1
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Jordan J, Gibb CL, Tran T, Yao W, Rose A, Mague JT, Easson MW, Gibb BC. Anion Binding to Ammonium and Guanidinium Hosts: Implications for the Reverse Hofmeister Effects Induced by Lysine and Arginine Residues. J Org Chem 2024; 89:6877-6891. [PMID: 38662908 PMCID: PMC11110012 DOI: 10.1021/acs.joc.4c00242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024]
Abstract
Anions have a profound effect on the properties of soluble proteins. Such Hofmeister effects have implications in biologics stability, protein aggregation, amyloidogenesis, and crystallization. However, the interplay between the important noncovalent interactions (NCIs) responsible for Hofmeister effects is poorly understood. To contribute to improving this state of affairs, we report on the NCIs between anions and ammonium and guanidinium hosts 1 and 2, and the consequences of these. Specifically, we investigate the properties of cavitands designed to mimic two prime residues for anion-protein NCIs─lysines and arginines─and the solubility consequences of complex formation. Thus, we report NMR and ITC affinity studies, X-ray analysis, MD simulations, and anion-induced critical precipitation concentrations. Our findings emphasize the multitude of NCIs that guanidiniums can form and how this repertoire qualitatively surpasses that of ammoniums. Additionally, our studies demonstrate the ease by which anions can dispense with a fraction of their hydration-shell waters, rearrange those that remain, and form direct NCIs with the hosts. This raises many questions concerning how solvent shell plasticity varies as a function of anion, how the energetics of this impact the different NCIs between anions and ammoniums/guanidiniums, and how this affects the aggregation of solutes at high anion concentrations.
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Affiliation(s)
- Jacobs
H. Jordan
- The
Southern Regional Research Center, Agricultural Research Service, US Department of Agriculture, 1100 Allen Toussaint Blvd., New Orleans, Louisiana 70124, United States
| | - Corinne L.D. Gibb
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Thien Tran
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Wei Yao
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Austin Rose
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Joel T. Mague
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Michael W. Easson
- The
Southern Regional Research Center, Agricultural Research Service, US Department of Agriculture, 1100 Allen Toussaint Blvd., New Orleans, Louisiana 70124, United States
| | - Bruce C. Gibb
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
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2
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Liu Z, Cao X, Ma Z, Xu L, Wang L, Li J, Xiao M, Jiang X. Enhanced Sampling Molecular Dynamics Simulations Reveal Transport Mechanism of Glycoconjugate Drugs through GLUT1. Int J Mol Sci 2024; 25:5486. [PMID: 38791523 PMCID: PMC11122603 DOI: 10.3390/ijms25105486] [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: 04/17/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Glucose transporters GLUT1 belong to the major facilitator superfamily and are essential to human glucose uptake. The overexpression of GLUT1 in tumor cells designates it as a pivotal target for glycoconjugate anticancer drugs. However, the interaction mechanism of glycoconjugate drugs with GLUT1 remains largely unknown. Here, we employed all-atom molecular dynamics simulations, coupled to steered and umbrella sampling techniques, to examine the thermodynamics governing the transport of glucose and two glycoconjugate drugs (i.e., 6-D-glucose-conjugated methane sulfonate and 6-D-glucose chlorambucil) by GLUT1. We characterized the specific interactions between GLUT1 and substrates at different transport stages, including substrate recognition, transport, and releasing, and identified the key residues involved in these procedures. Importantly, our results described, for the first time, the free energy profiles of GLUT1-transporting glycoconjugate drugs, and demonstrated that H160 and W388 served as important gates to regulate their transport via GLUT1. These findings provide novel atomic-scale insights for understanding the transport mechanism of GLUT1, facilitating the discovery and rational design of GLUT1-targeted anticancer drugs.
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Affiliation(s)
- Zhuo Liu
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Xueting Cao
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Zhenyu Ma
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Limei Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Jian Li
- Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - Min Xiao
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
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3
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Bennett AL, Cranford KN, Bates AL, Sabatini CR, Lee HS. A molecular dynamics study of cell-penetrating peptide transportan-10 (TP10): Binding, folding and insertion to transmembrane state in zwitterionic membrane. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184218. [PMID: 37634858 PMCID: PMC10843101 DOI: 10.1016/j.bbamem.2023.184218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/05/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023]
Abstract
Transportan 10 (TP10) is a 21-residue, cationic, α-helical cell-penetrating peptide that can be used as a delivery vector for various bioactive molecules. Based on recent confocal microscopy studies, it is believed that TP10 can translocate across neutral lipid membrane passively, possibly as a monomer, without the formation of permanent pore. Here, we performed extensive molecular dynamics (MD) simulations of TP10W (Y3W variant of TP10) to find the microscopic details of binding, folding and insertion of TP10W to transmembrane state in POPC bilayer. Binding study with CHARMM36 force field showed that TP10W initially binds to the membrane surface in unstructured configuration, but it spontaneously folds into α-helical conformation under the lipid head groups. Further insertion of TP10W, changing from a surface bound state to a vertically oriented transmembrane state, was investigated via umbrella simulations. The resulting free energy profile shows a relatively small barrier between two states, suggesting a possible translocation pathway as a monomer. In fact, unbiased simulation of transmembrane TP10W revealed how a charged Lys side chain can move from one leaflet to the other without a significant free energy cost. Finally, we compared the results of TP10W simulations with those of point mutated variants (TP10W-K12A18 and TP10W-K19L) to understand the effect of charge distribution on the peptide. It was observed that such a conservative mutation can cause noticeable changes in the conformations of both surface bound and transmembrane states. The results of present study will be discussed in relation to the experimentally observed activities of TP10W against neutral membrane.
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Affiliation(s)
- Ashley L Bennett
- Department of Chemistry and Biochemistry, University of North Carolina, Wilmington, NC 28403, United States of America
| | - Kristen N Cranford
- Department of Chemistry and Biochemistry, University of North Carolina, Wilmington, NC 28403, United States of America
| | - Austin L Bates
- Department of Chemistry and Biochemistry, University of North Carolina, Wilmington, NC 28403, United States of America
| | - Christopher R Sabatini
- Department of Chemistry and Biochemistry, University of North Carolina, Wilmington, NC 28403, United States of America
| | - Hee-Seung Lee
- Department of Chemistry and Biochemistry, University of North Carolina, Wilmington, NC 28403, United States of America.
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4
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Jiang X, Patil NA, Xu Y, Wickremasinghe H, Zhou QT, Zhou F, Thompson PE, Wang L, Xiao M, Roberts KD, Velkov T, Li J. Structure-Interaction Relationship of Polymyxins with Lung Surfactant. J Med Chem 2023; 66:16109-16119. [PMID: 38019899 DOI: 10.1021/acs.jmedchem.3c01497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Multidrug-resistant Gram-negative bacteria present an urgent and formidable threat to the global public health. Polymyxins have emerged as a last-resort therapy against these 'superbugs'; however, their efficacy against pulmonary infection is poor. In this study, we integrated chemical biology and molecular dynamics simulations to examine how the alveolar lung surfactant significantly reduces polymyxin antibacterial activity. We discovered that lung surfactant is a phospholipid-based permeability barrier against polymyxins, compromising their efficacy against target bacteria. Next, we unraveled the structure-interaction relationship between polymyxins and lung surfactant, elucidating the thermodynamics that govern the penetration of polymyxins through this critical surfactant layer. Moreover, we developed a novel analog, FADDI-235, which exhibited potent activity against Gram-negative bacteria, both in the presence and absence of lung surfactant. These findings shed new light on the sequestration mechanism of lung surfactant on polymyxins and importantly pave the way for the rational design of new-generation lipopeptide antibiotics to effectively treat Gram-negative bacterial pneumonia.
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Affiliation(s)
- Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Nitin A Patil
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Yuwen Xu
- Shandong Institute for Food and Drug Control, Jinan 250000, China
| | - Hasini Wickremasinghe
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Qi Tony Zhou
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette 47907, United States of America
| | - Fanfan Zhou
- Faculty of Medicine and Health, Sydney Pharmacy School, The University of Sydney, Sydney 2006, Australia
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne 3052, Australia
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Min Xiao
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Kade D Roberts
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Tony Velkov
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne 3010, Australia
| | - Jian Li
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
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5
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Gori A, Lodigiani G, Colombarolli SG, Bergamaschi G, Vitali A. Cell Penetrating Peptides: Classification, Mechanisms, Methods of Study, and Applications. ChemMedChem 2023; 18:e202300236. [PMID: 37389978 DOI: 10.1002/cmdc.202300236] [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: 05/02/2023] [Revised: 06/28/2023] [Accepted: 06/28/2023] [Indexed: 07/02/2023]
Abstract
Cell-penetrating peptides (CPPs) encompass a class of peptides that possess the remarkable ability to cross cell membranes and deliver various types of cargoes, including drugs, nucleic acids, and proteins, into cells. For this reason, CPPs are largely investigated in drug delivery applications in the context of many diseases, such as cancer, diabetes, and genetic disorders. While sharing this functionality and some common structural features, such as a high content of positively charged amino acids, CPPs represent an extremely diverse group of elements, which can differentiate under many aspects. In this review, we summarize the most common characteristics of CPPs, introduce their main distinctive features, mechanistic aspects that drive their function, and outline the most widely used techniques for their structural and functional studies. We highlight current gaps and future perspectives in this field, which have the potential to significantly impact the future field of drug delivery and therapeutics.
