study, we postulate that this problem can be overcome by locating cationic amino acids at the energetically preferred membrane surface. All amino acids have an energetically preferred or less preferred membrane position profile, and this profile is strongly related to membrane insertion. However, most AMPs do not follow this profile. One exception is protegrin-1, a powerful but neglected AMP. In the present study, we found that a potent AMP, WCopW5, strongly resembles protegrin-1 and that the match between its sequence and the preferred position profile closely correlates with its antimicrobial activity. One of its derivatives, WCopW43, has antimicrobial activity comparable to that of the most effective AMPs in clinical use.
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14
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Construction strategies and the development trend of antibacterial surfaces. Biointerphases 2022; 17:050801. [DOI: 10.1116/6.0002147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The construction of antibacterial surfaces is an efficient way to respond to the problem of microbial contamination. In this review, we first describe the formation process and characteristics of microbial contamination and the current research status of antibacterial surfaces. Then, the passive antiadhesion, active killing, and combination construction strategies of the antibacterial surface are discussed in detail. Based on different antibacterial mechanisms and existing problems of current antibacterial strategies, we then discuss the future development trends of the next generation of antibacterial surfaces.
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Membranolytic Mechanism of Amphiphilic Antimicrobial β-Stranded [KL]n Peptides. Biomedicines 2022; 10:biomedicines10092071. [PMID: 36140173 PMCID: PMC9495826 DOI: 10.3390/biomedicines10092071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
Amphipathic peptides can act as antibiotics due to membrane permeabilization. KL peptides with the repetitive sequence [Lys-Leu]n-NH2 form amphipathic β-strands in the presence of lipid bilayers. As they are known to kill bacteria in a peculiar length-dependent manner, we suggest here several different functional models, all of which seem plausible, including a carpet mechanism, a β-barrel pore, a toroidal wormhole, and a β-helix. To resolve their genuine mechanism, the activity of KL peptides with lengths from 6–26 amino acids (plus some inverted LK analogues) was systematically tested against bacteria and erythrocytes. Vesicle leakage assays served to correlate bilayer thickness and peptide length and to examine the role of membrane curvature and putative pore diameter. KL peptides with 10–12 amino acids showed the best therapeutic potential, i.e., high antimicrobial activity and low hemolytic side effects. Mechanistically, this particular window of an optimum β-strand length around 4 nm (11 amino acids × 3.7 Å) would match the typical thickness of a lipid bilayer, implying the formation of a transmembrane pore. Solid-state 15N- and 19F-NMR structure analysis, however, showed that the KL backbone lies flat on the membrane surface under all conditions. We can thus refute any of the pore models and conclude that the KL peptides rather disrupt membranes by a carpet mechanism. The intriguing length-dependent optimum in activity can be fully explained by two counteracting effects, i.e., membrane binding versus amyloid formation. Very short KL peptides are inactive, because they are unable to bind to the lipid bilayer as flexible β-strands, whereas very long peptides are inactive due to vigorous pre-aggregation into β-sheets in solution.
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16
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Moreno-Morales J, Guardiola S, Ballesté-Delpierre C, Giralt E, Vila J. A new synthetic protegrin as a promising peptide with antibacterial activity against MDR Gram-negative pathogens. J Antimicrob Chemother 2022; 77:3077-3085. [PMID: 35972429 DOI: 10.1093/jac/dkac284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/30/2022] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Protegrins are a family of natural peptides from the innate immune system of vertebrates, with broad-spectrum antimicrobial activity. However, the toxicity and haemolysis of protegrin-1 (PG-1) at low concentrations renders it useless for therapeutic application. We rationally designed PLP-3, a novel synthetic PG-1-like peptide, comprising key activity features of protegrins in a constrained bicyclic structure. Our main objective was to investigate PLP-3's activity against MDR strains of Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae and to analyse its haemolysis and cytotoxicity. METHODS Peptide synthesis was performed via solid phase and intramolecular ligation in solution, and the correct folding of the peptide was verified by circular dichroism. Antimicrobial activity was performed through broth microdilution. The test panel contained 45 bacterial strains belonging to A. baumannii, P. aeruginosa and K. pneumoniae (15 strains per species) comprising colistin-resistant and MDR strains. Cytotoxicity was assessed by XTT cell viability assays using HeLa and A549 cells and haemolysis of human erythrocytes. RESULTS PLP-3 was successfully synthesized, and its antiparallel β-sheet conformation was confirmed. Antimicrobial activity screening showed MIC90 values of 2 mg/L for A. baumannii, 16 mg/L for K. pneumoniae and 8 mg/L for P. aeruginosa. The haemolysis IC50 value was 48.53 mg/L. Cytotoxicity against human HeLa and A549 cells showed values of ca. 200 mg/L in both cell lines resulting in a 100-fold selectivity window for bacterial over human cells. CONCLUSIONS PLP-3 has potent antimicrobial activity, especially against A. baumannii, while maintaining low haemolysis and toxicity against human cell lines at antimicrobial concentrations. These characteristics make PLP-3 a promising peptide with an interesting therapeutic window.
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Affiliation(s)
| | | | - Clara Ballesté-Delpierre
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto Salud Carlos III, Madrid, Spain
| | - Ernest Giralt
- IRB Barcelona, Barcelona, Spain.,Department of Inorganic and Organic Chemistry, Universitat de Barcelona, Barcelona, Spain
| | - Jordi Vila
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto Salud Carlos III, Madrid, Spain.,Department of Clinical Microbiology, Hospital Clinic, Barcelona, Spain
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17
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Canepa E, Relini A, Bochicchio D, Lavagna E, Mescola A. Amphiphilic Gold Nanoparticles: A Biomimetic Tool to Gain Mechanistic Insights into Peptide-Lipid Interactions. MEMBRANES 2022; 12:673. [PMID: 35877876 PMCID: PMC9324301 DOI: 10.3390/membranes12070673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023]
Abstract
Functional peptides are now widely used in a myriad of biomedical and clinical contexts, from cancer therapy and tumor targeting to the treatment of bacterial and viral infections. Underlying this diverse range of applications are the non-specific interactions that can occur between peptides and cell membranes, which, in many contexts, result in spontaneous internalization of the peptide within cells by avoiding energy-driven endocytosis. For this to occur, the amphipathicity and surface structural flexibility of the peptides play a crucial role and can be regulated by the presence of specific molecular residues that give rise to precise molecular events. Nevertheless, most of the mechanistic details regulating the encounter between peptides and the membranes of bacterial or animal cells are still poorly understood, thus greatly limiting the biomimetic potential of these therapeutic molecules. In this arena, finely engineered nanomaterials-such as small amphiphilic gold nanoparticles (AuNPs) protected by a mixed thiol monolayer-can provide a powerful tool for mimicking and investigating the physicochemical processes underlying peptide-lipid interactions. Within this perspective, we present here a critical review of membrane effects induced by both amphiphilic AuNPs and well-known amphiphilic peptide families, such as cell-penetrating peptides and antimicrobial peptides. Our discussion is focused particularly on the effects provoked on widely studied model cell membranes, such as supported lipid bilayers and lipid vesicles. Remarkable similarities in the peptide or nanoparticle membrane behavior are critically analyzed. Overall, our work provides an overview of the use of amphiphilic AuNPs as a highly promising tailor-made model to decipher the molecular events behind non-specific peptide-lipid interactions and highlights the main affinities observed both theoretically and experimentally. The knowledge resulting from this biomimetic approach could pave the way for the design of synthetic peptides with tailored functionalities for next-generation biomedical applications, such as highly efficient intracellular delivery systems.
