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Ma J, Wehrle J, Frank D, Lorenzen L, Popp C, Driever W, Grosse R, Jessen HJ. Intracellular delivery and deep tissue penetration of nucleoside triphosphates using photocleavable covalently bound dendritic polycations. Chem Sci 2024; 15:6478-6487. [PMID: 38699261 PMCID: PMC11062083 DOI: 10.1039/d3sc05669d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/15/2024] [Indexed: 05/05/2024] Open
Abstract
Nucleoside triphosphates (NTPs) are essential in various biological processes. Cellular or even organismal controlled delivery of NTPs would be highly desirable, yet in cellulo and in vivo applications are hampered owing to their negative charge leading to cell impermeability. NTP transporters or NTP prodrugs have been developed, but a spatial and temporal control of the release of the investigated molecules remains challenging with these strategies. Herein, we describe a general approach to enable intracellular delivery of NTPs using covalently bound dendritic polycations, which are derived from PAMAM dendrons and their guanidinium derivatives. By design, these modifications are fully removable through attachment on a photocage, ready to deliver the native NTP upon irradiation enabling spatiotemporal control over nucleotide release. We study the intracellular distribution of the compounds depending on the linker and dendron generation as well as side chain modifications. Importantly, as the polycation is bound covalently, these molecules can also penetrate deeply into the tissue of living organisms, such as zebrafish.
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Affiliation(s)
- Jiahui Ma
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg Albertstr. 21 79104 Freiburg Germany
- CIBSS-Centre for Integrative Biological Signaling Studies, University of Freiburg 79104 Freiburg Germany
| | - Johanna Wehrle
- CIBSS-Centre for Integrative Biological Signaling Studies, University of Freiburg 79104 Freiburg Germany
- Faculty of Biology, University of Freiburg Hauptstr. 1 79104 Freiburg Germany
| | - Dennis Frank
- CIBSS-Centre for Integrative Biological Signaling Studies, University of Freiburg 79104 Freiburg Germany
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg Albertstr. 25 79104 Freiburg Germany
| | - Lina Lorenzen
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg Albertstr. 25 79104 Freiburg Germany
| | - Christoph Popp
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg Albertstr. 21 79104 Freiburg Germany
| | - Wolfgang Driever
- CIBSS-Centre for Integrative Biological Signaling Studies, University of Freiburg 79104 Freiburg Germany
- Faculty of Biology, University of Freiburg Hauptstr. 1 79104 Freiburg Germany
| | - Robert Grosse
- CIBSS-Centre for Integrative Biological Signaling Studies, University of Freiburg 79104 Freiburg Germany
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg Albertstr. 25 79104 Freiburg Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg Albertstr. 21 79104 Freiburg Germany
- CIBSS-Centre for Integrative Biological Signaling Studies, University of Freiburg 79104 Freiburg Germany
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2
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Singh D, Singh L, Kaur S, Arora A. Nucleic acids based integrated macromolecular complexes for SiRNA delivery: Recent advancements. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-24. [PMID: 38693628 DOI: 10.1080/15257770.2024.2347499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/18/2024] [Indexed: 05/03/2024]
Abstract
The therapeutic potential of small interfering RNA (siRNA) is monumental, offering a pathway to silence disease-causing genes with precision. However, the delivery of siRNA to target cells in-vivo remains a formidable challenge, owing to degradation by nucleases, poor cellular uptake and immunogenicity. This overview examines recent advancements in the design and application of nucleic acid-based integrated macromolecular complexes for the efficient delivery of siRNA. We dissect the innovative delivery vectors developed in recent years, including lipid-based nanoparticles, polymeric carriers, dendrimer complexes and hybrid systems that incorporate stimuli-responsive elements for targeted and controlled release. Advancements in bioconjugation techniques, active targeting strategies and nanotechnology-enabled delivery platforms are evaluated for their contribution to enhancing siRNA delivery. It also addresses the complex interplay between delivery system design and biological barriers, highlighting the dynamic progress and remaining hurdles in translating siRNA therapies from bench to bedside. By offering a comprehensive overview of current strategies and emerging technologies, we underscore the future directions and potential impact of siRNA delivery systems in personalized medicine.
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Affiliation(s)
- Dilpreet Singh
- University Institute of Pharma Sciences, Chandigarh University, Mohali, India
- University Centre for Research and Development, Chandigarh University, Mohali, India
| | - Lovedeep Singh
- University Institute of Pharma Sciences, Chandigarh University, Mohali, India
| | - Simranjeet Kaur
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab, India
| | - Akshita Arora
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab, India
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3
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Wong KH, Guo Z, Law MK, Chen M. Functionalized PAMAM constructed nanosystems for biomacromolecule delivery. Biomater Sci 2023; 11:1589-1606. [PMID: 36692071 DOI: 10.1039/d2bm01677j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Polyamidoamines (PAMAMs) are a class of dendrimer with monodispersity and controlled topology, which can deliver biologically active macromolecules (e.g., genes and proteins) to specific regions with high efficiency and minimum side effects. In detail, PAMAMs can be functionalized easily by core modification or surface amendment to encapsulate a wide range of biomacromolecules. Besides, self-assembled, cross-linked and hybrid PAMAMs with customized therapeutic purposes are developed as delivery vehicles, which makes PAMAMs promising for biomacromolecule therapy. In this review, we comprehensively summarize the application of PAMAMs in biomacromolecule delivery from the synthesis of functionalized PAMAM carriers to the development of PAMAM-based drug delivery systems. The underlying strategies for PAMAM functionalization and assembly are first systematically discussed, and then the current applications of PAMAMs for biomacromolecule delivery are reviewed. Finally, a brief perspective on the further applications of PAMAMs concludes, aiming to provide insights into developing PAMAM-based biomacromolecule delivery systems.
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Affiliation(s)
- Ka Hong Wong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau SAR, China.
| | - Zhaopei Guo
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau SAR, China.
| | - Man-Kay Law
- State Key Laboratory of Analog and Mixed-Signal VLSI, IME and FST-ECE, University of Macau, Macau SAR, China
| | - Meiwan Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau SAR, China.
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4
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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.
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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.
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5
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Cationic Dendrimers for siRNA Delivery: Computational Approaches for Characterization. Methods Mol Biol 2021. [PMID: 33928581 DOI: 10.1007/978-1-0716-1298-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Nowadays, computer simulations have been established as a fundamental tool in the design and development of new dendrimer-based nanocarriers for drug and gene delivery. Moreover, the level of detail contained in the information that can be gathered by performing atomistic-scale simulations cannot be obtained with any other available experimental technique. In this chapter we describe the main computational toolbox that can be exploited in the different stages of novel dendritic nanocarrier production-from the initial conception to the stage of biological intermolecular interactions.