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Affiliation(s)
- Alessandro Gori
- SCITEC - Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milano, Italy
| | - Giulia Lodigiani
- SCITEC - Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milano, Italy
| | - Stella G Colombarolli
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy, L.go F. Vito 1, 00168, Roma, Italy
| | - Greta Bergamaschi
- SCITEC - Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milano, Italy
| | - Alberto Vitali
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy, L.go F. Vito 1, 00168, Roma, Italy
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6
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Zakany F, Mándity IM, Varga Z, Panyi G, Nagy P, Kovacs T. Effect of the Lipid Landscape on the Efficacy of Cell-Penetrating Peptides. Cells 2023; 12:1700. [PMID: 37443733 PMCID: PMC10340183 DOI: 10.3390/cells12131700] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Every cell biological textbook teaches us that the main role of the plasma membrane is to separate cells from their neighborhood to allow for a controlled composition of the intracellular space. The mostly hydrophobic nature of the cell membrane presents an impenetrable barrier for most hydrophilic molecules larger than 1 kDa. On the other hand, cell-penetrating peptides (CPPs) are capable of traversing this barrier without compromising membrane integrity, and they can do so on their own or coupled to cargos. Coupling biologically and medically relevant cargos to CPPs holds great promise of delivering membrane-impermeable drugs into cells. If the cargo is able to interact with certain cell types, uptake of the CPP-drug complex can be tailored to be cell-type-specific. Besides outlining the major membrane penetration pathways of CPPs, this review is aimed at deciphering how properties of the membrane influence the uptake mechanisms of CPPs. By summarizing an extensive body of experimental evidence, we argue that a more ordered, less flexible membrane structure, often present in the very diseases planned to be treated with CPPs, decreases their cellular uptake. These correlations are not only relevant for understanding the cellular biology of CPPs, but also for rationally improving their value in translational or clinical applications.
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Affiliation(s)
- Florina Zakany
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (F.Z.); (Z.V.); (G.P.)
| | - István M. Mándity
- Department of Organic Chemistry, Faculty of Pharmacy, Semmelweis University, 1085 Budapest, Hungary;
- TTK Lendület Artificial Transporter Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Zoltan Varga
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (F.Z.); (Z.V.); (G.P.)
| | - Gyorgy Panyi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (F.Z.); (Z.V.); (G.P.)
| | - Peter Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (F.Z.); (Z.V.); (G.P.)
| | - Tamas Kovacs
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (F.Z.); (Z.V.); (G.P.)
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7
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Drexler CI, Cyran JD, Webb LJ. Lipid-Specific Direct Translocation of the Cell-Penetrating Peptide NAF-1 44-67 across Bilayer Membranes. J Phys Chem B 2023; 127:2002-2010. [PMID: 36827970 PMCID: PMC10127249 DOI: 10.1021/acs.jpcb.2c08076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
The cell-penetrating peptide NAF-1 has recently emerged as a promising candidate for selective penetration and destruction of cancer cells. It displays numerous membrane-selective behaviors including cell-specific uptake and organelle-specific degradation. In this work, we explore membrane penetration and translocation of NAF-1 in model lipid bilayer vesicles as a function of lipid identity in zwitterionic phosphatidylcholine lipids mixed with anionic phosphatidylserine, phosphatidylglycerol, and phosphatidic acid lipids. By monitoring the digestion of NAF-1 using the protease trypsin located inside but not outside the vesicles, we determined that the translocation of NAF-1 was significantly enhanced by the presence of phosphatidic acid in the membrane compared to the other three anionic or zwitterionic lipids. These findings were correlated to fluorescence measurements of dansyl-labeled NAF-1, which revealed whether noncovalent interactions between NAF-1 and the bilayer were most stable either at the membrane/solution interface or within the membrane interior. Phosphatidic acid promoted interactions with fatty acid tails, while phosphatidylcholine, phosphatidylserine, and phosphatidylglycerol stabilized interactions with polar lipid headgroups. Interfacial vibrational sum frequency spectroscopy experiments revealed that the phosphate moiety on phosphatidic acid headgroups was better hydrated than on the other three lipids, which helped to shuttle NAF-1 into the hydrophobic region. Our findings demonstrate that permeation does not depend on the net charge on phospholipid lipid headgroups in these model vesicles and suggest a model wherein NAF-1 crosses membranes selectively due to lipid-specific interactions at bilayer surfaces.
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Affiliation(s)
- Chad I Drexler
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jenée D Cyran
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Lauren J Webb
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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8
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Choe S. Translocation of a single Arg[Formula: see text] peptide across a DOPC/DOPG(4:1) model membrane using the weighted ensemble method. Sci Rep 2023; 13:1168. [PMID: 36670187 PMCID: PMC9860060 DOI: 10.1038/s41598-023-28493-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/19/2023] [Indexed: 01/21/2023] Open
Abstract
It is difficult to observe a spontaneous translocation of cell-penetrating peptides(CPPs) within a short time scale (e.g., a few hundred ns) in all-atom molecular dynamics(MD) simulations because the time required for the translocation of usual CPPs is on the order of minutes or so. In this work, we report a spontaneous translocation of a single Arg[Formula: see text](R9) across a DOPC/DOPG(4:1) model membrane within an order of a few tens ns scale by using the weighted ensemble(WE) method. We identify how water molecules and the orientation of Arg[Formula: see text] play a role in translocation. We also show how lipid molecules are transported along with Arg[Formula: see text]. In addition, we present free energy profiles of the translocation across the membrane using umbrella sampling and show that a single Arg[Formula: see text] translocation is energetically unfavorable. We expect that the WE method can help study interactions of CPPs with various model membranes within MD simulation approaches.
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Affiliation(s)
- Seungho Choe
- Department of Energy Science & Engineering, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, 42988 South Korea
- Energy Science & Engineering Research Center, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, 42988 South Korea
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9
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Jeong KJ, Jeong S, Lee S, Son CY. Predictive Molecular Models for Charged Materials Systems: From Energy Materials to Biomacromolecules. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2204272. [PMID: 36373701 DOI: 10.1002/adma.202204272] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/05/2022] [Indexed: 06/16/2023]
Abstract
Electrostatic interactions play a dominant role in charged materials systems. Understanding the complex correlation between macroscopic properties with microscopic structures is of critical importance to develop rational design strategies for advanced materials. But the complexity of this challenging task is augmented by interfaces present in the charged materials systems, such as electrode-electrolyte interfaces or biological membranes. Over the last decades, predictive molecular simulations that are founded in fundamental physics and optimized for charged interfacial systems have proven their value in providing molecular understanding of physicochemical properties and functional mechanisms for diverse materials. Novel design strategies utilizing predictive models have been suggested as promising route for the rational design of materials with tailored properties. Here, an overview of recent advances in the understanding of charged interfacial systems aided by predictive molecular simulations is presented. Focusing on three types of charged interfaces found in energy materials and biomacromolecules, how the molecular models characterize ion structure, charge transport, morphology relation to the environment, and the thermodynamics/kinetics of molecular binding at the interfaces is discussed. The critical analysis brings two prominent field of energy materials and biological science under common perspective, to stimulate crossover in both research field that have been largely separated.
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Affiliation(s)
- Kyeong-Jun Jeong
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, South Korea
| | - Seungwon Jeong
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, South Korea
| | - Sangmin Lee
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, South Korea
| | - Chang Yun Son
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, South Korea
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10
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Rajapaksha SP, Nawagamuwage SU. Anticorrelated position fluctuation of lipids in forming membrane water pores: molecular dynamics simulations study with dengue virus capsid protein. J Biomol Struct Dyn 2022; 40:11395-11404. [PMID: 34343444 DOI: 10.1080/07391102.2021.1958698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The traffic of molecules into or out of cells is regulated by many membrane-associated mechanisms. Membrane pores are considered as one of the major passage mechanisms, although molecular-level understanding of pore formation is still vague. The opening of a membrane pore depends on many factors, including the influence of some proteins. The ability of the cell-penetrating peptides and supercharged proteins to form membrane pores has been reported. We studied pore formation through dipalmitoylphosphatidylcholine (DPPC) lipid bilayers by supercharged dengue virus capsid (C) protein. Atomistic molecular dynamics simulations confirmed the formation of membrane pores by a combined effect of the C protein and the membrane electric field. Analyses of simulated trajectories showed highly correlated vertical position fluctuations between the Cα atom of the membrane-anchored arginine residues and the phosphorus atoms of the surrounding DPPC lipids. Certain regions of the bilayer were negatively correlated while the others were positively correlated with respect to the fluctuations of the Cα atom of the anchored arginine residues. When positively correlated lipids in one leaflet vertically aligned with the negatively correlated lipids in the other leaflet, a local anticorrelated region was generated by weakening the bilayer. The membrane pore was always formed close to this anticorrelated region. Once formed, the C protein followed the hydrated pathway provided by the water-filled pores to cross the membrane.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suneth P Rajapaksha
- Department of Chemistry, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Sithara U Nawagamuwage
- Department of Chemistry, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
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11
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Ouyang J, Sheng Y, Wang W. Recent Advances of Studies on Cell-Penetrating Peptides Based on Molecular Dynamics Simulations. Cells 2022; 11:cells11244016. [PMID: 36552778 PMCID: PMC9776715 DOI: 10.3390/cells11244016] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
With the ability to transport cargo molecules across cell membranes with low toxicity, cell-penetrating peptides (CPPs) have become promising candidates for next generation peptide-based drug delivery vectors. Over the past three decades since the first CPP was discovered, a great deal of work has been done on the cellular uptake mechanisms and the applications for the delivery of therapeutic molecules, and significant advances have been made. But so far, we still do not have a precise and unified understanding of the structure-activity relationship of the CPPs. Molecular dynamics (MD) simulations provide a method to reveal peptide-membrane interactions at the atomistic level and have become an effective complement to experiments. In this paper, we review the progress of the MD simulations on CPP-membrane interactions, including the computational methods and technical improvements in the MD simulations, the research achievements in the CPP internalization mechanism, CPP decoration and coupling, and the peptide-induced membrane reactions during the penetration process, as well as the comparison of simulated and experimental results.
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Affiliation(s)
- Jun Ouyang
- School of Public Courses, Bengbu Medical College, Bengbu 233030, China
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yuebiao Sheng
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- High Performance Computing Center, Nanjing University, Nanjing 210093, China
- Correspondence: (Y.S.); (W.W.)
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- Correspondence: (Y.S.); (W.W.)