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Affiliation(s)
- Ester Canepa
- Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy; (E.C.); (A.R.); (D.B.)
| | - Annalisa Relini
- Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy; (E.C.); (A.R.); (D.B.)
| | - Davide Bochicchio
- Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy; (E.C.); (A.R.); (D.B.)
| | - Enrico Lavagna
- Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy; (E.C.); (A.R.); (D.B.)
| | - Andrea Mescola
- CNR-Nanoscience Institute-S3, Via Campi 213/A, 41125 Modena, Italy
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18
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Blair JMA, Zeth K, Bavro VN, Sancho-Vaello E. The role of bacterial transport systems in the removal of host antimicrobial peptides in Gram-negative bacteria. FEMS Microbiol Rev 2022; 46:6617596. [PMID: 35749576 PMCID: PMC9629497 DOI: 10.1093/femsre/fuac032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/23/2022] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
Antibiotic resistance is a global issue that threatens our progress in healthcare and life expectancy. In recent years, antimicrobial peptides (AMPs) have been considered as promising alternatives to the classic antibiotics. AMPs are potentially superior due to their lower rate of resistance development, since they primarily target the bacterial membrane ('Achilles' heel' of the bacteria). However, bacteria have developed mechanisms of AMP resistance, including the removal of AMPs to the extracellular space by efflux pumps such as the MtrCDE or AcrAB-TolC systems, and the internalization of AMPs to the cytoplasm by the Sap transporter, followed by proteolytic digestion. In this review, we focus on AMP transport as a resistance mechanism compiling all the experimental evidence for the involvement of efflux in AMP resistance in Gram-negative bacteria and combine this information with the analysis of the structures of the efflux systems involved. Finally, we expose some open questions with the aim of arousing the interest of the scientific community towards the AMPs-efflux pumps interactions. All the collected information broadens our understanding of AMP removal by efflux pumps and gives some clues to assist the rational design of AMP-derivatives as inhibitors of the efflux pumps.
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Affiliation(s)
- Jessica M A Blair
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Kornelius Zeth
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - Vassiliy N Bavro
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Enea Sancho-Vaello
- Corresponding author. College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom. E-mail:
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Umegawa Y, Yamamoto T, Dixit M, Funahashi K, Seo S, Nakagawa Y, Suzuki T, Matsuoka S, Tsuchikawa H, Hanashima S, Oishi T, Matsumori N, Shinoda W, Murata M. Amphotericin B assembles into seven-molecule ion channels: An NMR and molecular dynamics study. SCIENCE ADVANCES 2022; 8:eabo2658. [PMID: 35714188 PMCID: PMC9205587 DOI: 10.1126/sciadv.abo2658] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/04/2022] [Indexed: 05/30/2023]
Abstract
Amphotericin B, an antifungal drug with a long history of use, forms fungicidal ion-permeable channels across cell membranes. Using solid-state nuclear magnetic resonance spectroscopy and molecular dynamics simulations, we experimentally elucidated the three-dimensional structure of the molecular assemblies formed by this drug in membranes in the presence of the fungal sterol ergosterol. A stable assembly consisting of seven drug molecules was observed to form an ion conductive channel. The structure is somewhat similar to the upper half of the barrel-stave model proposed in the 1970s but substantially different in the number of molecules and in their arrangement. The present structure explains many previous findings, including structure-activity relationships of the drug, which will be useful for improving drug efficacy and reducing adverse effects.
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Affiliation(s)
- Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Project Research Center for Fundamental Sciences, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Tomoya Yamamoto
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Mayank Dixit
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Kosuke Funahashi
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Sangjae Seo
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Yasuo Nakagawa
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Taiga Suzuki
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Shigeru Matsuoka
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Japan Science and Technology Agency, ERATO, Lipid Active Structure Project, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Tohru Oishi
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
- Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Project Research Center for Fundamental Sciences, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Japan Science and Technology Agency, ERATO, Lipid Active Structure Project, Osaka University, Toyonaka, Osaka 560-0043, Japan
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Atomic-Resolution Structures and Mode of Action of Clinically Relevant Antimicrobial Peptides. Int J Mol Sci 2022; 23:ijms23094558. [PMID: 35562950 PMCID: PMC9100274 DOI: 10.3390/ijms23094558] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/18/2022] [Accepted: 04/18/2022] [Indexed: 02/01/2023] Open
Abstract
Global rise of infections and deaths caused by drug-resistant bacterial pathogens are among the unmet medical needs. In an age of drying pipeline of novel antibiotics to treat bacterial infections, antimicrobial peptides (AMPs) are proven to be valid therapeutics modalities. Direct in vivo applications of many AMPs could be challenging; however, works are demonstrating encouraging results for some of them. In this review article, we discussed 3-D structures of potent AMPs e.g., polymyxin, thanatin, MSI, protegrin, OMPTA in complex with bacterial targets and their mode of actions. Studies on human peptide LL37 and de novo-designed peptides are also discussed. We have focused on AMPs which are effective against drug-resistant Gram-negative bacteria. Since treatment options for the infections caused by super bugs of Gram-negative bacteria are now extremely limited. We also summarize some of the pertinent challenges in the field of clinical trials of AMPs.
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21
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Salnikov E, Aisenbrey C, Bechinger B. Lipid saturation and head group composition have a pronounced influence on the membrane insertion equilibrium of amphipathic helical polypeptides. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183844. [PMID: 34954200 DOI: 10.1016/j.bbamem.2021.183844] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 10/19/2022]
Abstract
The histidine-rich peptides of the LAH4 family were designed using cationic antimicrobial peptides such as magainin and PGLa as templates. The LAH4 amphipathic helical sequences exhibit a multitude of interesting biological properties such as antimicrobial activity, cell penetration of a large variety of cargo and lentiviral transduction enhancement. The parent peptide associates with lipid bilayers where it changes from an orientation along the membrane interface into a transmembrane configuration in a pH-dependent manner. Here we show that LAH4 adopts a transmembrane configuration in fully saturated DMPC membranes already at pH 3.5, i.e. much below the pKa of the histidines whereas the transition pH in POPC correlates closely with histidine neutralization. In contrast in POPG membranes the in-planar configuration is stabilized by about one pH unit. The differences in pH can be converted into energetic contributions for the in-plane to transmembrane transition equilibrium, where the shift in the transition pH due to lipid saturation corresponds to energies which are otherwise obtained by the exchange of several cationic with hydrophobic residues. A similar dependence on lipid saturation has also been observed when the PGLa and magainin antimicrobial peptides interact within lipid bilayers suggesting that the quantitative evaluation presented in this paper also applies to other membrane polypeptides.
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Affiliation(s)
- Evgeniy Salnikov
- University of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics and NMR, Strasbourg, France
| | - Christopher Aisenbrey
- University of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics and NMR, Strasbourg, France
| | - Burkhard Bechinger
- University of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics and NMR, Strasbourg, France; Institut Universitaire de France, France.