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6
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Gupta S, Biswas P. Conformational properties of complexes of poly(propylene imine) dendrimers with linear polyelectrolytes in dilute solutions. J Chem Phys 2020; 153:194902. [PMID: 33218232 DOI: 10.1063/5.0030270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
This study investigates the conformational properties of complexes of poly(propylene imine) dendrimers with a linear polyelectrolyte (LPE) at neutral pH in an aqueous solution via molecular dynamics simulations. Various conformational properties, such as the atomic density profile, counterion density distribution, charge distribution, cavity volume, and the static structure factor are studied as a function of the charge and chain length of the LPE. The lower generation dendrimer complexes encapsulate the shorter linear PE chains, while the longer PE chains are adsorbed on the dendrimer surface that screen the surface charge and prevent the penetration of the counterions and water molecules. However, the overall charge of the higher generation dendrimers is not neutralized by the charge of the PE chains, which results in chloride counterion penetration within the dendrimers. The adsorption of the PE chains on the dendrimers is also verified from the charge distribution of the dendrimer-PE complexes. The charge on the lower generation dendrimer complexes is overcompensated by the longer PE chains resulting in an overall negative charge on the complexes, while the PE chains do not completely neutralize the charge of the higher generation dendrimers and produce positively charged complexes. The results of the structure factor indicate a conformational transition of the dendrimer-PE complexes from a dense compact structure to an open one with an increase in the PE chain length. This transition is characterized by an increase in the cavity volume in dendrimers with an increase in the PE chain length.
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Affiliation(s)
- Shilpa Gupta
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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7
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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.
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Affiliation(s)
- Anastassia N Rissanou
- Department of Chemical Engineering, University of Thessaloniki, P.O. BOX 420, 54124 Thessaloniki, Greece.
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8
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Pantatosaki E, Papadopoulos GK. Binding Dynamics of siRNA with Selected Lipopeptides: A Computer-Aided Study of the Effect of Lipopeptides' Functional Groups and Stereoisomerism. J Chem Theory Comput 2020; 16:3842-3855. [PMID: 32324997 DOI: 10.1021/acs.jctc.9b01261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The engineering issues pertaining to nanoparticle systems toward targeted gene therapies have not been fully probed. Recent experiments have identified specific structural characteristics of a novel class of lipopeptides (LP) that may lead to potent nanocarriers intended as RNAi therapeutics, albeit the molecular mechanism that underlies their performance remains unexplored. We conducted molecular dynamics simulations in atomistic detail coupled with free energy computations to study the dynamics and thermodynamics of an acrylate- and an epoxide-derived LP, members of the aforesaid class, upon their binding to siRNA in aqueous solution aiming at examining structure-potency relations. We found that the entropic part of the free energy of binding predominates; moreover, the first LP class tends to disrupt the Watson-Crick base pairing of siRNA, whereas the latter leaves the double helix intact. Moreover, the identified tug-of-war effect between LP-water and LP-siRNA hydrogen bonding in the supramolecular complex can underpin synthesis routes toward tuning the association dynamics. Our simulations on two diastereomers of the epoxide-derived LP showed significant structural and energetics differences upon binding, as a result of steric effects imposed by the different absolute configurations at their chiral centers. These findings may serve as crucial design parameters toward modulating the interplay between complex stability and ease of releasing the nucleic acid drug into the cell.
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Affiliation(s)
- Evangelia Pantatosaki
- School of Chemical Engineering, National Technical University of Athens, 15780 Athens, Greece
| | - George K Papadopoulos
- School of Chemical Engineering, National Technical University of Athens, 15780 Athens, Greece.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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9
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Avila-Salas F, González RI, Ríos PL, Araya-Durán I, Camarada MB. Effect of the Generation of PAMAM Dendrimers on the Stabilization of Gold Nanoparticles. J Chem Inf Model 2020; 60:2966-2976. [DOI: 10.1021/acs.jcim.0c00052] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Fabián Avila-Salas
- Centro de Nanotecnologı́a Aplicada, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
- Núcleo de Quı́mica y Bioquímica, Facultad de Estudios Interdisciplinarios, Universidad Mayor, Santiago 8580745, Chile
| | - Rafael I. González
- Centro de Nanotecnologı́a Aplicada, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
- Center for the Development of Nanoscience and Nanotechnology—CEDENNA, Santiago 9170124, Chile
| | - Paulina L. Ríos
- Centro de Nanotecnologı́a Aplicada, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| | - Ingrid Araya-Durán
- Centro de Nanotecnologı́a Aplicada, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| | - María B. Camarada
- Centro de Nanotecnologı́a Aplicada, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
- Núcleo de Quı́mica y Bioquímica, Facultad de Estudios Interdisciplinarios, Universidad Mayor, Santiago 8580745, Chile
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10
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Evolution from Covalent to Self-Assembled PAMAM-Based Dendrimers as Nanovectors for siRNA Delivery in Cancer by Coupled In Silico-Experimental Studies. Part I: Covalent siRNA Nanocarriers. Pharmaceutics 2019; 11:pharmaceutics11070351. [PMID: 31323863 PMCID: PMC6680565 DOI: 10.3390/pharmaceutics11070351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/10/2019] [Accepted: 07/16/2019] [Indexed: 12/28/2022] Open
Abstract
Small interfering RNAs (siRNAs) represent a new approach towards the inhibition of gene expression; as such, they have rapidly emerged as promising therapeutics for a plethora of important human pathologies including cancer, cardiovascular diseases, and other disorders of a genetic etiology. However, the clinical translation of RNA interference (RNAi) requires safe and efficient vectors for siRNA delivery into cells. Dendrimers are attractive nanovectors to serve this purpose, as they present a unique, well-defined architecture and exhibit cooperative and multivalent effects at the nanoscale. This short review presents a brief introduction to RNAi-based therapeutics, the advantages offered by dendrimers as siRNA nanocarriers, and the remarkable results we achieved with bio-inspired, structurally flexible covalent dendrimers. In the companion paper, we next report our recent efforts in designing, characterizing and testing a series of self-assembled amphiphilic dendrimers and their related structural alterations to achieve unprecedented efficient siRNA delivery both in vitro and in vivo.
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11
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Laurini E, Marson D, Aulic S, Fermeglia M, Pricl S. Evolution from Covalent to Self-Assembled PAMAM-Based Dendrimers as Nanovectors for siRNA Delivery in Cancer by Coupled in Silico-Experimental Studies. Part II: Self-Assembled siRNA Nanocarriers. Pharmaceutics 2019; 11:pharmaceutics11070324. [PMID: 31295912 PMCID: PMC6680776 DOI: 10.3390/pharmaceutics11070324] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 01/07/2023] Open
Abstract
In part I of this review, the authors showed how poly(amidoamine) (PAMAM)-based dendrimers can be considered as promising delivering platforms for siRNA therapeutics. This is by virtue of their precise and unique multivalent molecular architecture, characterized by uniform branching units and a plethora of surface groups amenable to effective siRNA binding and delivery to e.g., cancer cells. However, the successful clinical translation of dendrimer-based nanovectors requires considerable amounts of good manufacturing practice (GMP) compounds in order to conform to the guidelines recommended by the relevant authorizing agencies. Large-scale GMP-standard high-generation dendrimer production is technically very challenging. Therefore, in this second part of the review, the authors present the development of PAMAM-based amphiphilic dendrons, that are able to auto-organize themselves into nanosized micelles which ultimately outperform their covalent dendrimer counterparts in in vitro and in vivo gene silencing.
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Affiliation(s)
- Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), Department of Engineering and Architecture, University of Trieste, 34127 Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), Department of Engineering and Architecture, University of Trieste, 34127 Trieste, Italy.