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12
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Jiang X, Han M, Tran K, Patil NA, Ma W, Roberts KD, Xiao M, Sommer B, Schreiber F, Wang L, Velkov T, Li J. An Intelligent Strategy with All-Atom Molecular Dynamics Simulations for the Design of Lipopeptides against Multidrug-Resistant Pseudomonas aeruginosa. J Med Chem 2022; 65:10001-10013. [PMID: 35786900 DOI: 10.1021/acs.jmedchem.2c00657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Multidrug-resistant Gram-negative bacteria seriously threaten modern medicine due to the lack of efficacious therapeutic options. Their outer membrane (OM) is an essential protective fortress to exclude many antibiotics. Unfortunately, current structural biology methods are not able to resolve the membrane structure and it is difficult to examine the specific interaction between the OM and small molecules. These limitations hinder mechanistic understanding of antibiotic penetration through the OM and antibiotic discovery. Here, we developed biologically relevant OM models by quantitatively determining membrane lipidomics of Pseudomonas aeruginosa and elucidated how lipopolysaccharide modifications and OM vesicles mediated resistance to polymyxins. Supported by chemical biology and pharmacological assays, our multiscale molecular dynamics simulations provide an intelligent platform to quantify the membrane-penetrating thermodynamics of peptides and predict their antimicrobial activity. Through experimental validations with our in-house polymyxin analogue library, our computational strategy may have significant potential in accelerating the discovery of lipopeptides against bacterial "superbugs".
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Affiliation(s)
- Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Meiling Han
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Kevin Tran
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Nitin A Patil
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Wendong Ma
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Kade D Roberts
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Min Xiao
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Bjorn Sommer
- Department of Computer and Information Science, University of Konstanz, Konstanz 78457, Germany
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz 78457, Germany
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Tony Velkov
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne 3010, Australia
| | - Jian Li
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
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13
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Translocating Peptides of Biomedical Interest Obtained from the Spike (S) Glycoprotein of the SARS-CoV-2. MEMBRANES 2022; 12:membranes12060600. [PMID: 35736307 PMCID: PMC9229458 DOI: 10.3390/membranes12060600] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 02/01/2023]
Abstract
At the beginning of 2020, the pandemic caused by the SARS-CoV-2 virus led to the fast sequencing of its genome to facilitate molecular engineering strategies to control the pathogen’s spread. The spike (S) glycoprotein has been identified as the leading therapeutic agent due to its role in localizing the ACE2 receptor in the host’s pulmonary cell membrane, binding, and eventually infecting the cells. Due to the difficulty of delivering bioactive molecules to the intracellular space, we hypothesized that the S protein could serve as a source of membrane translocating peptides. AHB-1, AHB-2, and AHB-3 peptides were identified and analyzed on a membrane model of DPPC (dipalmitoylphosphatidylcholine) using molecular dynamics (MD) simulations. An umbrella sampling approach was used to quantify the energy barrier necessary to cross the boundary (13.2 to 34.9 kcal/mol), and a flat-bottom pulling helped to gain a deeper understanding of the membrane’s permeation dynamics. Our studies revealed that the novel peptide AHB-1 exhibited comparable penetration potential of already known potent cell-penetrating peptides (CPPs) such as TP2, Buforin II, and Frenatin 2.3s. Results were confirmed by in vitro analysis of the peptides conjugated to chitosan nanoparticles, demonstrating its ability to reach the cytosol and escape endosomes, while maintaining high biocompatibility levels according to standardized assays.
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14
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Cardenas AE, Drexler CI, Nechushtai R, Mittler R, Friedler A, Webb LJ, Elber R. Peptide Permeation across a Phosphocholine Membrane: An Atomically Detailed Mechanism Determined through Simulations and Supported by Experimentation. J Phys Chem B 2022; 126:2834-2849. [PMID: 35388695 PMCID: PMC9074375 DOI: 10.1021/acs.jpcb.1c10966] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell-penetrating peptides (CPPs) facilitate translocation across biological membranes and are of significant biological and medical interest. Several CPPs can permeate into specific cells and organelles. We examine the incorporation and translocation of a novel anticancer CPP in a dioleoylphosphatidylcholine (DOPC) lipid bilayer membrane. The peptide, NAF-144-67, is a short fragment of a transmembrane protein, consisting of hydrophobic N-terminal and charged C-terminal segments. Experiments using fluorescently labeled NAF-144-67 in ∼100 nm DOPC vesicles and atomically detailed simulations conducted with Milestoning support a model in which a significant barrier for peptide-membrane entry is found at the interface between the aqueous solution and membrane. The initial step is the insertion of the N-terminal segment and the hydrophobic helix into the membrane, passing the hydrophilic head groups. Both experiments and simulations suggest that the free energy difference in the first step of the permeation mechanism in which the hydrophobic helix crosses the phospholipid head groups is -0.4 kcal mol-1 slightly favoring motion into the membrane. Milestoning calculations of the mean first passage time and the committor function underscore the existence of an early polar barrier followed by a diffusive barrierless motion in the lipid tail region. Permeation events are coupled to membrane fluctuations that are examined in detail. Our study opens the way to investigate in atomistic resolution the molecular mechanism, kinetics, and thermodynamics of CPP permeation to diverse membranes.
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Affiliation(s)
- Alfredo E Cardenas
- Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Chad I Drexler
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Rachel Nechushtai
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 91904, Israel
| | - Ron Mittler
- The Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, Missouri 65201, United States
| | - Assaf Friedler
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 91904, Israel
| | - Lauren J Webb
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ron Elber
- Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas 78712, United States.,Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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15
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Li J, Kannan S, Aronica P, Brown CJ, Partridge AW, Verma CS. Molecular descriptors suggest stapling as a strategy for optimizing membrane permeability of cyclic peptides. J Chem Phys 2022; 156:065101. [DOI: 10.1063/5.0078025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jianguo Li
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix, Singapore 138671
- Singapore Eye Research Institute, Singapore 169856, Singapore
| | | | - Pietro Aronica
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix, Singapore 138671
| | | | - Anthony W. Partridge
- MSD International, Translation Medicine Research Centre, 8 Biomedical Grove, #04-01/05 Neuros Building, Singapore 138665, Singapore
| | - Chandra S. Verma
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix, Singapore 138671
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
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16
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Choe S. Free Energy Analyses of Cell-Penetrating Peptides Using the Weighted Ensemble Method. MEMBRANES 2021; 11:membranes11120974. [PMID: 34940475 PMCID: PMC8706838 DOI: 10.3390/membranes11120974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/27/2021] [Accepted: 12/01/2021] [Indexed: 12/22/2022]
Abstract
Cell-penetrating peptides (CPPs) have been widely used for drug-delivery agents; however, it has not been fully understood how they translocate across cell membranes. The Weighted Ensemble (WE) method, one of the most powerful and flexible path sampling techniques, can be helpful to reveal translocation paths and free energy barriers along those paths. Within the WE approach we show how Arg9 (nona-arginine) and Tat interact with a DOPC/DOPG(4:1) model membrane, and we present free energy (or potential mean of forces, PMFs) profiles of penetration, although a translocation across the membrane has not been observed in the current simulations. Two different compositions of lipid molecules were also tried and compared. Our approach can be applied to any CPPs interacting with various model membranes, and it will provide useful information regarding the transport mechanisms of CPPs.
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Affiliation(s)
- Seungho Choe
- Department of Energy Science & Engineering, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu 42988, Korea;
- Energy Science & Engineering Research Center, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu 42988, Korea
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17
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A Re-evaluation of the Free Energy Profiles for Cell-Penetrating Peptides Across DOPC Membranes. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10301-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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19
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Jiang X, Patil NA, Azad MAK, Wickremasinghe H, Yu H, Zhao J, Zhang X, Li M, Gong B, Wan L, Ma W, Thompson PE, Yang K, Yuan B, Schreiber F, Wang L, Velkov T, Roberts KD, Li J. A novel chemical biology and computational approach to expedite the discovery of new-generation polymyxins against life-threatening Acinetobacter baumannii. Chem Sci 2021; 12:12211-12220. [PMID: 34667587 PMCID: PMC8457388 DOI: 10.1039/d1sc03460j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/12/2021] [Indexed: 01/20/2023] Open
Abstract
Multidrug-resistant Gram-negative bacteria represent a major medical challenge worldwide. New antibiotics are desperately required with 'old' polymyxins often being the only available therapeutic option. Here, we systematically investigated the structure-activity relationship (SAR) of polymyxins using a quantitative lipidomics-informed outer membrane (OM) model of Acinetobacter baumannii and a series of chemically synthesized polymyxin analogs. By integrating chemical biology and all-atom molecular dynamics simulations, we deciphered how each residue of the polymyxin molecule modulated its conformational folding and specific interactions with the bacterial OM. Importantly, a novel designed polymyxin analog FADDI-287 with predicted stronger OM penetration showed improved in vitro antibacterial activity. Collectively, our study provides a novel chemical biology and computational strategy to expedite the discovery of new-generation polymyxins against life-threatening Gram-negative 'superbugs'.