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22
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Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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23
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Rani L, Arora A, Majhi S, Mishra A, Mallajosyula SS. Experimental and simulation studies reveal mechanism of action of human defensin derivatives. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183824. [PMID: 34838874 DOI: 10.1016/j.bbamem.2021.183824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 06/13/2023]
Abstract
Antimicrobial peptides (AMPs) are naturally occurring promising candidates which can be used as antibiotics against a wide variety of bacteria. The key component for using them as a potent antibiotic is that their mechanism of action is less prone to bacterial resistance. However, the molecular details of their mechanism of action is not yet fully understood. In this study, we try to shed light on the mode of action of AMPs, possible reason behind it, and their interaction with lipid bilayers through experimental as well as molecular dynamics (MD) simulation studies. The focal of our study was Human beta defensin 3 (hBD-3) which is a naturally occurring AMP. We chose three derivatives of hBD-3, namely CHRG01, KSR, and KLR for the detailed analysis presented in this study. These three peptides are evaluated for their antibacterial potency, secondary structure analysis and mechanism of action. The experimental results reveal that these peptides are active against gram positive as well as gram negative bacteria and kill bacteria by forming membrane pores. The MD simulation results correlate well with the antibacterial activity and shed light into the early membrane insertion dynamics. Moreover, the specific amino acids responsible for membrane disruptions are also identified from the MD simulations. Understanding the molecular level interaction of individual amino acids with the lipid bilayer will greatly help in the design of more efficient antimicrobial peptides.
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Affiliation(s)
- Lata Rani
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Ankita Arora
- Department of Materials Science and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Sasmita Majhi
- Department of Materials Science and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Abhijit Mishra
- Department of Materials Science and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India.
| | - Sairam S Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India.
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Booth V. Deuterium Solid State NMR Studies of Intact Bacteria Treated With Antimicrobial Peptides. FRONTIERS IN MEDICAL TECHNOLOGY 2022; 2:621572. [PMID: 35047897 PMCID: PMC8757836 DOI: 10.3389/fmedt.2020.621572] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
Solid state NMR has been tremendously useful in characterizing the structure and dynamics of model membranes composed of simple lipid mixtures. Model lipid studies employing solid state NMR have included important work revealing how membrane bilayer structure and dynamics are affected by molecules such as antimicrobial peptides (AMPs). However, solid state NMR need not be applied only to model membranes, but can also be used with living, intact cells. NMR of whole cells holds promise for helping resolve some unsolved mysteries about how bacteria interact with AMPs. This mini-review will focus on recent studies using 2H NMR to study how treatment with AMPs affect membranes in intact bacteria.
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Affiliation(s)
- Valerie Booth
- Department of Biochemistry and Department of Physics and Physical Oceanograpy, Memorial University of Newfoundland, St. John's, NL, Canada
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25
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Zouhir A, Semmar N. Structure-activity trend analysis between amino-acids and minimal inhibitory concentration of antimicrobial peptides. Chem Biol Drug Des 2021; 99:438-455. [PMID: 34965022 DOI: 10.1111/cbdd.14003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 10/03/2021] [Accepted: 10/23/2021] [Indexed: 11/29/2022]
Abstract
Antimicrobial peptides (AMPs) provide large structural libraries of molecules with high variability of constitutional amino-acids (AAs). Highlighting structural organization and structure-activity trends in such molecular systems provide key information on structural associations and functional conditions that could usefully help for drug design. This work presents link analyses between minimal inhibitory concentration (MIC) and different types of constitutional AAs of anti-Pseudomonas aeruginosa AMPs. This scope was based on a dataset of 328 published molecules. Regulation levels of AAs in AMPs were statistically ordinated by correspondence analysis helping for classification of the 328 AMPs into nine structurally homogeneous peptide clusters (PCs 1-9) characterized by high/low relative occurrences of different AAs. Within each PC, negative trends between MIC and AAs were highlighted by iterated multiple linear regression models built by bootstrap processes (bagging). MIC-decrease was linked to different AAs that varied with PCs: alcohol type AAs (Thr, Ser) in Cys-rich and low Arg PCs (PCs 1-3); basic AAs (Lys, Arg) in Pro-rich and low Val PCs (PCs 4-8); Trp (heterocyclic AA) in Arg-rich PCs (PCs 6, 7, 9). Aliphatic AAs (more particularly Gly) showed MIC-reduction effects in different PCs essentially under interactive forms.
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Affiliation(s)
- Abdelmajid Zouhir
- University of Tunis El Manar, Institut Supérieur des Sciences Biologiques Appliquées de Tunis
| | - Nabil Semmar
- University of Tunis El Manar, Laboratory of BioInformatics, bioMathematics and bioStatistics (BIMS), Pasteur Institute of Tunis, Tunisia
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26
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Liu AY, Aguayo-Ortiz R, Guerrero-Serna G, Wang N, Blin MG, Goldstein DR, Michel Espinoza-Fonseca L. Homologous cardiac calcium pump regulators phospholamban and sarcolipin adopt distinct oligomeric states in the membrane. Comput Struct Biotechnol J 2021; 20:380-384. [PMID: 35035790 PMCID: PMC8748397 DOI: 10.1016/j.csbj.2021.12.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 11/23/2022] Open
Abstract
Phospholamban (PLN) and Sarcolipin (SLN) are homologous membrane proteins that belong to the family of proteins that regulate the activity of the cardiac calcium pump (sarcoplasmic reticulum Ca2+-ATPase, SERCA). PLN and SLN share highly conserved leucine zipper motifs that control self-association; consequently, it has been proposed that both PLN and SLN assemble into stable pentamers in the membrane. In this study, we used molecular dynamics (MD) simulations and Western blot analysis to investigate the precise molecular architecture of the PLN and SLN oligomers. Analysis showed that the PLN pentamer is the predominant oligomer present in mouse ventricles and ventricle-like human iPSC-derived cardiomyocytes, in agreement with the MD simulations showing stable leucine zipper interactions across all protomer-protomer interfaces and MD replicates. Interestingly, we found that the PLN pentamer populates an asymmetric structure of the transmembrane region, which is likely an intrinsic feature of the oligomer in a lipid bilayer. The SLN pentamer is not favorably formed across MD replicates and species of origin; instead, SLN from human and mouse atria primarily populate coexisting dimeric and trimeric states. In contrast to previous studies, our findings indicate that the SLN pentamer is not the predominant oligomeric state populated in the membrane. We conclude that despite their structural homology, PLN and SLN adopt distinct oligomeric states in the membrane. We propose that the distinct oligomeric states populated by PLN and SLN may contribute to tissue-specific SERCA regulation via differences in protomer-oligomer exchange, oligomer-SERCA dynamics, and noise filtering during β-adrenergic stimulation in the heart.