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), Department of Engineering and Architecture, University of Trieste, 34127 Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), Department of Engineering and Architecture, University of Trieste, 34127 Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), Department of Engineering and Architecture, University of Trieste, 34127 Trieste, Italy
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12
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Abedi-Gaballu F, Dehghan G, Ghaffari M, Yekta R, Abbaspour-Ravasjani S, Baradaran B, Dolatabadi JEN, Hamblin MR. PAMAM dendrimers as efficient drug and gene delivery nanosystems for cancer therapy. APPLIED MATERIALS TODAY 2018; 12:177-190. [PMID: 30511014 PMCID: PMC6269116 DOI: 10.1016/j.apmt.2018.05.002] [Citation(s) in RCA: 243] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Drug delivery systems for cancer chemotherapy are employed to improve the effectiveness and decrease the side-effects of highly toxic drugs. Most chemotherapy agents have indiscriminate cytotoxicity that affects normal, as well as cancer cells. To overcome these problems, new more efficient nanosystems for drug delivery are increasingly being investigated. Polyamidoamine (PAMAM) dendrimers are an example of a versatile and reproducible type of nanocarrier that can be loaded with drugs, and modified by attaching target-specific ligands that recognize receptors that are over-expressed on cancer cells. PAMAM dendrimers with a high density of cationic charges display electrostatic interactions with nucleic acids (DNA, siRNA, miRNA, etc.), creating dendriplexes that can preserve the nucleic acids from degradation. Dendrimers are prepared by conducting several successive "generations" of synthetic reactions so their size can be easily controlled and they have good uniformity. Dendrimers are particularly well-suited to co-delivery applications (simultaneous delivery of drugs and/or genes). In the current review, we discuss dendrimer-based targeted delivery of drugs/genes and co-delivery systems mainly for cancer therapy.
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Affiliation(s)
- Fereydoon Abedi-Gaballu
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Gholamreza Dehghan
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Maryam Ghaffari
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Reza Yekta
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | | | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Dermatology, Harvard Medical School, Boston, MA 02115, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
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13
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Camarada MB, Comer J, Poblete H, Azhagiya Singam ER, Marquez-Miranda V, Morales-Verdejo C, Gonzalez-Nilo FD. Experimental and Computational Characterization of the Interaction between Gold Nanoparticles and Polyamidoamine Dendrimers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:10063-10072. [PMID: 30074805 DOI: 10.1021/acs.langmuir.8b01809] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Dendrimers provide a means to control the synthesis of gold nanoparticles and stabilize their suspensions. However, design of improved dendrimers for this application is hindered by a lack of understanding how the dendrimers and synthesis conditions determine nanoparticle morphology and suspension stability. In the present work, we evaluate the effect of polyamidoamine (PAMAM) dendrimers terminated with different functional groups (-OH or -NH3+) and different synthesis conditions on the morphology of the resulting gold nanoparticles and their stability in solution. We leverage molecular dynamics (MD) simulations to identify the atomic interactions that underlie adsorption of PAMAM dendrimers to gold surface and how the thermodynamics of this adsorption depends on the terminal functional groups of the dendrimers. We find that gold nanoparticles formed with hydroxyl-terminated PAMAM (PAMAM-OH) rapidly aggregate, whereas those formed with PAMAM-NH3+ are stable in solution for months of storage. Synthesis under ultrasound sonication is shown to be more rapid than that under agitation, with sonication producing smaller nanoparticles. Free-energy calculations in MD simulations show that all dendrimers have a high affinity for the gold surface, although PAMAM-OH and its oxidized aldehyde form (PAMAM-CHO) have a greater affinity for the nanoparticle surface than PAMAM-NH3+. Although adsorption of PAMAM-OH and PAMAM-CHO has both favorable entropy and enthalpy, adsorption of PAMAM-NH3+ is driven by a strong enthalpic component subject to an unfavorable entropic component.
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Affiliation(s)
- M B Camarada
- Centro de Nanotecnología Aplicada, Facultad de Ciencias , Universidad Mayor , Camino la Pirámide 5750 , Huechuraba , Santiago 8580745 , Chile
| | - J Comer
- Nanotechnology Innovation Center of Kansas State, Institute of Computational Comparative Medicine, Department of Anatomy and Physiology , Kansas State University , 1800 Denison Avenue , Manhattan , Kansas 66506 , United States
| | - H Poblete
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería; Nucleo Científico Multidiciplinario-DI; Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD) , Universidad de Talca , 2 Norte 685 , Casilla 721 , Talca , Chile
| | - E R Azhagiya Singam
- Nanotechnology Innovation Center of Kansas State, Institute of Computational Comparative Medicine, Department of Anatomy and Physiology , Kansas State University , 1800 Denison Avenue , Manhattan , Kansas 66506 , United States
| | - V Marquez-Miranda
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida , Universidad Andrés Bello , Av. República 330 , Santiago 8370186 , Chile
| | - C Morales-Verdejo
- Centro de Nanotecnología Aplicada, Facultad de Ciencias , Universidad Mayor , Camino la Pirámide 5750 , Huechuraba , Santiago 8580745 , Chile
| | - F D Gonzalez-Nilo
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida , Universidad Andrés Bello , Av. República 330 , Santiago 8370186 , Chile
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14
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Antipina AY, Gurtovenko AA. Toward Understanding Liposome-Based siRNA Delivery Vectors: Atomic-Scale Insight into siRNA-Lipid Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8685-8693. [PMID: 29932659 DOI: 10.1021/acs.langmuir.8b01211] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Liposome carriers for delivering small interfering RNA (siRNA) into target cells are of tremendous importance because the siRNA-based therapy offers a completely new approach for treating a wide range of diseases, including cancer and viral infections. In this paper, we employ the state-of-the-art computer simulations to get an atomic-scale insight into the interactions of siRNA with zwitterionic (neutral) lipids. Our computational findings clearly demonstrate that siRNA does adsorb on the surface of a neutral lipid bilayer. The siRNA adsorption, being rather weak and unstable, is driven by attractive interactions of overhanging unpaired nucleotides with choline moieties of lipid molecules. It is the presence of the unpaired terminal nucleotides that underlies a drastic difference between siRNA and DNA; the latter is not able to bind to the zwitterionic lipid bilayer. We also show that adding divalent Ca ions leads to the formation of stable siRNA-lipid system complexes; these complexes are stabilized by Ca-mediated aggregates of siRNA and lipid molecules rather than by the overhanging siRNA nucleotides. Furthermore, the molecular mechanism of interactions between siRNA and the lipid bilayer in the presence of divalent cations seems to involve exchange of Ca ions between the outer mouth of the major groove of siRNA and the lipid/water interface. Overall, our findings contribute significantly to a deeper understanding of the structure and function of liposome carriers used for siRNA delivery and can be used as a theoretical basis for further development of siRNA-based therapeutics.
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Affiliation(s)
- Alexandra Yu Antipina
- Department of Photonics and Optical Information Technology , ITMO University , 49 Kronverksky Pr. , St. Petersburg 197101 , Russia
| | - Andrey A Gurtovenko
- Institute of Macromolecular Compounds , Russian Academy of Sciences , Bolshoi Prospect V.O. 31 , St. Petersburg 199004 , Russia
- Faculty of Physics , St. Petersburg State University , Ulyanovskaya Street 3, Petrodvorets , St. Petersburg 198504 , Russia
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15
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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.