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Affiliation(s)
- Xukai Jiang
- National Glycoengineering Research Center, Shandong University Qingdao China
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Nitin A Patil
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Mohammad A K Azad
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Hasini Wickremasinghe
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Heidi Yu
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Jinxin Zhao
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Xinru Zhang
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Mengyao Li
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Bin Gong
- School of Software, Shandong University Jinan China
| | - Lin Wan
- School of Software, Shandong University Jinan China
| | - Wendong Ma
- Centre for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University Suzhou China
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Science, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University Melbourne Australia
| | - Kai Yang
- Centre for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University Suzhou China
| | - Bing Yuan
- Centre for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University Suzhou China
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz Konstanz Germany
- Faculty of Information Technology, Monash University Melbourne Australia
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University Qingdao China
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, University of Melbourne Melbourne Australia
| | - Kade D Roberts
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Jian Li
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
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20
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Mineo S, Takahashi N, Yamada-Hara M, Tsuzuno T, Aoki-Nonaka Y, Tabeta K. Rice bran-derived protein fractions enhance sulforaphane-induced anti-oxidative activity in gingival epithelial cells. Arch Oral Biol 2021; 129:105215. [PMID: 34325345 DOI: 10.1016/j.archoralbio.2021.105215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/04/2021] [Accepted: 07/20/2021] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Food-derived bioactive peptides have been reported to exhibit various beneficial effects, including anti-microbial, anti-inflammatory, and anti-oxidant properties. Oxidative stress has been implicated in the development of several inflammatory diseases such as periodontal disease. However, the anti-oxidative effect of food-derived bioactive peptides in gingival epithelial cells (GECs) is unknown. Therefore, we examined the bioactivity of the peptides in GECs. DESIGN Food-derived peptide fractionations derived from rice bran, rice endosperm, corn, and soy were screened for anti-oxidative effects using anti-oxidant response element (ARE)-luciferase-transfected HEK 293 cells. The induction of anti-oxidation-related genes and proteins in GECs by the fractions were examined by quantitative PCR and Western blotting, respectively. Then, the fraction-mediated anti-oxidative effects were examined by measuring intracellular reactive oxygen species (ROS) levels using flow cytometry. Furthermore, the anti-oxidative response-related cellular signaling pathways were analyzed via Western blotting. RESULTS Although treatment with the food-derived peptides alone did not activate anti-oxidative responses, co-treatment with sulforaphane (SFN; a potent anti-oxidant) and certain food-derived peptides enhanced anti-oxidative responses in ARE-luciferase-transfected HEK 293 cells. The fractions augmented heme oxygenase-1 mRNA and protein expression in GECs. The percentage of ROS-positive cells was significantly decreased by co-treatment with SFN and peptide fractions derived from rice bran. Furthermore, the involvement of both nuclear factor erythroid 2-related factor 2 (Nrf2) and extracellular signal-regulated kinase (ERK) in the enhancement of anti-oxidative responses was demonstrated by Western blotting. CONCLUSIONS Peptides derived from rice bran enhances SFN-induced anti-oxidative responses in GECs through ERK-Nrf2-ARE signaling.
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Affiliation(s)
- Shuhei Mineo
- Division of Periodontology, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Naoki Takahashi
- Division of Periodontics, Niigata University Medical & Dental Hospital University Medical and Dental Hospital, 2-5274 Gakkocho-dori, Chuo-ku, 951-8514, Niigata, Japan.
| | - Miki Yamada-Hara
- Division of Periodontology, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan; Research Center for Advanced Oral Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Takahiro Tsuzuno
- Division of Periodontology, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yukari Aoki-Nonaka
- Division of Periodontology, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Koichi Tabeta
- Division of Periodontology, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
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21
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Jiang X, Yang K, Yuan B, Han M, Zhu Y, Roberts KD, Patil NA, Li J, Gong B, Hancock REW, Velkov T, Schreiber F, Wang L, Li J. Molecular dynamics simulations informed by membrane lipidomics reveal the structure-interaction relationship of polymyxins with the lipid A-based outer membrane of Acinetobacter baumannii. J Antimicrob Chemother 2021; 75:3534-3543. [PMID: 32911540 DOI: 10.1093/jac/dkaa376] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 08/04/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND MDR bacteria represent an urgent threat to human health globally. Polymyxins are a last-line therapy against life-threatening Gram-negative 'superbugs', including Acinetobacter baumannii. Polymyxins exert antimicrobial activity primarily via permeabilizing the bacterial outer membrane (OM); however, the mechanism of interaction between polymyxins and the OM remains unclear at the atomic level. METHODS We constructed a lipid A-based OM model of A. baumannii using quantitative membrane lipidomics data and employed all-atom molecular dynamics simulations with umbrella sampling techniques to elucidate the structure-interaction relationship and thermodynamics governing the penetration of polymyxins [B1 and E1 (i.e. colistin A) representing the two clinically used polymyxins] into the OM. RESULTS Polymyxin B1 and colistin A bound to the A. baumannii OM by the initial electrostatic interactions between the Dab residues of polymyxins and the phosphates of lipid A, competitively displacing the cations from the headgroup region of the OM. Both polymyxin B1 and colistin A formed a unique folded conformation upon approaching the hydrophobic centre of the OM, consistent with previous experimental observations. Polymyxin penetration induced reorientation of the headgroups of the OM lipids near the penetration site and caused local membrane disorganization, thereby significantly increasing membrane permeability and promoting the subsequent penetration of polymyxin molecules into the OM and periplasmic space. CONCLUSIONS The thermodynamics governing the penetration of polymyxins through the outer leaflet of the A. baumannii OM were examined and novel structure-interaction relationship information was obtained at the atomic and membrane level. Our findings will facilitate the discovery of novel polymyxins against MDR Gram-negative pathogens.
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Affiliation(s)
- Xukai Jiang
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Kai Yang
- Centre for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Bing Yuan
- Centre for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Meiling Han
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Yan Zhu
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Kade D Roberts
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Nitin A Patil
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Jingliang Li
- Institute for Frontier Materials, Deakin University, Geelong, Victoria, Australia
| | - Bin Gong
- School of Computer Science and Technology, Shandong University, Jinan, China
| | - Robert E W Hancock
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, University of Melbourne, Melbourne, Australia
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian Li
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
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22
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Morillas-Becerril L, Franco-Ulloa S, Fortunati I, Marotta R, Sun X, Zanoni G, De Vivo M, Mancin F. Specific and nondisruptive interaction of guanidium-functionalized gold nanoparticles with neutral phospholipid bilayers. Commun Chem 2021; 4:93. [PMID: 36697571 PMCID: PMC9814519 DOI: 10.1038/s42004-021-00526-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 05/05/2021] [Indexed: 01/28/2023] Open
Abstract
Understanding and controlling the interaction between nanoparticles and biological entities is fundamental to the development of nanomedicine applications. In particular, the possibility to realize nanoparticles capable of directly targeting neutral lipid membranes would be advantageous to numerous applications aiming at delivering nanoparticles and their cargos into cells and biological vesicles. Here, we use experimental and computational methodologies to analyze the interaction between liposomes and gold nanoparticles (AuNPs) featuring cationic headgroups in their protecting monolayer. We find that in contrast to nanoparticles decorated with other positively charged headgroups, guanidinium-coated AuNPs can bind to neutral phosphatidylcholine liposomes, inducing nondisruptive membrane permeabilization. Atomistic molecular simulations reveal that this ability is due to the multivalent H-bonding interaction between the phosphate residues of the liposome's phospholipids and the guanidinium groups. Our results demonstrate that the peculiar properties of arginine magic, an effect responsible for the membranotropic properties of some naturally occurring peptides, are also displayed by guanidinium-bearing functionalized AuNPs.
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Affiliation(s)
- Lucía Morillas-Becerril
- grid.5608.b0000 0004 1757 3470Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, Padova, Italy
| | - Sebastian Franco-Ulloa
- grid.25786.3e0000 0004 1764 2907Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa, Italy ,Present Address: Expert Analytics. Møllergata 8, Oslo, Norway
| | - Ilaria Fortunati
- grid.5608.b0000 0004 1757 3470Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, Padova, Italy
| | - Roberto Marotta
- grid.25786.3e0000 0004 1764 2907Electron Microscopy Facility (EMF), Istituto Italiano di Tecnologia, Via Morego 30, Genoa, Italy
| | - Xiaohuan Sun
- grid.268415.cSchool of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, Jiangsu People’s Republic of China
| | - Giordano Zanoni
- grid.5608.b0000 0004 1757 3470Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, Padova, Italy
| | - Marco De Vivo
- grid.25786.3e0000 0004 1764 2907Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa, Italy
| | - Fabrizio Mancin
- grid.5608.b0000 0004 1757 3470Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, Padova, Italy
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23
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Her Choong F, Keat Yap B. Cell-Penetrating Peptides: Correlation between Peptide-Lipid Interaction and Penetration Efficiency. Chemphyschem 2021; 22:493-498. [PMID: 33377300 DOI: 10.1002/cphc.202000873] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/28/2020] [Indexed: 12/27/2022]
Abstract
Cell-penetrating peptides are used in the delivery of peptides and biologics, with some cell-penetrating peptides found to be more efficient than others. The exact mechanism of how they interact with the cell membrane and penetrate it, however, remains unclear. This study attempts to investigate the difference in free energy profiles of three cell-penetrating peptides (TAT, CPP1 and CPP9) with a model lipid bilayer (DOPC) using molecular dynamics pulling simulations with umbrella sampling. Potential mean force (PMF) and free energy barrier between the peptides and DOPC are determined using WHAM analysis and MM-PBSA analysis, respectively. CPP9 is found to have the smallest PMF value, followed by CPP1 and TAT, consistent with the experimental data. YDEGE peptide, however, does not give the highest PMF value, although it is a non-cell-permeable peptide. YDEGE is also found to form water pores, alongside with TAT and CPP9, suggesting that it is difficult to distinguish true water pore formation from artefacts arising from pulling simulations. On the contrary, free energy analysis of the peptide-DOPC complex at the lipid-water interface with MM-PBSA provides results consistent with experimental data with CPP9 having the least interaction with DOPC and lowest free energy barrier, followed by CPP1, TAT and YDEGE. These findings suggest that peptide-lipid interaction at the lipid-water interface has a direct correlation with the penetration efficiency of peptides across the lipid bilayer.
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Affiliation(s)
- Fei Her Choong
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
| | - Beow Keat Yap
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
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24
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Albrecht C, Kuznetsov AS, Appert-Collin A, Dhaideh Z, Callewaert M, Bershatsky YV, Urban AS, Bocharov EV, Bagnard D, Baud S, Blaise S, Romier-Crouzet B, Efremov RG, Dauchez M, Duca L, Gueroult M, Maurice P, Bennasroune A. Transmembrane Peptides as a New Strategy to Inhibit Neuraminidase-1 Activation. Front Cell Dev Biol 2020; 8:611121. [PMID: 33392200 PMCID: PMC7772355 DOI: 10.3389/fcell.2020.611121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/27/2020] [Indexed: 12/31/2022] Open
Abstract
Sialidases, or neuraminidases, are involved in several human disorders such as neurodegenerative, infectious and cardiovascular diseases, and cancers. Accumulative data have shown that inhibition of neuraminidases, such as NEU1 sialidase, may be a promising pharmacological target, and selective inhibitors of NEU1 are therefore needed to better understand the biological functions of this sialidase. In the present study, we designed interfering peptides (IntPep) that target a transmembrane dimerization interface previously identified in human NEU1 that controls its membrane dimerization and sialidase activity. Two complementary strategies were used to deliver the IntPep into cells, either flanked to a TAT sequence or non-tagged for solubilization in detergent micelles. Combined with molecular dynamics simulations and heteronuclear nuclear magnetic resonance (NMR) studies in membrane-mimicking environments, our results show that these IntPep are able to interact with the dimerization interface of human NEU1, to disrupt membrane NEU1 dimerization and to strongly decrease its sialidase activity at the plasma membrane. In conclusion, we report here new selective inhibitors of human NEU1 of strong interest to elucidate the biological functions of this sialidase.