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Affiliation(s)
- Andy Y. Liu
- Center for Arrhythmia Research, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- McKetta Department of Chemical Engineering, The University of Texas, Austin, TX 78712, USA
| | - Rodrigo Aguayo-Ortiz
- Departamento de Farmacia, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Guadalupe Guerrero-Serna
- Center for Arrhythmia Research, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nulang Wang
- Center for Arrhythmia Research, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Muriel G. Blin
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel R. Goldstein
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
- Institute of Gerontology, University of Michigan, Ann Arbor, MI 48109, USA
| | - L. Michel Espinoza-Fonseca
- Center for Arrhythmia Research, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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27
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Shcherbakov AA, Medeiros-Silva J, Tran N, Gelenter MD, Hong M. From Angstroms to Nanometers: Measuring Interatomic Distances by Solid-State NMR. Chem Rev 2021; 122:9848-9879. [PMID: 34694769 DOI: 10.1021/acs.chemrev.1c00662] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Internuclear distances represent one of the main structural constraints in molecular structure determination using solid-state NMR spectroscopy, complementing chemical shifts and orientational restraints. Although a large number of magic-angle-spinning (MAS) NMR techniques have been available for distance measurements, traditional 13C and 15N NMR experiments are inherently limited to distances of a few angstroms due to the low gyromagnetic ratios of these nuclei. Recent development of fast MAS triple-resonance 19F and 1H NMR probes has stimulated the design of MAS NMR experiments that measure distances in the 1-2 nm range with high sensitivity. This review describes the principles and applications of these multiplexed multidimensional correlation distance NMR experiments, with an emphasis on 19F- and 1H-based distance experiments. Representative applications of these long-distance NMR methods to biological macromolecules as well as small molecules are reviewed.
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Affiliation(s)
- Alexander A Shcherbakov
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Nhi Tran
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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28
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Sutherland M, Kwon B, Hong M. Interactions of HIV gp41's membrane-proximal external region and transmembrane domain with phospholipid membranes from 31P NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183723. [PMID: 34352242 DOI: 10.1016/j.bbamem.2021.183723] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/22/2021] [Accepted: 07/30/2021] [Indexed: 11/30/2022]
Abstract
HIV-1 entry into cells requires coordinated changes of the conformation and dynamics of both the fusion protein, gp41, and the lipids in the cell membrane and virus envelope. Commonly proposed features of membrane deformation during fusion include high membrane curvature, lipid disorder, and membrane surface dehydration. The virus envelope and target cell membrane contain a diverse set of phospholipids and cholesterol. To dissect how different lipids interact with gp41 to contribute to membrane fusion, here we use 31P solid-state NMR spectroscopy to investigate the curvature, dynamics, and hydration of POPE, POPC and POPS membranes, with and without cholesterol, in the presence of a peptide comprising the membrane proximal external region (MPER) and transmembrane domain (TMD) of gp41. Static 31P NMR spectra indicate that the MPER-TMD induces strong negative Gaussian curvature (NGC) to the POPE membrane but little curvature to POPC and POPC:POPS membranes. The NGC manifests as an isotropic peak in the static NMR spectra, whose intensity increases with the peptide concentration. Cholesterol inhibits the NGC formation and stabilizes the lamellar phase. Relative intensities of magic-angle spinning 31P cross-polarization and direct-polarization spectra indicate that all three phospholipids become more mobile upon peptide binding. Finally, 2D 1H-31P correlation spectra show that the MPER-TMD enhances water 1H polarization transfer to the lipids, indicating that the membrane surfaces become more hydrated. These results suggest that POPE is an essential component of the high-curvature fusion site, and lipid dynamic disorder is a general feature of membrane restructuring during fusion.
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Affiliation(s)
- Madeleine Sutherland
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Byungsu Kwon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
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29
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Gabrielli V, Kuraite A, da Silva MA, Edler KJ, Angulo J, Nepravishta R, Muñoz-García JC, Khimyak YZ. Spin diffusion transfer difference (SDTD) NMR: An advanced method for the characterisation of water structuration within particle networks. J Colloid Interface Sci 2021; 594:217-227. [PMID: 33756365 DOI: 10.1016/j.jcis.2021.02.094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/13/2021] [Accepted: 02/23/2021] [Indexed: 11/26/2022]
Abstract
HYPOTHESIS The classical STD NMR protocol to monitor solvent interactions in gels is strongly dependent on gelator and solvent concentrations and does not report on the degree of structuration of the solvent at the particle/solvent interface. We hypothesised that, for suspensions of large gelator particles, solvent structuration could be characterised by STD NMR when taking into account the particle-to-solvent 1H-1H spin diffusion transfer using the 1D diffusion equation. EXPERIMENTS We have carried out a systematic study on effect of gelator and solvent concentrations, and gelator surface charge, affecting the behaviour of the classical STD NMR build-up curves. To do so, we have characterised solvent interactions in dispersions of starch and cellulose-like particles prepared in deuterated water and alcohol/D2O mixtures. FINDINGS The Spin Diffusion Transfer Difference (SDTD) NMR protocol is independent of the gelator and solvent concentrations, hence allowing the estimation of the degree of solvent structuration within different particle networks. In addition, the simulation of SDTD build-up curves using the general one-dimensional diffusion equation allows the determination of minimum distances (r) and spin diffusion rates (D) at the particle/solvent interface. This novel NMR protocol can be readily extended to characterise the solvent(s) organisation in any type of colloidal systems constituted by large particles.
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Affiliation(s)
- Valeria Gabrielli
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Agne Kuraite
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | | | - Karen J Edler
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Jesús Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Ridvan Nepravishta
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | - Juan C Muñoz-García
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | - Yaroslav Z Khimyak
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
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30
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Phyo P, Zhao X, Templeton AC, Xu W, Cheung JK, Su Y. Understanding molecular mechanisms of biologics drug delivery and stability from NMR spectroscopy. Adv Drug Deliv Rev 2021; 174:1-29. [PMID: 33609600 DOI: 10.1016/j.addr.2021.02.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/20/2021] [Accepted: 02/07/2021] [Indexed: 02/06/2023]
Abstract
Protein therapeutics carry inherent limitations of membrane impermeability and structural instability, despite their predominant role in the modern pharmaceutical market. Effective formulations are needed to overcome physiological and physicochemical barriers, respectively, for improving bioavailability and stability. Knowledge of membrane affinity, cellular internalization, encapsulation, and release of drug-loaded carrier vehicles uncover the structural basis for designing and optimizing biopharmaceuticals with enhanced delivery efficiency and therapeutic efficacy. Understanding stabilizing and destabilizing interactions between protein drugs and formulation excipients provide fundamental mechanisms for ensuring the stability and quality of biological products. This article reviews the molecular studies of biologics using solution and solid-state NMR spectroscopy on structural attributes pivotal to drug delivery and stability. In-depth investigation of the structure-function relationship of drug delivery systems based on cell-penetrating peptides, lipid nanoparticles and polymeric colloidal, and biophysical and biochemical stability of peptide, protein, monoclonal antibody, and vaccine, as the integrative efforts on drug product design, will be elaborated.
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Affiliation(s)
- Pyae Phyo
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Xi Zhao
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Allen C Templeton
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Wei Xu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Jason K Cheung
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Yongchao Su
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States.