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16
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Molecular Weight-Dependent Activity of Aminated Poly(α)glutamates as siRNA Nanocarriers. Polymers (Basel) 2018; 10:polym10050548. [PMID: 30966582 PMCID: PMC6415365 DOI: 10.3390/polym10050548] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 11/25/2022] Open
Abstract
RNA interference (RNAi) can contribute immensely to the area of personalized medicine by its ability to target any gene of interest. Nevertheless, its clinical use is limited by lack of efficient delivery systems. Polymer therapeutics can address many of the challenges encountered by the systemic delivery of RNAi, but suffer from inherent drawbacks such as polydispersity and batch to batch heterogeneity. These characteristics may have far-reaching consequences when dealing with therapeutic applications, as both the activity and the toxicity may be dependent on the length of the polymer chain. To investigate the consequences of polymers’ heterogeneity, we have synthesized two batches of aminated poly(α)glutamate polymers (PGAamine), differing in their degree of polymerization, but not in the monomer units or their conjugation. Isothermal titration calorimetry study was conducted to define the binding affinity of these polymers with siRNA. Molecular dynamics simulation revealed that Short PGAamine:siRNA polyplexes exposed a higher amount of amine moieties to the surroundings compared to Long PGAamine. This resulted in a higher zeta potential, leading to faster degradation and diminished gene silencing. Altogether, our study highlights the importance of an adequate physico-chemical characterization to elucidate the structure–function-activity relationship, for further development of tailor-designed RNAi delivery vehicles.
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17
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Camarada MB. PAMAM Dendrimers as Support for the Synthesis of Gold Nanoparticles: Understanding the Effect of the Terminal Groups. J Phys Chem A 2017; 121:8124-8135. [DOI: 10.1021/acs.jpca.7b08272] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. B. Camarada
- Centro de Genómica
y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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18
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Abstract
Gene therapy is an important therapeutic strategy in the treatment of a wide range of genetic disorders. Polymers forming stable complexes with nucleic acids (NAs) are non-viral gene carriers. The self-assembly of polymers and nucleic acids is typically a complex process that involves many types of interaction at different scales. Electrostatic interaction, hydrophobic interaction, and hydrogen bonds are three important and prevalent interactions in the polymer/nucleic acid system. Electrostatic interactions and hydrogen bonds are the main driving forces for the condensation of nucleic acids, while hydrophobic interactions play a significant role in the cellular uptake and endosomal escape of polymer-nucleic acid complexes. To design high-efficiency polymer candidates for the DNA and siRNA delivery, it is necessary to have a detailed understanding of the interactions between them in solution. In this chapter, we survey the roles of the three important interactions between polymers and nucleic acids during the formation of polyplexes and summarize recent understandings of the linear polyelectrolyte-NA interactions and dendrimer-NA interactions. We also review recent progress optimizing the gene delivery system by tuning these interactions.
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19
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Wei Z, Luijten E. Systematic coarse-grained modeling of complexation between small interfering RNA and polycations. J Chem Phys 2016; 143:243146. [PMID: 26723631 DOI: 10.1063/1.4937384] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
All-atom molecular dynamics simulations can provide insight into the properties of polymeric gene-delivery carriers by elucidating their interactions and detailed binding patterns with nucleic acids. However, to explore nanoparticle formation through complexation of these polymers and nucleic acids and study their behavior at experimentally relevant time and length scales, a reliable coarse-grained model is needed. Here, we systematically develop such a model for the complexation of small interfering RNA (siRNA) and grafted polyethyleneimine copolymers, a promising candidate for siRNA delivery. We compare the predictions of this model with all-atom simulations and demonstrate that it is capable of reproducing detailed binding patterns, charge characteristics, and water release kinetics. Since the coarse-grained model accelerates the simulations by one to two orders of magnitude, it will make it possible to quantitatively investigate nanoparticle formation involving multiple siRNA molecules and cationic copolymers.
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Affiliation(s)
- Zonghui Wei
- Graduate Program in Applied Physics, Northwestern University, Evanston, Illinois 60208, USA
| | - Erik Luijten
- Graduate Program in Applied Physics, Northwestern University, Evanston, Illinois 60208, USA
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20
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Jones DE, Lund AM, Ghandehari H, Facelli JC. Molecular dynamics simulations in drug delivery research: Calcium chelation of G3.5 PAMAM dendrimers. COGENT CHEMISTRY 2016; 2:1229830. [PMID: 29177183 PMCID: PMC5699217 DOI: 10.1080/23312009.2016.1229830] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/24/2016] [Indexed: 11/18/2022]
Abstract
Poly(amido amine) (PAMAM) dendrimers have been considered as possible delivery systems for anticancer drugs. One potential advantage of these carriers would be their use in oral formulations, which will require absorption in the intestinal lumen. This may require the opening of tight junctions which may be enabled by reducing the Ca2+ concentration in the intestinal lumen, which has been shown as an absorption mechanism for EDTA (ethylenediaminetetraacetic acid). Using molecular dynamics simulations, we show that the G3.5 PAMAM dendrimers are able to chelate Ca2+ at similar proportions to EDTA, providing support to the hypothesis that oral formulations of PAMAM dendrimers could use this high chelating efficiency as a potential mechanism for permeating the tight junctions of the intestines if other formulation barriers could be overcome.
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Affiliation(s)
- David E. Jones
- Department of Biomedical Informatics, University of Utah, 421 Wakara, Salt Lake City, UT 84108, USA
| | - Albert M. Lund
- Department of Biomedical Informatics, University of Utah, 421 Wakara, Salt Lake City, UT 84108, USA
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Hamidreza Ghandehari
- Departments of Bioengineering and Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112, USA
- Utah Center for Nanomedicine, Nano Institute of Utah, University of Utah, Salt Lake City, UT 84112, USA
| | - Julio C. Facelli
- Department of Biomedical Informatics, University of Utah, 421 Wakara, Salt Lake City, UT 84108, USA
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21
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Cooper BM, Putnam D. Polymers for siRNA Delivery: A Critical Assessment of Current Technology Prospects for Clinical Application. ACS Biomater Sci Eng 2016; 2:1837-1850. [PMID: 33440520 DOI: 10.1021/acsbiomaterials.6b00363] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The number of polymer-based vectors for siRNA delivery in clinical trials lags behind other delivery strategies; however, the molecular architectures and chemical compositions available to polymers make them attractive candidates for further exploration. Polymer vectors are extensively investigated in academic laboratories worldwide with fundamental progress having recently been made in the areas of high-throughput screening, synthetic methods, cellular internalization, endosomal escape and computational prediction and analysis. This review assesses recent advances within the field and highlights relevant developments from within the complementary fields of nanotechnology and protein chemistry with the intent to propose future work that addresses key gaps within the current body of knowledge, potentially advancing the development of the next generation of polymeric vectors.