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Affiliation(s)
- Camille Albrecht
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Andrey S Kuznetsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Higher School of Economics, Moscow, Russia.,Moscow Institute of Physics and Technology, National Research University, Dolgoprudny, Russia
| | - Aline Appert-Collin
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Zineb Dhaideh
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Maïté Callewaert
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7312, Institut de Chimie Moléculaire de Reims, Reims, France
| | - Yaroslav V Bershatsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, National Research University, Dolgoprudny, Russia
| | - Anatoly S Urban
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, National Research University, Dolgoprudny, Russia
| | - Eduard V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, National Research University, Dolgoprudny, Russia
| | - Dominique Bagnard
- Université de Strasbourg, Strasbourg, France.,INSERM U1119 Biopathologie de la Myéline, Neuroprotection et Stratégies Thérapeutiques, Labex Medalis, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Stéphanie Baud
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Sébastien Blaise
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Béatrice Romier-Crouzet
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Roman G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Higher School of Economics, Moscow, Russia.,Moscow Institute of Physics and Technology, National Research University, Dolgoprudny, Russia
| | - Manuel Dauchez
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France.,Plateau de Modélisation Moléculaire Multi-échelle, Reims, France
| | - Laurent Duca
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Marc Gueroult
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Pascal Maurice
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Amar Bennasroune
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
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25
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Sinha S, Ghosh Dastidar S. Shifting Polar Residues Across Primary Sequence Frames of Transmembrane Domains Calibrates Membrane Permeation Thermodynamics. Biochemistry 2020; 59:4353-4366. [PMID: 33136366 DOI: 10.1021/acs.biochem.0c00536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Permeation of the mitochondrial outer membrane (MOM) using the transmembrane domains (TMDs) is the key step of the Bcl-2 family of proteins to control apoptosis. The primary sequences of the TMDs of the family members like Bcl-xL, Bcl-2, Bak, etc. indicate the presence of charged residues at the C-terminal tip to be essential for drilling the membrane. However, Bax, a variant of the same family, is an exception, as the charged residues are shifted away from the tip by two positional frames in the primary sequence, but does it matter really? The free energy landscapes of membrane permeation, computed from a total of ∼13.3 μs of conformational sampling, show how such shifting of the amino acid frames in the primary sequence is correlated with the energy landscape that ensures the balance between membrane permeation and cytosolic population. Shifting the charged residues back to the terminal, in suitable mutants of Bax, proves the necessity of terminal charged residues by improving the insertion free energy but adds a high energy barrier unless some other polar residues are adjusted further. The difference in the TMDs of Bcl-xL and Bax is also reflected in their mechanism to drill the MOM-like anionic membrane; only Bax-TMD requires surface crowding to favorably shape the permeation landscape by weakening the bilayer integrity. So, this investigation suggests that such proteins can calibrate the free energy landscape of membrane permeation by adjusting the positions of the charged or polar residues in the primary sequence frames, a strategy analogous to the game of the "sliding tile puzzle" but played with primary sequence frames.
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Affiliation(s)
- Souvik Sinha
- Division of Bioinformatics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata 700054, India
| | - Shubhra Ghosh Dastidar
- Division of Bioinformatics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata 700054, India
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26
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Jiang X, Yang K, Han ML, Yuan B, Li J, Gong B, Velkov T, Schreiber F, Wang L, Li J. Outer Membranes of Polymyxin-Resistant Acinetobacter baumannii with Phosphoethanolamine-Modified Lipid A and Lipopolysaccharide Loss Display Different Atomic-Scale Interactions with Polymyxins. ACS Infect Dis 2020; 6:2698-2708. [PMID: 32871077 DOI: 10.1021/acsinfecdis.0c00330] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Resistance to the last-line polymyxins is increasingly reported in multidrug-resistant Gram-negative pathogens, including Acinetobacter baumannii, which develops resistance via either lipid A modification (e.g., with phosphoethanolamine [pEtN]) or even lipopolysaccharide (LPS) loss in the outer membrane (OM). Considering these two different mechanisms, quantitative membrane lipidomics data were utilized to develop three OM models representing polymyxin-susceptible and -resistant A. baumannii strains. Through all-atom molecular simulations with enhanced sampling techniques, the effect of lipid A-pEtN modification and LPS loss on the action of colistin (i.e., polymyxin E) was examined for the first time, with a focus on the dynamics and energetics of colistin penetration into these OMs. Lipid A-pEtN modification improved the OM stability, impeding the penetration of colistin into the OM; this differed from the current literature that lipid A-pEtN modification confers resistance by diminishing the initial interaction with polymyxins. In contrast, the LPS deficiency significantly reduced the negative charges on the OM surface, diminishing the binding of colistin. Moreover, both lipid A-pEtN modification and LPS loss also constituted colistin resistance through disturbing the conformational transitions of the colistin molecule. Collectively, atomic-scale interactions between polymyxins and different bacterial OMs are very different and the findings may facilitate the discovery of new-generation polymyxins against Gram-negative 'superbugs'.
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Affiliation(s)
- Xukai Jiang
- Biomedicine Discovery Institute, Infection & Immunity Program, Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia
| | - Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Mei-Ling Han
- Biomedicine Discovery Institute, Infection & Immunity Program, Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia
| | - Bing Yuan
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Jingliang Li
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3217, Australia
| | - Bin Gong
- School of Software, Shandong University, Jinan 250101, China
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz 78467, Germany
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Jian Li
- Biomedicine Discovery Institute, Infection & Immunity Program, Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia
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27
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Jiang X, Yang K, Yuan B, Gong B, Wan L, Patil NA, Swarbrick JD, Roberts KD, Schreiber F, Wang L, Velkov T, Li J. Simulations of octapeptin-outer membrane interactions reveal conformational flexibility is linked to antimicrobial potency. J Biol Chem 2020; 295:15902-15912. [PMID: 32913118 DOI: 10.1074/jbc.ra120.014856] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/09/2020] [Indexed: 12/22/2022] Open
Abstract
The octapeptins are lipopeptide antibiotics that are structurally similar to polymyxins yet retain activity against polymyxin-resistant Gram-negative pathogens, suggesting they might be used to treat recalcitrant infections. However, the basis of their unique activity is unclear because of the difficulty in generating high-resolution experimental data of the interaction of antimicrobial peptides with lipid membranes. To elucidate these structure-activity relationships, we employed all-atom molecular dynamics simulations with umbrella sampling to investigate the conformational and energetic landscape of octapeptins interacting with bacterial outer membrane (OM). Specifically, we examined the interaction of octapeptin C4 and FADDI-115, lacking a single hydroxyl group compared with octapeptin C4, with the lipid A-phosphoethanolamine modified OM of Acinetobacter baumannii Octapeptin C4 and FADDI-115 both penetrated into the OM hydrophobic center but experienced different conformational transitions from an unfolded to a folded state that was highly dependent on the structural flexibility of their respective N-terminal fatty acyl groups. The additional hydroxyl group present in the fatty acyl group of octapeptin C4 resulted in the molecule becoming trapped in a semifolded state, leading to a higher free energy barrier for OM penetration. The free energy barrier for the translocation through the OM hydrophobic layer was ∼72 kcal/mol for octapeptin C4 and 62 kcal/mol for FADDI-115. Our results help to explain the lower antimicrobial activity previously observed for octapeptin C4 compared with FADDI-115 and more broadly improve our understanding of the structure-function relationships of octapeptins. These findings may facilitate the discovery of next-generation octapeptins against polymyxin-resistant Gram-negative 'superbugs.'
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Affiliation(s)
- Xukai Jiang
- Biomedicine Discovery Institute, Infection & Immunity Program, Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Bing Yuan
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Bin Gong
- School of Software, Shandong University, Jinan, China
| | - Lin Wan
- School of Software, Shandong University, Jinan, China
| | - Nitin A Patil
- Biomedicine Discovery Institute, Infection & Immunity Program, Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - James D Swarbrick
- Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Victoria, Australia
| | - Kade D Roberts
- Biomedicine Discovery Institute, Infection & Immunity Program, Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Tony Velkov
- Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Victoria, Australia.
| | - Jian Li
- Biomedicine Discovery Institute, Infection & Immunity Program, Department of Microbiology, Monash University, Melbourne, Victoria, Australia.
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28
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Yusheng S, Chenjun M, Yingying H, Tiantian W, Liefeng Z. Multifunctional nanoparticles of paclitaxel and cyclodextrin-polypeptide conjugates with in vitro anticancer activity. Pharm Dev Technol 2020; 25:1071-1080. [PMID: 32589088 DOI: 10.1080/10837450.2020.1787441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In this study, the cyclodextrin polypeptide (R8-CMβCD) was successfully synthesized by the conjugation of a cell-penetrating peptide (R8) with carboxymethyl-β-cyclodextrin (CMβCD) via the carbon diamine reaction. Then, paclitaxel-loaded nanoparticles (PTX@R8-CMβCD NPs) was prepared. Results of transmission electron microscopy (TEM) showed that PTX@R8-CMβCD NPs were spherical with smooth surfaces and an average diameter about 144 nm. The amount of PTX released from NPs was less than 20% at pH7.4, but it increased significantly to 80% in the weakly acidic cytoplasm of tumors (pH5.0). Furthermore, PTX@R8-CMβCD NPs promoted the cellular uptake of PTX. Further studies on the mechanism showed that cellular uptake of PTX@R8-CMβCD NPs could rely on multiple pathways. In addition, the NPs had the ability to inhibit P-gp efflux pumps. Cytotoxicity tests showed that the NPs had no side effects. Taken together, PTX@R8-CMβCD NPs is an effective anticancer drug delivery system, and the material (R8-CMβCD) may be a promising anti-cancer drug carrier.