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31
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Gong H, Hu X, Liao M, Fa K, Ciumac D, Clifton LA, Sani MA, King SM, Maestro A, Separovic F, Waigh TA, Xu H, McBain AJ, Lu JR. Structural Disruptions of the Outer Membranes of Gram-Negative Bacteria by Rationally Designed Amphiphilic Antimicrobial Peptides. ACS APPLIED MATERIALS & INTERFACES 2021; 13:16062-16074. [PMID: 33797891 DOI: 10.1021/acsami.1c01643] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Gram-negative bacteria are covered by both an inner cytoplasmic membrane (IM) and an outer membrane (OM). Antimicrobial peptides (AMPs) must first permeate through the OM and cell wall before attacking the IM to cause cytoplasmic leakage and kill the bacteria. The bacterial OM is an asymmetric bilayer with the outer leaflet primarily composed of lipopolysaccharides (LPSs) and the inner leaflet composed of phospholipids (PLs). Two cationic α-helical AMPs were designed to target Gram-negative bacteria, a full peptide G(IIKK)3I-NH2 (G3), and a hydrophobic lipopeptide C8-G(IIKK)2I-NH2 (C8G2, with C8 denoting the octanoyl chain). LPS dominates OM functions as the first line of defense against antibiotics, thereby reducing drug susceptibility. This work explores how the two AMPs interact with LPS through several carefully chosen OM models that facilitated measurements from solid-state nuclear magnetic resonance (ss-NMR), small-angle neutron scattering (SANS), and neutron reflectivity (NR). The results revealed that G3 molecules bound preferably to the LPS head region and functioned as bridge molecules to reassemble the dislocated lipids into bilayer stacks. In contrast, C8G2 lipopeptides could quickly penetrate into the central region of the OM to cause direct removal of some membrane lipids. Different structural disruptions implicated different antimicrobial efficacies from these AMPs. The demonstration of the structural features underlying different susceptibilities of the OM to AMPs offers a useful route for the future development of strain-specific AMPs against antimicrobial-resistant pathogens.
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Affiliation(s)
- Haoning Gong
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Xuzhi Hu
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Mingrui Liao
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Ke Fa
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Daniela Ciumac
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Luke A Clifton
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Marc-Antoine Sani
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Stephen M King
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Armando Maestro
- Institute Laue Langevin, 71 Avenue des Martyrs, CS-20156, 38042 Grenoble, France
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Thomas A Waigh
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and the Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Andrew J McBain
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Jian Ren Lu
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
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32
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Huynh L, Velásquez J, Rabara R, Basu S, Nguyen HB, Gupta G. Rational design of antimicrobial peptides targeting Gram-negative bacteria. Comput Biol Chem 2021; 92:107475. [PMID: 33813188 DOI: 10.1016/j.compbiolchem.2021.107475] [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: 12/31/2020] [Revised: 03/02/2021] [Accepted: 03/09/2021] [Indexed: 01/16/2023]
Abstract
Membrane-targeting host antimicrobial peptides (AMPs) can kill or inhibit the growth of Gram-negative bacteria. However, the evolution of resistance among microbes poses a substantial barrier to the long-term utility of the host AMPs. Combining experiment and molecular dynamics simulations, we show that terminal carboxyl capping enhances both membrane insertion and antibacterial activity of an AMP called P1. Furthermore, we show that a bacterial strain with evolved resistance to this peptide becomes susceptible to P1 variants with either backbone capping or lysine-to-arginine substitutions. Our results suggest that cocktails of closely related AMPs may be useful in overcoming evolved resistance.
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Affiliation(s)
- Loan Huynh
- New Mexico Consortium, Los Alamos, NM, 87544, USA
| | | | - Roel Rabara
- New Mexico Consortium, Los Alamos, NM, 87544, USA
| | | | - Hau B Nguyen
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Goutam Gupta
- New Mexico Consortium, Los Alamos, NM, 87544, USA.
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33
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Panteleev PV, Tsarev AV, Safronova VN, Reznikova OV, Bolosov IA, Sychev SV, Shenkarev ZO, Ovchinnikova TV. Structure Elucidation and Functional Studies of a Novel β-hairpin Antimicrobial Peptide from the Marine Polychaeta Capitella teleta. Mar Drugs 2020; 18:md18120620. [PMID: 33291782 PMCID: PMC7761999 DOI: 10.3390/md18120620] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/27/2020] [Accepted: 12/02/2020] [Indexed: 12/21/2022] Open
Abstract
Endogenous antimicrobial peptides (AMPs) are evolutionary ancient molecular factors of innate immunity that play a key role in host defense. Among the most active and stable under physiological conditions AMPs are the peptides of animal origin that adopt a β-hairpin conformation stabilized by disulfide bridges. In this study, a novel BRICHOS-domain related AMP from the marine polychaeta Capitella teleta, named capitellacin, was produced as the recombinant analogue and investigated. The mature capitellacin exhibits high homology with the known β-hairpin AMP family—tachyplesins and polyphemusins from the horseshoe crabs. The β-hairpin structure of the recombinant capitellacin was proved by CD and NMR spectroscopy. In aqueous solution the peptide exists as monomeric right-handed twisted β-hairpin and its structure does not reveal significant amphipathicity. Moreover, the peptide retains this conformation in membrane environment and incorporates into lipid bilayer. Capitellacin exhibits a strong antimicrobial activity in vitro against a wide panel of bacteria including extensively drug-resistant strains. In contrast to other known β-hairpin AMPs, this peptide acts apparently via non-lytic mechanism at concentrations inhibiting bacterial growth. The molecular mechanism of the peptide antimicrobial action does not seem to be related to the inhibition of bacterial translation therefore other molecular targets may be assumed. The reduced cytotoxicity against human cells and high antibacterial cell selectivity as compared to tachyplesin-1 make it an attractive candidate compound for an anti-infective drug design.
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Affiliation(s)
- Pavel V. Panteleev
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia; (P.V.P.); (A.V.T.); (V.N.S.); (O.V.R.); (I.A.B.); (S.V.S.); (Z.O.S.)
| | - Andrey V. Tsarev
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia; (P.V.P.); (A.V.T.); (V.N.S.); (O.V.R.); (I.A.B.); (S.V.S.); (Z.O.S.)
| | - Victoria N. Safronova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia; (P.V.P.); (A.V.T.); (V.N.S.); (O.V.R.); (I.A.B.); (S.V.S.); (Z.O.S.)
| | - Olesia V. Reznikova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia; (P.V.P.); (A.V.T.); (V.N.S.); (O.V.R.); (I.A.B.); (S.V.S.); (Z.O.S.)
| | - Ilia A. Bolosov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia; (P.V.P.); (A.V.T.); (V.N.S.); (O.V.R.); (I.A.B.); (S.V.S.); (Z.O.S.)
| | - Sergei V. Sychev
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia; (P.V.P.); (A.V.T.); (V.N.S.); (O.V.R.); (I.A.B.); (S.V.S.); (Z.O.S.)
| | - Zakhar O. Shenkarev
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia; (P.V.P.); (A.V.T.); (V.N.S.); (O.V.R.); (I.A.B.); (S.V.S.); (Z.O.S.)
| | - Tatiana V. Ovchinnikova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia; (P.V.P.); (A.V.T.); (V.N.S.); (O.V.R.); (I.A.B.); (S.V.S.); (Z.O.S.)