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Affiliation(s)
- Bailey M Cooper
- Meinig School of Biomedical Engineering and ‡Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - David Putnam
- Meinig School of Biomedical Engineering and Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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22
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Hsu H, Bugno J, Lee S, Hong S. Dendrimer‐based nanocarriers: a versatile platform for drug delivery. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2016; 9. [DOI: 10.1002/wnan.1409] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Hao‐Jui Hsu
- Department of Biopharmaceutical Sciences, College of PharmacyUniversity of IllinoisChicagoILUSA
| | - Jason Bugno
- Department of Biopharmaceutical Sciences, College of PharmacyUniversity of IllinoisChicagoILUSA
| | - Seung‐ri Lee
- Department of Biopharmaceutical Sciences, College of PharmacyUniversity of IllinoisChicagoILUSA
| | - Seungpyo Hong
- Department of Biopharmaceutical Sciences, College of PharmacyUniversity of IllinoisChicagoILUSA
- Department of Integrated OMICs for Biomedical Science and Underwood International CollegeYonsei UniversitySeoulKorea
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23
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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.
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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
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24
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Ohyama A, Higashi T, Motoyama K, Arima H. In Vitro and In Vivo Tumor-Targeting siRNA Delivery Using Folate-PEG-appended Dendrimer (G4)/α-Cyclodextrin Conjugates. Bioconjug Chem 2016; 27:521-32. [PMID: 26715308 DOI: 10.1021/acs.bioconjchem.5b00545] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We previously reported that folate-polyethylene glycol (PEG)-appended dendrimer (generation 3)/α-cyclodextrin conjugate (Fol-PαC (G3)) shows folate receptor-α (FR-α)-overexpressing tumor cell-selective in vitro siRNA transfer activity. However, Fol-PαC (G3)/siRNA complex did not induce a significant in vivo RNAi effect after intravenous administration to tumor-bearing mice, possibly resulting from immediate dissociation of the complex in blood. Herein, to develop the novel siRNA carrier having high blood circulating ability, high in vivo siRNA transfer activity, and high safety profile, we newly prepared Fol-PαCs with higher generation (G4) and evaluated their potential as tumor-targeting siRNA carriers in vitro and in vivo. Fol-PαC (G4, average degree of substitution of α-cyclodextrin (DSC) 2.9, average degree of substitution of folate-PEG (DSF) 2)/siRNA complex had the prominent RNAi effect through adequate physicochemical properties, FR-α-mediated endocytosis, efficient endosomal escape, and siRNA delivery to cytoplasm with negligible cytotoxicity. Importantly, Fol-PαC (G4, DSC2.9, DSF2) improved the serum stability, blood circulating ability, and in vivo RNAi effects of siRNA, compared to Fol-PαC (G3). Furthermore, Fol-PαC (G4, DSC2.9, DSF2) complex with siRNA against Polo-like kinase 1 (siPLK1) suppressed the tumor growth compared to control siRNA complex. These results suggest that Fol-PαC (G4, DSC2.9, DSF2) has the potential as a novel tumor-targeting siRNA carrier in vitro and in vivo.
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Affiliation(s)
- Ayumu Ohyama
- Department of Physical Pharmaceutics, Graduate School of Pharmaceutical Sciences and ‡Program for Leading Graduate Schools "HIGO (Health life science: Interdisciplinary and Glocal Oriented) Program", Kumamoto University , 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Taishi Higashi
- Department of Physical Pharmaceutics, Graduate School of Pharmaceutical Sciences and ‡Program for Leading Graduate Schools "HIGO (Health life science: Interdisciplinary and Glocal Oriented) Program", Kumamoto University , 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Keiichi Motoyama
- Department of Physical Pharmaceutics, Graduate School of Pharmaceutical Sciences and ‡Program for Leading Graduate Schools "HIGO (Health life science: Interdisciplinary and Glocal Oriented) Program", Kumamoto University , 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Hidetoshi Arima
- Department of Physical Pharmaceutics, Graduate School of Pharmaceutical Sciences and ‡Program for Leading Graduate Schools "HIGO (Health life science: Interdisciplinary and Glocal Oriented) Program", Kumamoto University , 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
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25
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Torras J, Zanuy D, Aradilla D, Alemán C. Solvent effects on the properties of hyperbranched polythiophenes. Phys Chem Chem Phys 2016; 18:24610-9. [DOI: 10.1039/c6cp04812a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
QM/MM-MD simulations of dendrimers using explicit solvent molecules capture the conformational flexibility and microfluctuations induced by different types of solvents.
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Affiliation(s)
- Juan Torras
- Departament d'Enginyeria Química
- EEI
- Universitat Politècnica de Catalunya
- 08700 Igualada
- Spain
| | - David Zanuy
- Departament d'Enginyeria Química
- E.T.S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
| | - David Aradilla
- Departament d'Enginyeria Química
- E.T.S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química
- E.T.S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
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26
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Kanchi S, Suresh G, Priyakumar UD, Ayappa KG, Maiti PK. Molecular Dynamics Study of the Structure, Flexibility, and Hydrophilicity of PETIM Dendrimers: A Comparison with PAMAM Dendrimers. J Phys Chem B 2015; 119:12990-3001. [DOI: 10.1021/acs.jpcb.5b07124] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Subbarao Kanchi
- Center
for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India
- Department
of Chemical Engineering, Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Gorle Suresh
- Center
for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - U. Deva Priyakumar
- Center
for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - K. G. Ayappa
- Department
of Chemical Engineering, Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Prabal K Maiti
- Center
for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India
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27
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Biomimetics: From Bioinformatics to Rational Design of Dendrimers as Gene Carriers. PLoS One 2015; 10:e0138392. [PMID: 26382062 PMCID: PMC4575034 DOI: 10.1371/journal.pone.0138392] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 08/28/2015] [Indexed: 12/11/2022] Open
Abstract
Biomimetics, or the use of principles of Nature for developing new materials, is a paradigm that could help Nanomedicine tremendously. One of the current challenges in Nanomedicine is the rational design of new efficient and safer gene carriers. Poly(amidoamine) (PAMAM) dendrimers are a well-known class of nanoparticles, extensively used as non-viral nucleic acid carriers, due to their positively charged end-groups. Yet, there are still several aspects that can be improved for their successful application in in vitro and in vivo systems, including their affinity for nucleic acids as well as lowering their cytotoxicity. In the search of new functional groups that could be used as new dendrimer-reactive groups, we followed a biomimetic approach to determine the amino acids with highest prevalence in protein-DNA interactions. Then we introduced them individually as terminal groups of dendrimers, generating a new class of nanoparticles. Molecular dynamics studies of two systems: PAMAM-Arg and PAMAM-Lys were also performed in order to describe the formation of complexes with DNA. Results confirmed that the introduction of amino acids as terminal groups in a dendrimer increases their affinity for DNA and the interactions in the complexes were characterized at atomic level. We end up by briefly discussing additional modifications that can be made to PAMAM dendrimers to turned them into promising new gene carriers.
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28
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Bugno J, Hsu HJ, Hong S. Recent advances in targeted drug delivery approaches using dendritic polymers. Biomater Sci 2015; 3:1025-34. [PMID: 26221937 PMCID: PMC4519693 DOI: 10.1039/c4bm00351a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Since they were first synthesized over 30 years ago, dendrimers have seen rapid translation into various biomedical applications. A number of reports have not only demonstrated their clinical utility, but also revealed novel design approaches and strategies based on the elucidation of underlying mechanisms governing their biological interactions. This review focuses on presenting the latest advances in dendrimer design, discussing the current mechanistic understandings, and highlighting recent developments and targeted approaches using dendrimers in drug/gene delivery.