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Affiliation(s)
- Sun Yusheng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Ma Chenjun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Hua Yingying
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Wei Tiantian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Zhang Liefeng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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29
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Cao Z, Liu L, Hu G, Bian Y, Li H, Wang J, Zhou Y. Interplay of hydrophobic and hydrophilic interactions in sequence-dependent cell penetration of spontaneous membrane-translocating peptides revealed by bias-exchange metadynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183402. [PMID: 32569587 DOI: 10.1016/j.bbamem.2020.183402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 06/14/2020] [Accepted: 06/16/2020] [Indexed: 12/29/2022]
Abstract
Spontaneous Membrane Translocating Peptides (SMTPs) can translocate silently across the bilayer and, thus, have the best potential to improve the delivery of therapeutic molecules to cells without toxicity. However, how their translocation mechanisms are affected by a specific peptide sequence remains poorly understood. Here, bias-exchange metadynamics simulations were employed to investigate the translocation mechanisms of five SMTPs with the same composition of amino acids (LLRLR, LRLLR, LLLRR, RLLLR, and LRLRL). Simulation results yield sequence-dependent free energy barrier using the FESs along the z-directional distance. An in-depth analysis of sequence-dependent interactions in different regions of the bilayers indicates that the free-energy barrier height of a specific sequence is resulted from the accessibility balance of isolated or clustered hydrophobic residues (L) and hydrophilic residues (R) that leads to different levels of resistance for moving of a peptide into the hydrophobic center of the membrane. At the maximal of the free-energy barrier, all peptides have a conformation parallel to the membrane surface with the barrier height determined by their affinity to the hydrophobic region. The appropriate bilayer perturbation and GDM+ pairing are beneficial for peptide translocation. These results provide an improved microscopic understanding of how peptide sequence influences the translocation efficiency and mechanism.
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Affiliation(s)
- Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Lei Liu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China; College of Information Management, Dezhou University, Dezhou 253023, China.
| | - Guodong Hu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Yunqiang Bian
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Haiyan Li
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China; College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Yaoqi Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China; Institute for Glycomics, School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, QLD 4222, Australia.
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30
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Luca S, Seal P, Parekh HS, Tupally KR, Smith SC. Cell Membrane Penetration without Pore Formation: Chameleonic Properties of Dendrimers in Response to Hydrophobic and Hydrophilic Environments. ADVANCED THEORY AND SIMULATIONS 2020. [DOI: 10.1002/adts.201900152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sergio Luca
- Integrated Materials Design LaboratoryDepartment of Applied MathematicsResearch School of PhysicsAustralian National University Acton ACT 2601 Australia
| | - Prasenjit Seal
- Department of ChemistryUniversity of Helsinki P.O. Box 55 (A.I. Virtasen aukio 1) Helsinki 00014 Finland
| | - Harendra S. Parekh
- School of PharmacyThe University of Queensland Brisbane QLD 4072 Australia
| | | | - Sean C. Smith
- Integrated Materials Design LaboratoryDepartment of Applied MathematicsResearch School of PhysicsAustralian National University Acton ACT 2601 Australia
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31
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Biovacc-19: A Candidate Vaccine for Covid-19 (SARS-CoV-2) Developed from Analysis of its General Method of Action for Infectivity. QRB DISCOVERY 2020; 1:e6. [PMID: 34192262 PMCID: PMC7468800 DOI: 10.1017/qrd.2020.8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 02/07/2023] Open
Abstract
This study presents the background, rationale and method of action of Biovacc-19, a candidate vaccine for corona virus disease 2019 (Covid-19), now in advanced preclinical development, which has already passed the first acute toxicity testing. Unlike conventionally developed vaccines, Biovacc-19’s method of operation is upon nonhuman-like (NHL) epitopes in 21.6% of the composition of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)’s spike protein, which displays distinct distributed charge including the presence of a charged furin-like cleavage site. The logic of the design of the vaccine is explained, which starts with empirical analysis of the aetiology of SARS-CoV-2. Mistaken assumptions about SARS-CoV-2’s aetiology risk creating ineffective or actively harmful vaccines, including the risk of antibody-dependent enhancement. Such problems in vaccine design are illustrated from past experience in the human immunodeficiency viruses domain. We propose that the dual effect general method of action of this chimeric virus’s spike, including receptor binding domain, includes membrane components other than the angiotensin-converting enzyme 2 receptor, which explains clinical evidence of its infectivity and pathogenicity. We show the nonreceptor dependent phagocytic general method of action to be specifically related to cumulative charge from insertions placed on the SARS-CoV-2 spike surface in positions to bind efficiently by salt bridge formations; and from blasting the spike we display the NHL epitopes from which Biovacc-19 has been down-selected.
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32
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Caparotta M, Bustos DM, Masone D. Order–disorder skewness in alpha-synuclein: a key mechanism to recognize membrane curvature. Phys Chem Chem Phys 2020; 22:5255-5263. [DOI: 10.1039/c9cp04951g] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Currently, membrane curvature is understood as an active mechanism to control cells spatial organization and activity.
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Affiliation(s)
- Marcelo Caparotta
- Facultad de Ciencias Exactas y Naturales
- Universidad Nacional de Cuyo (UNCuyo)
- Mendoza
- Argentina
| | - Diego M. Bustos
- Facultad de Ciencias Exactas y Naturales
- Universidad Nacional de Cuyo (UNCuyo)
- Mendoza
- Argentina
- Instituto de Histología y Embriología de Mendoza (IHEM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
- Universidad Nacional de Cuyo (UNCuyo)
- Mendoza
- Argentina
- Facultad de Ingeniería
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33
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Ruseska I, Zimmer A. Internalization mechanisms of cell-penetrating peptides. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2020; 11:101-123. [PMID: 31976201 PMCID: PMC6964662 DOI: 10.3762/bjnano.11.10] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 12/18/2019] [Indexed: 05/19/2023]
Abstract
In today's modern era of medicine, macromolecular compounds such as proteins, peptides and nucleic acids are dethroning small molecules as leading therapeutics. Given their immense potential, they are highly sought after. However, their application is limited mostly due to their poor in vivo stability, limited cellular uptake and insufficient target specificity. Cell-penetrating peptides (CPPs) represent a major breakthrough for the transport of macromolecules. They have been shown to successfully deliver proteins, peptides, siRNAs and pDNA in different cell types. In general, CPPs are basic peptides with a positive charge at physiological pH. They are able to translocate membranes and gain entry to the cell interior. Nevertheless, the mechanism they use to enter cells still remains an unsolved piece of the puzzle. Endocytosis and direct penetration have been suggested as the two major mechanisms used for internalization, however, it is not all black and white in the nanoworld. Studies have shown that several CPPs are able to induce and shift between different uptake mechanisms depending on their concentration, cargo or the cell line used. This review will focus on the major internalization pathways CPPs exploit, their characteristics and regulation, as well as some of the factors that influence the cellular uptake mechanism.
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Affiliation(s)
- Ivana Ruseska
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology and Biopharmacy, University of Graz, 8010 Graz, Austria
| | - Andreas Zimmer
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology and Biopharmacy, University of Graz, 8010 Graz, Austria
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34
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Abstract
Approximately 75% of all disease-relevant human proteins, including those involved in intracellular protein-protein interactions (PPIs), are undruggable with the current drug modalities (i.e., small molecules and biologics). Macrocyclic peptides provide a potential solution to these undruggable targets because their larger sizes (relative to conventional small molecules) endow them the capability of binding to flat PPI interfaces with antibody-like affinity and specificity. Powerful combinatorial library technologies have been developed to routinely identify cyclic peptides as potent, specific inhibitors against proteins including PPI targets. However, with the exception of a very small set of sequences, the vast majority of cyclic peptides are impermeable to the cell membrane, preventing their application against intracellular targets. This Review examines common structural features that render most cyclic peptides membrane impermeable, as well as the unique features that allow the minority of sequences to enter the cell interior by passive diffusion, endocytosis/endosomal escape, or other mechanisms. We also present the current state of knowledge about the molecular mechanisms of cell penetration, the various strategies for designing cell-permeable, biologically active cyclic peptides against intracellular targets, and the assay methods available to quantify their cell-permeability.
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Affiliation(s)
- Patrick G. Dougherty
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
| | - Ashweta Sahni
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
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35
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Adhikari S, Leissa JA, Karlsson AJ. Beyond function: Engineering improved peptides for therapeutic applications. AIChE J 2019. [DOI: 10.1002/aic.16776] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Sayanee Adhikari
- Department of Chemical and Biomolecular Engineering University of Maryland College Park Maryland
| | - Jesse A. Leissa
- Department of Chemical and Biomolecular Engineering University of Maryland College Park Maryland
| | - Amy J. Karlsson
- Department of Chemical and Biomolecular Engineering University of Maryland College Park Maryland
- Fischell Department of Bioengineering University of Maryland College Park Maryland
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36
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Reid LM, Verma CS, Essex JW. The role of molecular simulations in understanding the mechanisms of cell-penetrating peptides. Drug Discov Today 2019; 24:1821-1835. [DOI: 10.1016/j.drudis.2019.06.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/12/2019] [Accepted: 06/17/2019] [Indexed: 01/06/2023]
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37
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The Utilization of Cell-Penetrating Peptides in the Intracellular Delivery of Viral Nanoparticles. MATERIALS 2019; 12:ma12172671. [PMID: 31443361 PMCID: PMC6747576 DOI: 10.3390/ma12172671] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/16/2019] [Accepted: 08/21/2019] [Indexed: 01/04/2023]
Abstract
Viral particles (VPs) have evolved so as to efficiently enter target cells and to deliver their genetic material. The current state of knowledge allows us to use VPs in the field of biomedicine as nanoparticles that are safe, easy to manipulate, inherently biocompatible, biodegradable, and capable of transporting various cargoes into specific cells. Despite the fact that these virus-based nanoparticles constitute the most common vectors used in clinical practice, the need remains for further improvement in this area. The aim of this review is to discuss the potential for enhancing the efficiency and versatility of VPs via their functionalization with cell-penetrating peptides (CPPs), short peptides that are able to translocate across cellular membranes and to transport various substances with them. The review provides and describes various examples of and means of exploitation of CPPs in order to enhance the delivery of VPs into permissive cells and/or to allow them to enter a broad range of cell types. Moreover, it is possible that CPPs are capable of changing the immunogenic properties of VPs, which could lead to an improvement in their clinical application. The review also discusses strategies aimed at the modification of VPs by CPPs so as to create a useful cargo delivery tool.
