1
|
Zhu X, Shi Z, Mao Y, Lächelt U, Huang R. Cell Membrane Perforation: Patterns, Mechanisms and Functions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310605. [PMID: 38344881 DOI: 10.1002/smll.202310605] [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: 11/18/2023] [Revised: 12/21/2023] [Indexed: 02/21/2024]
Abstract
Cell membrane is crucial for the cellular activities, and any disruption to it may affect the cells. It is demonstrated that cell membrane perforation is associated with some biological processes like programmed cell death (PCD) and infection of pathogens. Specific developments make it a promising technique to perforate the cell membrane controllably and precisely. The pores on the cell membrane provide direct pathways for the entry and exit of substances, and can also cause cell death, which means reasonable utilization of cell membrane perforation is able to assist intracellular delivery, eliminate diseased or cancerous cells, and bring about other benefits. This review classifies the patterns of cell membrane perforation based on the mechanisms into 1) physical patterns, 2) biological patterns, and 3) chemical patterns, introduces the characterization methods and then summarizes the functions according to the characteristics of reversible and irreversible pores, with the aim of providing a comprehensive summary of the knowledge related to cell membrane perforation and enlightening broad applications in biomedical science.
Collapse
Affiliation(s)
- Xinran Zhu
- Key Laboratory of Smart Drug Delivery (Ministry of Education), Huashan Hospital, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Zhifeng Shi
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 201203, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 201203, China
| | - Ulrich Lächelt
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, 1090, Austria
| | - Rongqin Huang
- Key Laboratory of Smart Drug Delivery (Ministry of Education), Huashan Hospital, School of Pharmacy, Fudan University, Shanghai, 201203, China
| |
Collapse
|
2
|
Rissanou AN, Karatasos K. Effects of the structure of lipid-based agents in their complexation with a single stranded mRNA fragment: a computational study. SOFT MATTER 2022; 18:6229-6245. [PMID: 35904818 DOI: 10.1039/d2sm00403h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this work we employed fully atomistic molecular dynamics simulations, aiming towards a better understanding of the mechanisms associated with the formation and the stability of lipid-based RNA nanoassemblies, in an aqueous environment. We examined two groups of lipid-based complexation agents, differing in the degree of hydrophobicity and in the overall charge. The first group was comprised of cationic ionizable agents while the second included electrically neutral amphoteric phosphatidylcholine lipids. It was found that the overall charge of the complexation agents played the most decisive role in the energetics of the lipid/RNA association, while their degree of hydrophobicity affected their self-assembly and their complexation kinetics. The latter also affected the structural stability of the formed complexes since the water entrapped within the clusters of the less hydrophobic agents appeared to reduce the coherence of the lipid-RNA nanoassemblies. The combined effects of the aforementioned attributes dictated also the RNA conformation after complexation. The results from the present study provide thus new insight towards controlling the morphology, the energetic stability and the structural integrity of the formed complexes.
Collapse
Affiliation(s)
- Anastassia N Rissanou
- Department of Chemical Engineering, University of Thessaloniki, P.O. BOX 420, 54124 Thessaloniki, Greece.
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409, Heraklion, Crete, Greece.
| | - Kostas Karatasos
- Department of Chemical Engineering, University of Thessaloniki, P.O. BOX 420, 54124 Thessaloniki, Greece.