- Department of Biotechnology, I.M. Sechenov First Moscow State Medical University, Trubetskaya str., 8–2, 119991 Moscow, Russia
- Correspondence: ; Tel.: +7-495-336-44-44
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Sinha S, Ng WJ, Bhattacharjya S. NMR structure and localization of the host defense antimicrobial peptide thanatin in zwitterionic dodecylphosphocholine micelle: Implications in antimicrobial activity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183432. [PMID: 32781154 DOI: 10.1016/j.bbamem.2020.183432] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/11/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023]
Abstract
Antimicrobial peptides (AMPs) are potentially vital as the next generation of antibiotics against multidrug resistant bacterial pathogens. Thanatin, an insect derived pathogen inducible 21-residue long antimicrobial peptide, demonstrates antimicrobial activity toward broad range of pathogens. Thanatin is an excellent candidate for antibiotics development due to potent in vivo activity in animal model and low toxicity to human cells. Recent studies indicated mode of action of thanatin could be intriguing and may comprise bacterial membrane permeabilization and interactions with periplasmic proteins. In order to better understand selectivity and membrane disruption, here, we determined 3-D structure of the thanatin in zwitterionic DPC-d38 micelle by NMR spectroscopy. The depth of insertion of thanatin into micelle structure was investigated by spin labelled doxyl lipids, 5-DSA and 16-DSA. DPC-bound structure of thanatin is defined by a β-hairpin structure and an extended and turn conformations, for residues G1-I8, at the N-terminus. The β-hairpin structure is delineated by two antiparallel β-strands, residues I9-C11 and residues K17-R20, which is connected by loop consisted of residues N12-G16. There are cross β-strands sidechain-sidechain packing interactions among hydrophobic and aromatic residues. Spin labelled lipid studies revealed a set of spatially proximal residues V6, I8, Q19, R20 and M21 may be deeply inserted into the hydrophobic core of the DPC micelle. While, residues including those at the turn/loop are merely surface localized. The atomic resolution structure and orientation of thanatin in zwitterionic DPC micelle may be utilized for understating mode of action in lipid membrane and further development of non-toxic analogs.
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Affiliation(s)
- Sheetal Sinha
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; Interdisciplinary Graduate School, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore
| | - Wun Jern Ng
- Environmental Bio-Innovation Group (EBiG), School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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Zhang Y, Zhang HX, Zheng QC. In Silico Study of Membrane Lipid Composition Regulating Conformation and Hydration of Influenza Virus B M2 Channel. J Chem Inf Model 2020; 60:3603-3615. [PMID: 32589410 DOI: 10.1021/acs.jcim.0c00329] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The proton conduction of transmembrane influenza virus B M2 (BM2) proton channel is possibly mediated by the membrane environment, but the detailed molecular mechanism is challenging to determine. In this work, how membrane lipid composition regulates the conformation and hydration of BM2 channel is elucidated in silico. The appearance of several important hydrogen-bond networks has been discovered, as the addition of negatively charged lipid palmitoyloleoyl phosphatidylglycerol (POPG) and cholesterol reduces membrane fluidity and augments membrane rigidity. A more rigid membrane environment is beneficial to expand the channel, allow more water to enter the channel, promote channel hydration, and then even affect the proton conduction facilitated by the hydrated channel. Thus, membrane environment could be identified as an important influence factor of conformation and hydration of BM2. These findings can provide a unique perspective for understanding the mechanism of membrane lipid composition regulating conformation and hydration of BM2 and have important significance to the further study of anti-influenza virus B drugs.
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Affiliation(s)
- Yue Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, College of Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Hong-Xing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, College of Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, College of Chemistry, Jilin University, Changchun 130023, People's Republic of China.,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130023, People's Republic of China
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Cai L, Cao M, Regenstein J. Slow-Release and Nontoxic Pickering Emulsion Platform for Antimicrobial Peptide. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:7453-7466. [PMID: 32559384 DOI: 10.1021/acs.jafc.0c00874] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The resistance in microorganisms against many conventional antibiotics has become a serious global health problem. However, antibacterial drug delivery materials are still limited in toxicity, short efficacy and reducing inflammation. The novel and natural Pickering emulsions stabilized by antimicrobial peptide nanoparticles were tested as promising platforms to control bacterial resistance development. The parasin I interacted or conjugated with lecithin or chitosan and formed nanoparticles encapsulated by Pickering emulsion. The protonation and deprotonation of amino groups in chitosan and parasin I resulted in nanoparticles in different aggregate states and changed emulsion stability. Moreover, the Pickering emulsion could induce severe bacterial agglomeration on both Gram-positive and Gram-negative bacteria than parasin I through the membrane disintegration mechanism. Furthermore, the Pickering emulsion could alleviate the cytotoxicity of human liver cells and hemolytic activity in rat blood cells. In combination with the lack of acute cytotoxicity in Kunming mice and milder, more effective anti-inflammatory effect in peritonitis demonstrated for these Pickering emulsions, especially chitosan peptide-embedded nanoparticles Pickering emulsion, a potential role in combating multidrug resistant bacteria in biomedical applications.
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Affiliation(s)
- Luyun Cai
- College of Biosystems Engineering and Food Science, National & Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, China
- Ningbo Research Institute, Zhejiang University, Ningbo 315400, China
| | - Minjie Cao
- College of Food Science and Engineering, Bohai University, Jinzhou 121013, China
| | - Joe Regenstein
- Department of Food Science, Cornell University, Ithaca, New York 14853-7201, United States
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Lu X, Huang C, Li M, Skomski D, Xu W, Yu L, Byrn SR, Templeton AC, Su Y. Molecular Mechanism of Crystalline-to-Amorphous Conversion of Pharmaceutical Solids from 19F Magic Angle Spinning NMR. J Phys Chem B 2020; 124:5271-5283. [PMID: 32378905 DOI: 10.1021/acs.jpcb.0c02131] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Crystalline and amorphous materials usually possess distinct physicochemical properties due to major variations in long-range and local molecular packings. Enhanced fundamental knowledge of the molecular details of crystalline-to-amorphous interconversions is necessary to correlate the intermolecular structure to material properties and functions. While crystal structures can be readily obtained by X-ray crystallography, the microstructure of amorphous materials has rarely been explored due to a lack of high-resolution techniques capable of probing local molecular structures. Moreover, there is increasing interest in understanding the molecular nature of amorphous solids in pharmaceutical sciences due to the widespread utilization of amorphous active pharmaceutical ingredients (APIs) in pharmaceutical development for solubility and bioavailability enhancement. In this study, we explore multidimensional 13C and 19F magic angle spinning (MAS) NMR spectroscopy to study the molecular packing of amorphous posaconazole (POSA) in conjunction with the crystalline counterpart. Utilizing methods integrating homonuclear and heteronuclear 1H, 13C, and 19F correlation spectroscopy and atomic 19F-to-13C distance measurements, we identified the major differences in molecular packing between crystalline and amorphous POSA. The intermolecular "head-to-head" interaction along the molecule's major axis, as well as the "head-to-tail" molecular packing perpendicular to the major axis in POSA crystals, was recapitulated by MAS NMR. Furthermore, critical intermolecular distances in the crystal lattice were determined. Most importantly, the head-to-tail contact of two neighboring molecules was found to be preserved in amorphous POSA, suggesting localized molecular order, whereas crucial interactions for head-to-head packing are absent in the amorphous form resulting in long-range disorder. Our study, likely one of the first documented examples, provides molecular-level structural details to understand the molecular mechanism of crystalline-to-amorphous conversion of fluorine-containing drug substances occurring in drug processing and development and establish a high-resolution experimental protocol for investigating amorphous materials.