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38
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Fathizadeh A, Kogan M, Anderson CM, Webb LJ, Elber R. Defect-Assisted Permeation Through a Phospholipid Membrane: Experimental and Computational Study of the Peptide WKW. J Phys Chem B 2019; 123:6792-6798. [PMID: 31304755 PMCID: PMC6687544 DOI: 10.1021/acs.jpcb.9b05414] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We investigate membrane permeation by the peptide WKW that is amidated at its C-terminus and therefore carries a positive charge of +2. To facilitate an efficient calculation, we introduce a novel set of simple coarse variables that measure permeation depth and membrane distortion. The phospholipid head groups shift toward the center of the membrane, following the permeating peptide, and create a defect that assists permeation. The Milestoning algorithm was used in the new coarse space to compute the free-energy profile and the mean first passage time. The barrier was lower than expected from a simple continuum estimate. This behavior is consistent with the known behavior of positively charged cell-penetrating peptides, and is explained by a detailed mechanism of defect formation and propagation revealed by the simulations.
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Affiliation(s)
- Arman Fathizadeh
- Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin. TX, 78712
| | - Molly Kogan
- Department of Chemistry, University of Texas at Austin, Austin TX, 78712
| | - Cari M. Anderson
- Department of Chemistry, University of Texas at Austin, Austin TX, 78712
| | - Lauren J. Webb
- Department of Chemistry, University of Texas at Austin, Austin TX, 78712
| | - Ron Elber
- Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin. TX, 78712
- Department of Chemistry, University of Texas at Austin, Austin TX, 78712
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39
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Quan X, Sun D, Zhou J. Molecular mechanism of HIV-1 TAT peptide and its conjugated gold nanoparticles translocating across lipid membranes. Phys Chem Chem Phys 2019; 21:10300-10310. [PMID: 31070638 DOI: 10.1039/c9cp01543d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The trans-acting activator of transcription (TAT) peptide, which is derived from human immunodeficiency virus-1 (HIV-1), has been widely used as an effective nanocarrier to transport extracellular substances into cells. However, the underlying translocation mechanism of TAT peptide across cell membranes still remains controversial. Besides, the molecular process of TAT peptide facilitating the transport of extracellular substances into cells is largely unknown. In this study, we explore the interactions of TAT peptides and their conjugated gold nanoparticles with lipid membranes by coarse-grained molecular dynamics simulations. It is found that the TAT peptides can hardly penetrate through the membrane at low peptide concentrations; after the concentration increases to a threshold value, they can cross the membrane through an induced nanopore due to the transmembrane electrostatic potential difference. The translocation of TAT peptides is mainly caused by the overall structural changes of membranes. Furthermore, we demonstrate that the translocation of gold nanoparticles (AuNPs) across the membrane is significantly affected by the number of grafted TAT peptides on the particle surface. The transmembrane efficiency of AuNPs may even be reduced when a small number of peptides modify them; whereas, when the number of grafted peptides increases to a certain value, the TAT-AuNP complex can translocate across the membrane in a pore-mediated way. Based on our findings, an effective strategy has been proposed to enhance the delivery efficiency of AuNPs. The present study can improve our understanding of the interactions between TAT peptides and cell membranes; it may also give some insightful suggestions on the design and development of nanocarriers with high efficiency for the delivery of nanoparticles and drugs.
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Affiliation(s)
- Xuebo Quan
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou, 510640, P. R. China.
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40
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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41
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Rivel T, Ramseyer C, Yesylevskyy S. The asymmetry of plasma membranes and their cholesterol content influence the uptake of cisplatin. Sci Rep 2019; 9:5627. [PMID: 30948733 PMCID: PMC6449338 DOI: 10.1038/s41598-019-41903-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 03/18/2019] [Indexed: 12/20/2022] Open
Abstract
The composition of the plasma membrane of malignant cells is thought to influence the cellular uptake of cisplatin and to take part in developing resistance to this widespread anti-cancer drug. In this work we study the permeation of cisplatin through the model membranes of normal and cancer cells using molecular dynamics simulations. A special attention is paid to lipid asymmetry and cholesterol content of the membranes. The loss of lipid asymmetry, which is common for cancer cells, leads to a decrease in their permeability to cisplatin by one order of magnitude in comparison to the membranes of normal cells. The change in the cholesterol molar ratio from 0% to 33% also decreases the permeability of the membrane by approximately one order of magnitude. The permeability of pure DOPC membrane is 5-6 orders of magnitude higher than one of the membranes with realistic lipid composition, which makes it as an inadequate model for the studies of drug permeability.
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Affiliation(s)
- Timothée Rivel
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030, Besançon, Cedex, France.
| | - Christophe Ramseyer
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030, Besançon, Cedex, France
| | - Semen Yesylevskyy
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030, Besançon, Cedex, France.,Department of Physics of Biological Systems, Institute of Physics of the National Academy of Sciences of Ukraine, Prospect Nauky 46, 03028, Kyiv, Ukraine
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42
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Gao X, Hong S, Liu Z, Yue T, Dobnikar J, Zhang X. Membrane potential drives direct translocation of cell-penetrating peptides. NANOSCALE 2019; 11:1949-1958. [PMID: 30644958 DOI: 10.1039/c8nr10447f] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cell-penetrating peptides (CPPs) are frequently employed as drug delivery agents with rapid cellular uptake, however, the uptake mechanism and the detailed translocation pathway are at present not completely understood. Both endocytosis and direct translocation through membrane pores have been observed in experiments and simulations under different conditions. Here we report the molecular dynamics simulations providing evidence for the direct translocation of CPPs across the membrane driven by the membrane electrostatic potential. The local membrane potential can be produced by the ion concentration imbalance across the membrane, which is ubiquitous in biological environments. Moreover, if positively charged CPPs are adsorbed on the membrane, this further enhances the membrane potential, opening membrane pores through which CPPs can be instantly transported in a chain-like configuration. The classical nucleation theory is applied to estimate the translocation time by calculating the changes in the free energy upon transferring CPPs across the membrane at different potentials, showing good agreement with available experimental measurements. The revealed CPP translocation mechanism can be broadly relevant for cellular processes in biology.
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Affiliation(s)
- Xinli Gao
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, China
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43
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Masone D, Bustos DM. Transmembrane domain dimerization induces cholesterol rafts in curved lipid bilayers. Phys Chem Chem Phys 2019; 21:268-274. [DOI: 10.1039/c8cp06783j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Are the dimerization of transmembrane (TM) domains and the reorganization of the lipid bilayer two independent events?
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Affiliation(s)
- Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
- Universidad Nacional de Cuyo (UNCuyo)
- Mendoza
- Argentina
- Facultad de Ingeniería
| | - Diego M. Bustos
- Instituto de Histología y Embriología de Mendoza (IHEM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
- Universidad Nacional de Cuyo (UNCuyo)
- Mendoza
- Argentina
- Facultad de Ciencias Exactas y Naturales
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44
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Anderson CM, Cardenas A, Elber R, Webb LJ. Preferential Equilibrium Partitioning of Positively Charged Tryptophan into Phosphatidylcholine Bilayer Membranes. J Phys Chem B 2018; 123:170-179. [PMID: 30481465 PMCID: PMC6331081 DOI: 10.1021/acs.jpcb.8b09872] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The interactions between small molecules
and lipid bilayers play
a critical role in the function of cellular membranes. Understanding
how a small molecule interacts with the lipid bilayer differently
based on its charge reveals primordial mechanisms of transport across
membranes and assists in the design of drug molecules that can penetrate
cells. We have previously reported that tryptophan permeated through
a phosphatidylcholine lipid bilayer membrane at a faster rate when
it was positively charged (Trp+) than when negatively charged (Trp−),
which corresponded to a lower potential of mean force (PMF) barrier
determined through simulations. In this report, we demonstrate that
Trp+ partitions into the lipid bilayer membrane to a greater degree
than Trp– by interacting with the ester linkage of a phosphatidylcholine
lipid, where it is stabilized by the electron withdrawing glycerol
functional group. These results are in agreement with tryptophan’s
known role as an anchor for transmembrane proteins, though the tendency
for binding of a positively charged tryptophan is surprising. We discuss
the implications of our results on the mechanisms of unassisted permeation
and penetration of small molecules within and across lipid bilayer
membranes based on molecular charge, shape, and molecular interactions
within the bilayer structure.