| |
Collapse
|
3
|
Paloncýová M, Čechová P, Šrejber M, Kührová P, Otyepka M. Role of Ionizable Lipids in SARS-CoV-2 Vaccines As Revealed by Molecular Dynamics Simulations: From Membrane Structure to Interaction with mRNA Fragments. J Phys Chem Lett 2021; 12:11199-11205. [PMID: 34761943 PMCID: PMC8609914 DOI: 10.1021/acs.jpclett.1c03109] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Recent advances in RNA-based medicine have provided new opportunities for the global current challenge, i.e., the COVID-19 pandemic. Novel vaccines are based on a messenger RNA (mRNA) motif with a lipid nanoparticle (LNP) vector, consisting of high content of unique pH-sensitive ionizable lipids (ILs). Here we provide molecular insights into the role of the ILs and lipid mixtures used in current mRNA vaccines. We observed that the lipid mixtures adopted a nonlamellar organization, with ILs separating into a very disordered, pH-sensitive phase. We describe structural differences of the two ILs leading to their different congregation, with implications for the vaccine stability. Finally, as RNA interacts preferentially with IL-rich phases located at the regions with high curvature of lipid phase, local changes in RNA flexibility and base pairing are induced by lipids. A proper atomistic understanding of RNA-lipid interactions may enable rational tailoring of LNP composition for efficient RNA delivery.
Collapse
Affiliation(s)
- Markéta Paloncýová
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Petra Čechová
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Martin Šrejber
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Petra Kührová
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Michal Otyepka
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
- IT4Innovations, VSB—Technical University of Ostrava, 17. listopadu 2172/15, 708 00 Ostrava-Poruba, Czech Republic
| |
Collapse
|
4
|
Rissanou AN, Ouranidis A, Karatasos K. Complexation of single stranded RNA with an ionizable lipid: an all-atom molecular dynamics simulation study. SOFT MATTER 2020; 16:6993-7005. [PMID: 32667026 DOI: 10.1039/d0sm00736f] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Complexation of a lipid-based ionizable cationic molecule (referred to as DML: see main text) with RNA in an aqueous medium was examined in detail by means of fully atomistic molecular dynamics simulations. The different stages of the DML-RNA association process were explored, while the structural characteristics of the final complex were described. The self-assembly process of the DML molecules was examined in the absence and in the presence of nucleotide sequences of different lengths. The formed DML clusters were described in detail in terms of their size and composition and were found to share common features in all the examined systems. Different timescales related to their self-assembly and their association with RNA were identified. It was found that beyond a time period of a few tens of ns, a conformationally stable DML-RNA complex was formed, characterized by DML clusters covering the entire contour of RNA. In a system with a 642-nucleotide sequence, the average size of the complex in the longest dimension was found to be close to 40 nm. The DML clusters were characterized by a rather low surface charge, while a propensity for the formation of larger size clusters close to RNA was noted. Apart from hydrophobic and electrostatic interactions, hydrogen bonding was found to play a key-role in the DML-DML and in the DML-RNA association. The information obtained regarding the structural features of the final complex, the timescales and the driving forces associated with the complexation and the self-assembly processes provide new insight towards a rational design of optimized lipid-based ionizable cationic gene delivery vectors.
Collapse
Affiliation(s)
- Anastassia N Rissanou
- Department of Chemical Engineering, University of Thessaloniki, P.O. BOX 420, 54124 Thessaloniki, Greece.