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Affiliation(s)
- Xingyu Lu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Chengbin Huang
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Mingyue Li
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Daniel Skomski
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Wei Xu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Lian Yu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Stephen R Byrn
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Allen C Templeton
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Yongchao Su
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States.,Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States.,Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
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Rodnin MV, Vasquez-Montes V, Nepal B, Ladokhin AS, Lazaridis T. Experimental and Computational Characterization of Oxidized and Reduced Protegrin Pores in Lipid Bilayers. J Membr Biol 2020; 253:287-298. [PMID: 32500172 DOI: 10.1007/s00232-020-00124-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/23/2020] [Indexed: 12/16/2022]
Abstract
Protegrin-1 (PG-1), an 18-residue β-hairpin stabilized by two disulfide bonds, is a member of a family of powerful antimicrobial peptides which are believed to act through membrane permeabilization. Here we used a combination of experimental and computational approaches to characterize possible structural arrangements of PG-1 in lipid bilayers mimicking bacterial membranes. We have measured the dose-response function of the PG-1-induced leakage of markers of various sizes from vesicles and found it to be consistent with the formation of pores of two different sizes. The first one allows the release of small dyes and occurs at peptide:lipid ratios < 0.006. Above this ratio, larger pores are observed through which the smallest of dextrans FD4 can be released. In parallel with pore formation, we observe a general large-scale destabilization of vesicles which is probably related to complete rupture of some vesicles. The population of vesicles that are completely ruptured depends linearly on PG-1:lipid ratio. Neither pore size, nor vesicle rupture are influenced by the formation of disulfide bonds. Previous computational work on oxidized protegrin is complemented here by all-atom MD simulations of PG-1 with reduced disulfide bonds both in solution (monomer) and in a bilayer (dimer and octamer). The simulations provide molecular insights into the influence of disulfide bonds on peptide conformation, aggregation, and oligomeric structure.
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Affiliation(s)
- Mykola V Rodnin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Binod Nepal
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Themis Lazaridis
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA. .,Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, NY, 10016, USA.
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40
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Yun H, Min HJ, Lee CW. NMR structure and bactericidal activity of KR-12 analog derived from human LL-37 as a potential cosmetic preservative. J Anal Sci Technol 2020. [DOI: 10.1186/s40543-020-00213-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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41
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Lu X, Li M, Huang C, Lowinger MB, Xu W, Yu L, Byrn SR, Templeton AC, Su Y. Atomic-Level Drug Substance and Polymer Interaction in Posaconazole Amorphous Solid Dispersion from Solid-State NMR. Mol Pharm 2020; 17:2585-2598. [DOI: 10.1021/acs.molpharmaceut.0c00268] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xingyu Lu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Mingyue Li
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Chengbin Huang
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Michael B. Lowinger
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Wei Xu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Lian Yu
- School of Pharmacy and Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53705, United States
| | - Stephen R. Byrn
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, Indiana 47907, United States
| | - Allen C. Templeton
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Yongchao Su
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, Indiana 47907, United States
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
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Kang X, Elson C, Penfield J, Kirui A, Chen A, Zhang L, Wang T. Integrated solid-state NMR and molecular dynamics modeling determines membrane insertion of human β-defensin analog. Commun Biol 2019; 2:402. [PMID: 31701030 PMCID: PMC6825183 DOI: 10.1038/s42003-019-0653-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/15/2019] [Indexed: 12/11/2022] Open
Abstract
Human β-defensins (hBD) play central roles in antimicrobial activities against various microorganisms and in immune-regulation. These peptides perturb phospholipid membranes for function, but it is not well understood how defensins approach, insert and finally disrupt membranes on the molecular level. Here we show that hBD-3 analogs interact with lipid bilayers through a conserved surface that is formed by two adjacent loops in the solution structure. By integrating a collection of 13C, 1H and 31P solid-state NMR methods with long-term molecular dynamic simulations, we reveal that membrane-binding rigidifies the peptide, enhances structural polymorphism, and promotes β-strand conformation. The peptide colocalizes with negatively charged lipids, confines the headgroup motion, and deforms membrane into smaller, ellipsoidal vesicles. This study designates the residue-specific, membrane-bound topology of hBD-3 analogs, serves as the basis for further elucidating the function-relevant structure and dynamics of other defensins, and facilitates the development of defensin-mimetic antibiotics, antifungals, and anti-inflammatories.
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Affiliation(s)
- Xue Kang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Christopher Elson
- Department of Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505 USA
| | - Jackson Penfield
- Department of Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505 USA
| | - Alex Kirui
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Adrian Chen
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Liqun Zhang
- Department of Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505 USA
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803 USA
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43
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Beyond electrostatics: Antimicrobial peptide selectivity and the influence of cholesterol-mediated fluidity and lipid chain length on protegrin-1 activity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:182977. [DOI: 10.1016/j.bbamem.2019.04.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/11/2019] [Accepted: 04/28/2019] [Indexed: 12/31/2022]
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Soundrarajan N, Park S, Le Van Chanh Q, Cho HS, Raghunathan G, Ahn B, Song H, Kim JH, Park C. Protegrin-1 cytotoxicity towards mammalian cells positively correlates with the magnitude of conformational changes of the unfolded form upon cell interaction. Sci Rep 2019; 9:11569. [PMID: 31399625 PMCID: PMC6689069 DOI: 10.1038/s41598-019-47955-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/25/2019] [Indexed: 12/23/2022] Open
Abstract
Porcine protegrin-1 (PG-1) is a broad-spectrum antimicrobial peptide (AMP) with potent antimicrobial activities. We produced recombinant PG-1 and evaluated its cytotoxicity toward various types of mammalian cell lines, including embryonic fibroblasts, retinal cells, embryonic kidney cells, neuroblastoma cells, alveolar macrophage cells, and neutrophils. The sensitivity of the different mammalian cells to cytotoxic damage induced by PG-1 differed significantly among the cell types, with retinal neuron cells and neutrophils being the most significantly affected. A circular dichroism analysis showed there was a precise correlation between conformational changes in PG-1 and the magnitude of cytotoxicity among the various cell type. Subsequently, a green fluorescent protein (GFP) penetration assay using positively charged GFPs indicated there was a close correlation between the degree of penetration of charged GFP into cells and the magnitude of PG-1 cytotoxicity. Furthermore, we also showed that inhibition of the synthesis of anionic sulphated proteoglycans on the cell surface decreases the cytotoxic damage induced by PG-1 treatment. Taken together, the observed cytotoxicity of PG-1 towards different membrane surfaces is highly driven by the membrane’s anionic properties. Our results reveal a possible mechanism underlying cell-type dependent differences in cytotoxicity of AMPs, such as PG-1, toward mammalian cells.
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Affiliation(s)
| | - Suhyun Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Quy Le Van Chanh
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Hye-Sun Cho
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Govindan Raghunathan
- Department of Chemistry, University of Konstanz, Universitӓtsstraße 10, 78457, Konstanz, Germany
| | - Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Hyuk Song
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea.
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45
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Characterization of antibacterial activity and mechanisms of two linear derivatives of bactenecin. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.02.073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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46
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Abstract
Membrane permeabilizing peptides (MPPs) are as ubiquitous as the lipid bilayer membranes they act upon. Produced by all forms of life, most membrane permeabilizing peptides are used offensively or defensively against the membranes of other organisms. Just as nature has found many uses for them, translational scientists have worked for decades to design or optimize membrane permeabilizing peptides for applications in the laboratory and in the clinic ranging from antibacterial and antiviral therapy and prophylaxis to anticancer therapeutics and drug delivery. Here, we review the field of membrane permeabilizing peptides. We discuss the diversity of their sources and structures, the systems and methods used to measure their activities, and the behaviors that are observed. We discuss the fact that "mechanism" is not a discrete or a static entity for an MPP but rather the result of a heterogeneous and dynamic ensemble of structural states that vary in response to many different experimental conditions. This has led to an almost complete lack of discrete three-dimensional active structures among the thousands of known MPPs and a lack of useful or predictive sequence-structure-function relationship rules. Ultimately, we discuss how it may be more useful to think of membrane permeabilizing peptides mechanisms as broad regions of a mechanistic landscape rather than discrete molecular processes.