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45
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Liang H, Hu A, Chen X, Jin R, Wang K, Ke B, Nie Y. Structure optimization of dendritic lipopeptide based gene vectors with the assistance from molecular dynamic simulation. J Mater Chem B 2018; 7:915-926. [PMID: 32255097 DOI: 10.1039/c8tb02650e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Disulfide modified lipopeptide assemblies with an arginine-rich dendritic periphery provide a promising platform for effective gene transfer. Dendritic arginine peptides that mimic the cell-penetrating peptides of a virus envelope are vital for complexation, interaction with physical barriers, and final gene release. Here, we report three lipopeptides with different-generation dendritic peripheries (R1LS, R2LS and R3LS), each of which contains a dioleoyl-l-lysinate hydrophobic tail. Such molecules were proven to self-assemble in aqueous solution with different morphologies, sizes, and surface zeta potentials. R2LS and R3LS assemblies showed spherical and spindle shapes with zeta potentials of 27.2 and 32.8 mV, respectively. They exhibited complete condensation of pDNA at a low N/P ratio, while R1LS assemblies displayed a fiber pattern with a relatively low electric potential of 10.9 mV with poor DNA binding ability. In a cellular viability experiment, R1LS and R2LS have no significant cytotoxicity even at high dosage, while R3LS showed conspicuous toxicity. As a gene vector, R2LS presented high gene transfection efficiency either in the presence or the absence of serum, which was 58.7% greater than liposome 2000 and PEI in the condition of 10% fetal bovine serum for HeLa cells. While R3LS showed good results just without serum and R1LS was unserviceable in all situations. Moreover, molecular dynamic simulation was exploited to analyze the kinestate of the signal molecule and the interactions of multiple molecules, which could assist us in better understanding the experimental phenomena. The simulation results indicated that the R2LS molecule has better flexibility, which was favorable for interaction with the cell membrane. And it could generate tight integration in self-assembly while R1LS and R3LS assemblies have a large molecular interval, which led to a controllable release of cargos for R2LS in a reductive environment. In summary, the generation of the dendrimer in lipopeptides is vital for the gene transfer effect. For optimization, it is necessary to study the structure-function relationship, and molecular dynamic simulation is an effective strategy for screening the molecular structure and even for predicting experimental results.
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Affiliation(s)
- Hong Liang
- National Engineering Research Center for Biomaterials, Sichuan University, No. 29, Wangjiang Road, Chengdu 610064, P. R. China.
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46
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Via MA, Klug J, Wilke N, Mayorga LS, Del Pópolo MG. The interfacial electrostatic potential modulates the insertion of cell-penetrating peptides into lipid bilayers. Phys Chem Chem Phys 2018; 20:5180-5189. [PMID: 29393934 DOI: 10.1039/c7cp07243k] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cell-penetrating peptides (CPP) are short sequences of cationic amino-acids that show a surprising ability to traverse lipid bilayers. CPP are considered to be some of the most effective vectors to introduce membrane-impermeable cargos into cells, but the molecular basis of the membrane translocation mechanisms and its dependence on relevant membrane physicochemical properties have yet to be fully determined. In this paper we resort to Molecular Dynamics simulations and experiments to investigate how the electrostatic potential across the lipid/water interface affects the insertion of hydrophilic and amphipathic CPP into two-dimensional lipid structures. Simulations are used to quantify the effect of the transmembrane potential on the free-energy profile associated with the transfer of the CPP across a neutral lipid bilayer. It is found that the electrostatic bias has a relatively small effect on the binding of the peptides to the membrane surface, but that it significantly lowers the permeation barrier. A charge compensation mechanism, arising from the segregation of counter-ions while the peptide traverses the membrane, determines the shape and symmetry of the free-energy curves and underlines relevant mechanistic considerations. Langmuir monolayer experiments performed with a variety of amphiphiles model the incorporation of the CPP into the external membrane leaflet. It is shown that the dipole potential of the monolayer controls the extent of penetration of the CPP into the lipid aggregate, to a greater degree than its surface charge.
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Affiliation(s)
- Matías A Via
- CONICET & Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, CP5500, Argentina.
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47
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Vazdar M, Heyda J, Mason PE, Tesei G, Allolio C, Lund M, Jungwirth P. Arginine "Magic": Guanidinium Like-Charge Ion Pairing from Aqueous Salts to Cell Penetrating Peptides. Acc Chem Res 2018; 51:1455-1464. [PMID: 29799185 DOI: 10.1021/acs.accounts.8b00098] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
It is a textbook knowledge that charges of the same polarity repel each other. For two monovalent ions in the gas phase at a close contact this repulsive interaction amounts to hundreds of kilojoules per mole. In aqueous solutions, however, this Coulomb repulsion is strongly attenuated by a factor equal to the dielectric constant of the medium. The residual repulsion, which now amounts only to units of kilojoules per mole, may be in principle offset by attractive interactions. Probably the smallest cationic pair, where a combination of dispersion and cavitation forces overwhelms the Coulomb repulsion, consists of two guanidinium ions in water. Indeed, by a combination of molecular dynamics with electronic structure calculations and electrophoretic, as well as spectroscopic, experiments, we have demonstrated that aqueous guanidinium cations form (weakly) thermodynamically stable like-charge ion pairs. The importance of pairing of guanidinium cations in aqueous solutions goes beyond a mere physical curiosity, since it has significant biochemical implications. Guanidinium chloride is known to be an efficient and flexible protein denaturant. This is due to the ability of the orientationally amphiphilic guanidinium cations to disrupt various secondary structural motifs of proteins by pairing promiscuously with both hydrophobic and hydrophilic groups, including guanidinium-containing side chains of arginines. The fact that the cationic guanidinium moiety forms the dominant part of the arginine side chain implies that the like-charge ion pairing may also play a role for interactions between peptides and proteins. Indeed, arginine-arginine pairing has been frequently found in structural protein databases. In particular, when strengthened by a presence of negatively charged glutamate, aspartate, or C-terminal carboxylic groups, this binding motif helps to stabilize peptide or protein dimers and is also found in or near active sites of several enzymes. The like-charge pairing of the guanidinium side-chain groups may also hold the key to the understanding of the arginine "magic", that is, the extraordinary ability of arginine-rich polypeptides to passively penetrate across cellular membranes. Unlike polylysines, which are also highly cationic but lack the ease in crossing membranes, polyarginines do not exhibit mutual repulsion. Instead, they accumulate at the membrane, weaken it, and might eventually cross in a concerted, "train-like" manner. This behavior of arginine-rich cell penetrating peptides can be exploited when devising smart strategies how to deliver in a targeted way molecular cargos into the cell.
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Affiliation(s)
- Mario Vazdar
- Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technicka 5, 16628 Prague, Czech Republic
| | - Philip E. Mason
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
| | - Giulio Tesei
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Christoph Allolio
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Giv’at Ram, Jerusalem 9190401, Israel
| | - Mikael Lund
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
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48
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Alaybeyoglu B, Sariyar Akbulut B, Ozkirimli E. pVEC hydrophobic N-terminus is critical for antibacterial activity. J Pept Sci 2018; 24:e3083. [DOI: 10.1002/psc.3083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/08/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Begum Alaybeyoglu
- Chemical Engineering Department; Bogazici University; Bebek 34342 Istanbul Turkey
| | | | - Elif Ozkirimli
- Chemical Engineering Department; Bogazici University; Bebek 34342 Istanbul Turkey
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49
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Grasso G, Muscat S, Rebella M, Morbiducci U, Audenino A, Danani A, Deriu MA. Cell penetrating peptide modulation of membrane biomechanics by Molecular dynamics. J Biomech 2018; 73:137-144. [PMID: 29631749 DOI: 10.1016/j.jbiomech.2018.03.036] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/14/2018] [Accepted: 03/21/2018] [Indexed: 11/17/2022]
Abstract
The efficacy of a pharmaceutical treatment is often countered by the inadequate membrane permeability, that prevents drugs from reaching their specific intracellular targets. Cell penetrating peptides (CPPs) are able to route across cells' membrane various types of cargo, including drugs and nanoparticles. However, CPPs internalization mechanisms are not yet fully understood and depend on a wide variety of aspects. In this contest, the entry of a CPP into the lipid bilayer might induce molecular conformational changes, including marked variations on membrane's mechanical properties. Understanding how the CPP does influence the mechanical properties of cells membrane is crucial to design, engineer and improve new and existing penetrating peptides. Here, all atom Molecular Dynamics (MD) simulations were used to investigate the interaction between different types of CPPs embedded in a lipid bilayer of dioleoyl phosphatidylcholine (DOPC). In a greater detail, we systematically highlighted how CPP properties are responsible for modulating the membrane bending modulus. Our findings highlighted the CPP hydropathy strongly correlated with penetration of water molecules in the lipid bilayer, thus supporting the hypothesis that the amount of water each CPP can route inside the membrane is modulated by the hydrophobic and hydrophilic character of the peptide. Water penetration promoted by CPPs leads to a local decrease of the lipid order, which emerges macroscopically as a reduction of the membrane bending modulus.
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Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, Manno CH-6928, Switzerland
| | - Stefano Muscat
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy
| | - Martina Rebella
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy
| | - Alberto Audenino
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy
| | - Andrea Danani
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, Manno CH-6928, Switzerland
| | - Marco A Deriu
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, Manno CH-6928, Switzerland.
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50
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Cao Z, Bian Y, Hu G, Zhao L, Kong Z, Yang Y, Wang J, Zhou Y. Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids. Int J Mol Sci 2018; 19:E885. [PMID: 29547563 PMCID: PMC5877746 DOI: 10.3390/ijms19030885] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/11/2018] [Accepted: 03/12/2018] [Indexed: 11/16/2022] Open
Abstract
Thermodynamics of the permeation of amino acids from water to lipid bilayers is an important first step for understanding the mechanism of cell-permeating peptides and the thermodynamics of membrane protein structure and stability. In this work, we employed bias-exchange metadynamics simulations to simulate the membrane permeation of all 20 amino acids from water to the center of a dipalmitoylphosphatidylcholine (DPPC) membrane (consists of 256 lipids) by using both directional and torsion angles for conformational sampling. The overall accuracy for the free energy profiles obtained is supported by significant correlation coefficients (correlation coefficient at 0.5-0.6) between our results and previous experimental or computational studies. The free energy profiles indicated that (1) polar amino acids have larger free energy barriers than nonpolar amino acids; (2) negatively charged amino acids are the most difficult to enter into the membrane; and (3) conformational transitions for many amino acids during membrane crossing is the key for reduced free energy barriers. These results represent the first set of simulated free energy profiles of membrane crossing for all 20 amino acids.
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Affiliation(s)
- Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Yunqiang Bian
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Guodong Hu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Liling Zhao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Zhenzhen Kong
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Life Science, Shandong Normal University, Jinan 250014, China.
| | - Yuedong Yang
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, QLD 4222, Australia.
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou 510275, China.
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Yaoqi Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, QLD 4222, Australia.
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