| | | | | |
Collapse
|
5
|
Badu S, Melnik R, Singh S. Mathematical and computational models of RNA nanoclusters and their applications in data-driven environments. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1804564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Shyam Badu
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Roderick Melnik
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
- BCAM-Basque Center for Applied Mathematics, Bilbao, Spain
| | - Sundeep Singh
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
| |
Collapse
|
6
|
Singh RP, Hidalgo T, Cazade PA, Darcy R, Cronin MF, Dorin I, O’Driscoll CM, Thompson D. Self-Assembled Cationic β-Cyclodextrin Nanostructures for siRNA Delivery. Mol Pharm 2019; 16:1358-1366. [DOI: 10.1021/acs.molpharmaceut.8b01307] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Tania Hidalgo
- School of Pharmacy, Cavanagh Pharmacy Building, University College Cork, Cork, Ireland
| | - Pierre-Andre Cazade
- Department of Physics, Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland
| | - Raphael Darcy
- School of Pharmacy, Cavanagh Pharmacy Building, University College Cork, Cork, Ireland
| | - Michael F. Cronin
- School of Pharmacy, Cavanagh Pharmacy Building, University College Cork, Cork, Ireland
| | - Irina Dorin
- Malvern Panalytical Ltd., Grovewood Road, Malvern, Worcestershire WR14 1XZ, U.K
| | | | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland
| |
Collapse
|
7
|
The Mechanism for siRNA Transmembrane Assisted by PMAL. Molecules 2018; 23:molecules23071586. [PMID: 29966273 PMCID: PMC6099945 DOI: 10.3390/molecules23071586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/10/2018] [Accepted: 06/19/2018] [Indexed: 11/29/2022] Open
Abstract
The capacity of silencing genes makes small interfering RNA (siRNA) appealing for curing fatal diseases. However, the naked siRNA is vulnerable to and degraded by endogenous enzymes and is too large and too negatively charged to cross cellular membranes. An effective siRNA carrier, PMAL (poly(maleic anhydride-alt-1-decene) substituted with 3-(dimethylamino) propylamine), has been demonstrated to be able to assist siRNA transmembrane by both experiments and molecular simulation. In the present work, the mechanism of siRNA transmembrane assisted by PMAL was studied using steered molecular dynamics simulations based on the martini coarse-grained model. Here two pulling rates, i.e., 10−6 and 10−5 nm·ps−1, were chosen to imitate the passive and active transport of siRNA, respectively. Potential of mean force (PMF) and interactions among siRNA, PMAL, and lipid bilayer membrane were calculated to describe the energy change during siRNA transmembrane processes at various conditions. It is shown that PMAL-assisted siRNA delivery is in the mode of passive transport. The PMAL can help siRNA insert into lipid bilayer membrane by lowering the energy barrier caused by siRNA and lipid bilayer membrane. PMAL prefers to remain in the lipid bilayer membrane and release siRNA. The above simulations establish a molecular insight of the interaction between siRNA and PMAL and are helpful for the design and applications of new carriers for siRNA delivery.
Collapse
|
8
|
Lu Y, Li J, Lu D. The mechanism for the complexation and dissociation between siRNA and PMAL: a molecular dynamics simulation study based on a coarse-grained model. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1350663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Yanfei Lu
- Key Laboratory of Industrial Biocatalysis, Chinese Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Jipeng Li
- Key Laboratory of Industrial Biocatalysis, Chinese Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Diannan Lu
- Key Laboratory of Industrial Biocatalysis, Chinese Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| |
Collapse
|
9
|
Ramezanpour M, Leung SSW, Delgado-Magnero KH, Bashe BYM, Thewalt J, Tieleman DP. Computational and experimental approaches for investigating nanoparticle-based drug delivery systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1688-709. [PMID: 26930298 DOI: 10.1016/j.bbamem.2016.02.028] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 02/20/2016] [Accepted: 02/23/2016] [Indexed: 12/21/2022]
Abstract
Most therapeutic agents suffer from poor solubility, rapid clearance from the blood stream, a lack of targeting, and often poor translocation ability across cell membranes. Drug/gene delivery systems (DDSs) are capable of overcoming some of these barriers to enhance delivery of drugs to their right place of action, e.g. inside cancer cells. In this review, we focus on nanoparticles as DDSs. Complementary experimental and computational studies have enhanced our understanding of the mechanism of action of nanocarriers and their underlying interactions with drugs, biomembranes and other biological molecules. We review key biophysical aspects of DDSs and discuss how computer modeling can assist in rational design of DDSs with improved and optimized properties. We summarize commonly used experimental techniques for the study of DDSs. Then we review computational studies for several major categories of nanocarriers, including dendrimers and dendrons, polymer-, peptide-, nucleic acid-, lipid-, and carbon-based DDSs, and gold nanoparticles. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
Collapse
Affiliation(s)
- M Ramezanpour
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - S S W Leung
- Department of Physics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - K H Delgado-Magnero
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - B Y M Bashe
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - J Thewalt
- Department of Physics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - D P Tieleman
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| |
Collapse
|