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Affiliation(s)
- Jason Bugno
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, IL 60612, USA.
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29
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Meneksedag-Erol D, Tang T, Uludağ H. Probing the Effect of miRNA on siRNA–PEI Polyplexes. J Phys Chem B 2015; 119:5475-86. [DOI: 10.1021/acs.jpcb.5b00415] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Deniz Meneksedag-Erol
- Department of Biomedical Engineering, Faculties of Medicine & Dentistry and Engineering, University of Alberta, Alberta, Canada
- Department of Chemical & Materials Engineering, Faculty of Engineering, University of Alberta, Alberta, Canada
| | - Tian Tang
- Department of Biomedical Engineering, Faculties of Medicine & Dentistry and Engineering, University of Alberta, Alberta, Canada
- Department
of Mechanical Engineering, Faculty of Engineering, University of Alberta, Alberta, Canada
| | - Hasan Uludağ
- Department of Biomedical Engineering, Faculties of Medicine & Dentistry and Engineering, University of Alberta, Alberta, Canada
- Department of Chemical & Materials Engineering, Faculty of Engineering, University of Alberta, Alberta, Canada
- Faculty
of Pharmacy and Pharmaceutical Sciences, University of Alberta, Alberta, Canada
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30
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Camarada MB, Márquez-Miranda V, Araya-Durán I, Yévenes A, González-Nilo F. PAMAM G4 dendrimers as inhibitors of the iron storage properties of human L-chain ferritin. Phys Chem Chem Phys 2015; 17:19001-11. [DOI: 10.1039/c5cp02594j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cationic dendrimers, such as PAMAM, are known to be positively charged at neutral pH allowing their unspecific interaction with proteins and other cellular components.
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Affiliation(s)
- M. B. Camarada
- Universidad Bernardo O Higgins
- Laboratorio de Bionanotecnología
- Santiago
- Chile
| | - V. Márquez-Miranda
- Universidad Andres Bello
- Facultad de Biología
- Center for Bioinformatics and Integrative Biology (CBIB)
- Santiago
- Chile
| | - I. Araya-Durán
- Universidad Andres Bello
- Facultad de Biología
- Center for Bioinformatics and Integrative Biology (CBIB)
- Santiago
- Chile
| | - A. Yévenes
- Pontificia Universidad Católica de Chile
- Facultad de Química
- Macul
- Santiago
| | - F. González-Nilo
- Universidad Andres Bello
- Facultad de Biología
- Center for Bioinformatics and Integrative Biology (CBIB)
- Santiago
- Chile
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31
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Mehrabadi FS, Hirsch O, Zeisig R, Posocco P, Laurini E, Pricl S, Haag R, Kemmner W, Calderón M. Structure–activity relationship study of dendritic polyglycerolamines for efficient siRNA transfection. RSC Adv 2015. [DOI: 10.1039/c5ra10944b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Structure–activity relationship studies were performed through in vitro, in silico, and in vivo analysis in order to evaluate the gene transfection potential of dendritic polyglycerolamines with different amine loadings.
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Affiliation(s)
| | - Ole Hirsch
- Physikalisch-Technische Bundesanstalt
- 10587 Berlin
- Germany
| | - Reiner Zeisig
- Experimental Pharmacology & Oncology GmbH
- 13125 Berlin
- Germany
| | - Paola Posocco
- Molecular Simulation Engineering (MOSE) Laboratory
- DICAMP
- University of Trieste
- 34127 Trieste
- Italy
| | - Erik Laurini
- Molecular Simulation Engineering (MOSE) Laboratory
- DICAMP
- University of Trieste
- 34127 Trieste
- Italy
| | - Sabrina Pricl
- Molecular Simulation Engineering (MOSE) Laboratory
- DICAMP
- University of Trieste
- 34127 Trieste
- Italy
| | - Rainer Haag
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- 14195 Berlin
- Germany
| | - Wolfgang Kemmner
- Translational Oncology
- Experimental and Clinical Research Center
- 13125 Berlin
- Germany
| | - Marcelo Calderón
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- 14195 Berlin
- Germany
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32
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Li J, Ouyang Y, Kong X, Zhu J, Lu D, Liu Z. A multi-scale molecular dynamics simulation of PMAL facilitated delivery of siRNA. RSC Adv 2015. [DOI: 10.1039/c5ra10965e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
PMAL as a novel carrier for the delivery of siRNA into lipid bilayer membranes.
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Affiliation(s)
- Jipeng Li
- Department of Chemical Engineering
- Tsinghua University
- Beijing 100084
- China
| | - Yiyun Ouyang
- Department of Chemical Engineering
- Tsinghua University
- Beijing 100084
- China
| | - Xian Kong
- Department of Chemical Engineering
- Tsinghua University
- Beijing 100084
- China
| | - Jingying Zhu
- Department of Chemical Engineering
- Tsinghua University
- Beijing 100084
- China
| | - Diannan Lu
- Department of Chemical Engineering
- Tsinghua University
- Beijing 100084
- China
| | - Zheng Liu
- Department of Chemical Engineering
- Tsinghua University
- Beijing 100084
- China
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33
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Ottaviani MF, Cangiotti M, Fattori A, Coppola C, Posocco P, Laurini E, Liu X, Liu C, Fermeglia M, Peng L, Pricl S. Copper(II) binding to flexible triethanolamine-core PAMAM dendrimers: a combined experimental/in silico approach. Phys Chem Chem Phys 2014; 16:685-94. [PMID: 24256926 DOI: 10.1039/c3cp54005g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The structure of copper(II) complexes formed with triethanolamine (TEA) core poly(amidoamine) (PAMAM) dendrimers from generation 0 (G0) to 4 (G4) were investigated by the electron paramagnetic resonance (EPR) technique and molecular simulations. Different square planar coordination modes were detected as a function of copper(II) concentration, whose dynamic evolution relates to the high structural flexibility peculiar to this dendrimer family. Modulated by generation and solvation effects, copper(II) complexation begins at the dendrimer core and progresses to the dendrimer periphery. Differently from the ethylenediamine (EDA) core PAMAM dendrimers, the copper complexes involving the TEA core showed high mobility and saturation of the internal sites above the 1 : 1 molar ratio between the dendrimers and the ions. Therefore, by combining EPR and molecular simulations for the first time, ultimately we obtained unique information on structure, dynamics and copper interacting ability of these dendrimers which could be successfully exploited in biomedical applications.
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Affiliation(s)
- Maria Francesca Ottaviani
- Department of Earth, Life and Environment Sciences, University of Urbino, Località Crocicchia, 61029 Urbino, Italy.