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Affiliation(s)
- Shantanu Guha
- Department of Biochemistry and Molecular Biology Tulane University School of Medicine , New Orleans , Louisiana 70112 , United States
| | - Jenisha Ghimire
- Department of Biochemistry and Molecular Biology Tulane University School of Medicine , New Orleans , Louisiana 70112 , United States
| | - Eric Wu
- Department of Biochemistry and Molecular Biology Tulane University School of Medicine , New Orleans , Louisiana 70112 , United States
| | - William C Wimley
- Department of Biochemistry and Molecular Biology Tulane University School of Medicine , New Orleans , Louisiana 70112 , United States
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47
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Zhang AH, Edwards IA, Mishra BP, Sharma G, Healy MD, Elliott AG, Blaskovich MAT, Cooper MA, Collins BM, Jia X, Mobli M. Elucidating the Lipid Binding Properties of Membrane-Active Peptides Using Cyclised Nanodiscs. Front Chem 2019; 7:238. [PMID: 31058133 PMCID: PMC6477933 DOI: 10.3389/fchem.2019.00238] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/26/2019] [Indexed: 01/02/2023] Open
Abstract
The lipid composition of the cellular membrane plays an important role in a number of biological processes including the binding of membrane-active peptides. Characterization of membrane binding remains challenging, due to the technical limitations associated with the use of standard biophysical techniques and available membrane models. Here, we investigate the lipid binding properties of two membrane-active peptides, VSTx1, a well characterized ion-channel inhibitor, identified from spider venom, that preferentially binds to anionic lipid mixtures, and AA139 an antimicrobial β-hairpin peptide with uncharacterised lipid binding properties, currently in pre-clinical development. The lipid binding properties of these peptides are elucidated using nanodiscs formed by both linear and circularized (sortase-mediated) forms of a membrane scaffold protein (MSP1D1ΔH5). We find that nanodiscs formed by circularized MSPs—in contrast to those formed by linear MSPs—are sufficiently stable under sample conditions typically used for biophysical measurements (including lipid composition, a range of buffers, temperatures and concentrations). Using these circularized nanodiscs, we are able to extract detailed thermodynamic data using isothermal titration calorimetry (ITC) as well as atomic resolution mapping of the lipid binding interfaces of our isotope labeled peptides using solution-state, heteronuclear, nuclear magnetic resonance (NMR) spectroscopy. This represents a novel and general approach for elucidating the thermodynamics and molecular interface of membrane-active peptides toward flat lipid bilayers of variable composition. Our approach is validated by first determining the thermodynamic parameters and binding interface of VSTx1 toward the lipid bilayer, which shows good agreement with previous studies using lipid micelles and liposomes. The method is then applied to AA139, where the membrane binding properties are unknown. This characterization, involved solving the high-resolution structure of AA139 in solution using NMR spectroscopy and the development of a suitable expression system for isotope labeling. AA139 was found to bind exclusively to anionic membranes with moderate affinity (Kd~low μM), and was found to have a lipid binding interface involving the termini of the β-hairpin structure. The preference of AA139 for anionic lipids supports a role for membrane binding in the mode-of-action of this peptide, which is also consistent with its higher inhibitory activity against bacterial cells compared to mammalian cells. The described approach is a powerful method for investigation of the membrane binding properties of this important class of molecules.
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Affiliation(s)
- Alan H Zhang
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Ingrid A Edwards
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Biswa P Mishra
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Gagan Sharma
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Michael D Healy
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Alysha G Elliott
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Mark A T Blaskovich
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Matthew A Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Brett M Collins
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Xinying Jia
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
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Bhattacharyya D, Kim M, Mroue KH, Park M, Tiwari A, Saleem M, Lee D, Bhunia A. Role of non-electrostatic forces in antimicrobial potency of a dengue-virus derived fusion peptide VG16KRKP: Mechanistic insight into the interfacial peptide-lipid interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:798-809. [DOI: 10.1016/j.bbamem.2019.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 12/28/2018] [Accepted: 01/22/2019] [Indexed: 10/27/2022]
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49
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Ren J, Shang T, Sherry AD, Malloy CR. Unveiling a hidden 31 P signal coresonating with extracellular inorganic phosphate by outer-volume-suppression and localized 31 P MRS in the human brain at 7T. Magn Reson Med 2018; 80:1289-1297. [PMID: 29427295 PMCID: PMC6085175 DOI: 10.1002/mrm.27121] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/22/2017] [Accepted: 01/15/2018] [Indexed: 01/19/2023]
Abstract
PURPOSE The study was undertaken to demonstrate that there is more than 1 component in the extracellular Pi31 P signal ( Piex) acquired from human head using nonlocalized 31 P MRS. METHODS Outer-volume-suppression (OVS) saturation and 1D/2D 31 P CSI were utilized to reveal the presence of an additional component in the Piex signal. RESULTS 67% of the head extracellular Pi signal was attenuated upon OVS saturation of the peripheral meningeal tissues, likely reflecting elimination of the Pi signal in the meningeal fluids (the blood and CSF). Localized 1D/2D CSI data provided further support for this assignment. Upon correction for the meningeal contribution, the extracellular Pi concentration was 0.51 ± 0.07 mM, whereas the intracellular Pi was 0.85 ± 0.10 mM. The extracellular pH was measured as 7.32 ± 0.04 when using OVS, as compared to 7.39 ± 0.03 when measured without OVS (N = 7 subjects). CONCLUSION The extracellular Pi signal acquired from the human head using nonlocalized 31 P MRS contains a significant component likely contributed by peripheral blood and CSF in meninges that must be removed in order to use this signal as an endogenous probe for measuring extracellular pH and other properties in the brain.
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Affiliation(s)
- Jimin Ren
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Ty Shang
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - A. Dean Sherry
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Chemistry, University of Texas at Dallas, Richardson, TX 75080
| | - Craig R. Malloy
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
- VA North Texas Health Care System, Dallas, TX 75216
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de Paula VS, Valente AP. A Dynamic Overview of Antimicrobial Peptides and Their Complexes. Molecules 2018; 23:molecules23082040. [PMID: 30111717 PMCID: PMC6222744 DOI: 10.3390/molecules23082040] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/05/2018] [Accepted: 08/09/2018] [Indexed: 01/06/2023] Open
Abstract
In this narrative review, we comprehensively review the available information about the recognition, structure, and dynamics of antimicrobial peptides (AMPs). Their complex behaviors occur across a wide range of time scales and have been challenging to portray. Recent advances in nuclear magnetic resonance and molecular dynamics simulations have revealed the importance of the molecular plasticity of AMPs and their abilities to recognize targets. We also highlight experimental data obtained using nuclear magnetic resonance methodologies, showing that conformational selection is a major mechanism of target interaction in AMP families.
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Affiliation(s)
- Viviane Silva de Paula
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Ana Paula Valente
- Centro de Biologia Estrutural e Bioimagem, Instituto de Bioquímica Médica, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil.
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