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Pandav G, Ganesan V. Computer Simulations of Dendrimer–Polyelectrolyte Complexes. J Phys Chem B 2014; 118:10297-310. [DOI: 10.1021/jp505645r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Gunja Pandav
- Department
of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Venkat Ganesan
- Department of Chemical Engineering and Institute for
Computational and Engineering Sciences, University of Texas at Austin, Austin, Texas 78712, United States
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Jiang Y, Zhang D, Zhang Y, Deng Z, Zhang L. The adsorption-desorption transition of double-stranded DNA interacting with an oppositely charged dendrimer induced by multivalent anions. J Chem Phys 2014; 140:204912. [DOI: 10.1063/1.4878508] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Meneksedag-Erol D, Tang T, Uludağ H. Molecular modeling of polynucleotide complexes. Biomaterials 2014; 35:7068-76. [PMID: 24856107 DOI: 10.1016/j.biomaterials.2014.04.103] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 04/28/2014] [Indexed: 11/30/2022]
Abstract
Delivery of polynucleotides into patient cells is a promising strategy for treatment of genetic disorders. Gene therapy aims to either synthesize desired proteins (DNA delivery) or suppress expression of endogenous genes (siRNA delivery). Carriers constitute an important part of gene therapeutics due to limitations arising from the pharmacokinetics of polynucleotides. Non-viral carriers such as polymers and lipids protect polynucleotides from intra and extracellular threats and facilitate formation of cell-permeable nanoparticles through shielding and/or bridging multiple polynucleotide molecules. Formation of nanoparticulate systems with optimal features, their cellular uptake and intracellular trafficking are crucial steps for an effective gene therapy. Despite the great amount of experimental work pursued, critical features of the nanoparticles as well as their processing mechanisms are still under debate due to the lack of instrumentation at atomic resolution. Molecular modeling based computational approaches can shed light onto the atomic level details of gene delivery systems, thus provide valuable input that cannot be readily obtained with experimental techniques. Here, we review the molecular modeling research pursued on critical gene therapy steps, highlight the knowledge gaps in the field and providing future perspectives. Existing modeling studies revealed several important aspects of gene delivery, such as nanoparticle formation dynamics with various carriers, effect of carrier properties on complexation, carrier conformations in endosomal stages, and release of polynucleotides from carriers. Rate-limiting steps related to cellular events (i.e. internalization, endosomal escape, and nuclear uptake) are now beginning to be addressed by computational approaches. Limitations arising from current computational power and accuracy of modeling have been hindering the development of more realistic models. With the help of rapidly-growing computational power, the critical aspects of gene therapy are expected to be better investigated and direct comparison between more realistic molecular modeling and experiments may open the path for design of next generation gene therapeutics.
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Affiliation(s)
- Deniz Meneksedag-Erol
- Department of Biomedical Engineering, University of Alberta, Edmonton, Canada; Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada
| | - Tian Tang
- Department of Biomedical Engineering, University of Alberta, Edmonton, Canada; Department of Mechanical Engineering, University of Alberta, Edmonton, Canada.
| | - Hasan Uludağ
- Department of Biomedical Engineering, University of Alberta, Edmonton, Canada; Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada; Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Canada.
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Mese F, Congur G, Erdem A. Voltammetric and impedimetric detection of DNA hybridization by using dendrimer modified graphite electrodes. J Electroanal Chem (Lausanne) 2014. [DOI: 10.1016/j.jelechem.2014.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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38
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Kala S, Mak ASC, Liu X, Posocco P, Pricl S, Peng L, Wong AST. Combination of Dendrimer-Nanovector-Mediated Small Interfering RNA Delivery to Target Akt with the Clinical Anticancer Drug Paclitaxel for Effective and Potent Anticancer Activity in Treating Ovarian Cancer. J Med Chem 2014; 57:2634-42. [DOI: 10.1021/jm401907z] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Shashwati Kala
- School
of Biological Sciences, University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong
| | - Abby Sin Chi Mak
- School
of Biological Sciences, University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong
| | - Xiaoxuan Liu
- Aix-Marseille University, CNRS, Centre Interdisciplinaire
de Nanoscience de Marseille, CINaM UMR 7325, Marseille Cedex 09, France
| | - Paola Posocco
- Molecular
Simulation Engineering Laboratory (MOSE), Department of Engineering
and Architecture (DEA), University of Trieste, Via Valerio 10, 34127 Trieste, Italy
- Research
Unit MOSE-DEA, National Interuniversity Consortium for Material Science
and Technology (INSTM), University of Trieste, Via Valerio 6, 34127 Trieste, Italy
| | - Sabrina Pricl
- Molecular
Simulation Engineering Laboratory (MOSE), Department of Engineering
and Architecture (DEA), University of Trieste, Via Valerio 10, 34127 Trieste, Italy
- Research
Unit MOSE-DEA, National Interuniversity Consortium for Material Science
and Technology (INSTM), University of Trieste, Via Valerio 6, 34127 Trieste, Italy
| | - Ling Peng
- Aix-Marseille University, CNRS, Centre Interdisciplinaire
de Nanoscience de Marseille, CINaM UMR 7325, Marseille Cedex 09, France
| | - Alice Sze Tsai Wong
- School
of Biological Sciences, University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong
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Tintaru A, Chendo C, Wang Q, Viel S, Quéléver G, Peng L, Posocco P, Pricl S, Charles L. Conformational sensitivity of conjugated poly(ethylene oxide)-poly(amidoamine) molecules to cations adducted upon electrospray ionization – A mass spectrometry, ion mobility and molecular modeling study. Anal Chim Acta 2014; 808:163-74. [DOI: 10.1016/j.aca.2013.08.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/05/2013] [Accepted: 08/19/2013] [Indexed: 10/26/2022]
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40
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Molecular Dynamics Simulations of Polyplexes and Lipoplexes Employed in Gene Delivery. INTRACELLULAR DELIVERY II 2014. [DOI: 10.1007/978-94-017-8896-0_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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41
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Dendrimers as carriers for siRNA delivery and gene silencing: a review. ScientificWorldJournal 2013; 2013:630654. [PMID: 24288498 PMCID: PMC3830781 DOI: 10.1155/2013/630654] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 09/19/2013] [Indexed: 12/12/2022] Open
Abstract
RNA interference (RNAi) was first literaturally reported in 1998 and has become rapidly a promising tool for therapeutic applications in gene therapy. In a typical RNAi process, small interfering RNAs (siRNA) are used to specifically downregulate the expression of the targeted gene, known as the term "gene silencing." One key point for successful gene silencing is to employ a safe and efficient siRNA delivery system. In this context, dendrimers are emerging as potential nonviral vectors to deliver siRNA for RNAi purpose. Dendrimers have attracted intense interest since their emanating research in the 1980s and are extensively studied as efficient DNA delivery vectors in gene transfer applications, due to their unique features based on the well-defined and multivalent structures. Knowing that DNA and RNA possess a similar structure in terms of nucleic acid framework and the electronegative nature, one can also use the excellent DNA delivery properties of dendrimers to develop effective siRNA delivery systems. In this review, the development of dendrimer-based siRNA delivery vectors is summarized, focusing on the vector features (siRNA delivery efficiency, cytotoxicity, etc.) of different types of dendrimers and the related investigations on structure-activity relationship to promote safe and efficient siRNA delivery system.
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Chou ST, Hom K, Zhang D, Leng Q, Tricoli LJ, Hustedt JM, Lee A, Shapiro MJ, Seog J, Kahn JD, Mixson AJ. Enhanced silencing and stabilization of siRNA polyplexes by histidine-mediated hydrogen bonds. Biomaterials 2013; 35:846-55. [PMID: 24161165 DOI: 10.1016/j.biomaterials.2013.10.019] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 10/04/2013] [Indexed: 01/27/2023]
Abstract
Branched peptides containing histidines and lysines (HK) have been shown to be effective carriers for DNA and siRNA. We anticipate that elucidation of the binding mechanism of HK with siRNA will provide greater insight into the self-assembly and delivery of the HK:siRNA polyplex. Non-covalent bonds between histidine residues and nucleic acids may enhance the stability of siRNA polyplexes. We first compared the polyplex biophysical properties of a branched HK with those of branched asparagine-lysine peptide (NK). Consistent with siRNA silencing experiments, gel electrophoresis demonstrated that the HK siRNA polyplex maintained its integrity with prolonged incubation in serum, whereas siRNA in complex with NK was degraded in a time-dependent manner. Isothermal titration calorimetry of various peptides binding to siRNA at pH 7.3 showed that branched polylysine, interacted with siRNA was initially endothermic, whereas branched HK exhibited an exothermic reaction at initial binding. The exothermic interaction indicates formation of non-ionic bonds between histidines and siRNA; purely electrostatic interaction is entropy-driven and endothermic. To investigate the type of non-ionic bond, we studied the protonation state of imidazole rings of a selectively (15)N labeled branched HK by heteronuclear single quantum coherence NMR. The peak of Nδ1-H tautomers of imidazole shifted downfield (in the direction of deprotonation) by 0.5-1.0 ppm with addition of siRNA, providing direct evidence that histidines formed hydrogen bonds with siRNA at physiological pH. These results establish that histidine-rich peptides form hydrogen bonds with siRNA, thereby enhancing the stability and biological activity of the polyplex in vitro and in vivo.
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Affiliation(s)
- Szu-Ting Chou
- Department of Pathology, University of Maryland Baltimore, MSTF Building, 10 South Pine Street, Baltimore, MD 21201, United States; Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, United States.
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43
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Posocco P, Liu X, Laurini E, Marson D, Chen C, Liu C, Fermeglia M, Rocchi P, Pricl S, Peng L. Impact of siRNA Overhangs for Dendrimer-Mediated siRNA Delivery and Gene Silencing. Mol Pharm 2013; 10:3262-73. [DOI: 10.1021/mp400329g] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Paola Posocco
- Molecular Simulation Engineering
(MOSE) Laboratory, Department of Engineering and Architecture (DEA), University of Trieste, Via Valerio 10, 34127 Trieste,
Italy
| | - Xiaoxuan Liu
- Aix-Marseille Université & CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, 13288 Marseille, France
- Centre de Recherche en Cancérologie
de Marseille, Inserm, UMR1068, 13009 Marseille,
France
- Institut Paoli-Calmettes, 13009 Marseille, France
- Aix-Marseille Université, 13284 Marseille, France
- CNRS, UMR7258,
13009 Marseille, France
| | - Erik Laurini
- Molecular Simulation Engineering
(MOSE) Laboratory, Department of Engineering and Architecture (DEA), University of Trieste, Via Valerio 10, 34127 Trieste,
Italy
| | - Domenico Marson
- Molecular Simulation Engineering
(MOSE) Laboratory, Department of Engineering and Architecture (DEA), University of Trieste, Via Valerio 10, 34127 Trieste,
Italy
| | - Chao Chen
- Aix-Marseille Université & CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, 13288 Marseille, France
- Aix-Marseille Université & CNRS, Institut de Chimie Radicalaire, UMR 7273, 13390 Marseille, France
| | - Cheng Liu
- Aix-Marseille Université & CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, 13288 Marseille, France
- State Key Laboratory of Virology,
College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Maurizio Fermeglia
- Molecular Simulation Engineering
(MOSE) Laboratory, Department of Engineering and Architecture (DEA), University of Trieste, Via Valerio 10, 34127 Trieste,
Italy
| | - Palma Rocchi
- Centre de Recherche en Cancérologie
de Marseille, Inserm, UMR1068, 13009 Marseille,
France
- Institut Paoli-Calmettes, 13009 Marseille, France
- Aix-Marseille Université, 13284 Marseille, France
- CNRS, UMR7258,
13009 Marseille, France
| | - Sabrina Pricl
- Molecular Simulation Engineering
(MOSE) Laboratory, Department of Engineering and Architecture (DEA), University of Trieste, Via Valerio 10, 34127 Trieste,
Italy
- National Interuniversity Consortium
for Material Science and Technology (INSTM), Research Unit MOSE-DEA, University of Trieste, 34127 Trieste, Italy
| | - Ling Peng
- Aix-Marseille Université & CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, 13288 Marseille, France
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44
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Rossi D, Pedrali A, Gaggeri R, Marra A, Pignataro L, Laurini E, Dal Col V, Fermeglia M, Pricl S, Schepmann D, Wünsch B, Peviani M, Curti D, Collina S. Chemical, Pharmacological, and in vitro Metabolic Stability Studies on Enantiomerically Pure RC‐33 Compounds: Promising Neuroprotective Agents Acting as σ
1
Receptor Agonists. ChemMedChem 2013; 8:1514-27. [DOI: 10.1002/cmdc.201300218] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Daniela Rossi
- Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section, University of Pavia, Viale Taramelli 12, 27100 Pavia (Italy)
| | - Alice Pedrali
- Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section, University of Pavia, Viale Taramelli 12, 27100 Pavia (Italy)
| | - Raffaella Gaggeri
- Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section, University of Pavia, Viale Taramelli 12, 27100 Pavia (Italy)
| | - Annamaria Marra
- Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section, University of Pavia, Viale Taramelli 12, 27100 Pavia (Italy)
| | - Luca Pignataro
- Dipartimento di Chimica, Università degli Studi di Milano, Istituto di Scienze e Tecnologie Molecolari (ISTM) del CNR, Via Golgi 19, 20133 Milan (Italy)
| | - Erik Laurini
- MOSE‐DEA, University of Trieste, Via Valerio 10, 34127 Trieste (Italy)
| | - Valentina Dal Col
- MOSE‐DEA, University of Trieste, Via Valerio 10, 34127 Trieste (Italy)
| | | | - Sabrina Pricl
- MOSE‐DEA, University of Trieste, Via Valerio 10, 34127 Trieste (Italy)
- National Interuniversity Consortium for Material Science and Technology (INSTM), Research Unit MOSE‐DEA, University of Trieste, Trieste (Italy)
| | - Dirk Schepmann
- Institute of Pharmaceutical and Medicinal Chemistry, University of Muenster, Correnstrasse 48, 48149 Münster (Germany)
| | - Bernhard Wünsch
- Institute of Pharmaceutical and Medicinal Chemistry, University of Muenster, Correnstrasse 48, 48149 Münster (Germany)
| | - Marco Peviani
- Department of Biology and Biotechnology “L. Spallanzani”, Laboratory of Cellular and Molecular Neuropharmacology, University of Pavia, Via Ferrata 9, 27100 Pavia (Italy)
| | - Daniela Curti
- Department of Biology and Biotechnology “L. Spallanzani”, Laboratory of Cellular and Molecular Neuropharmacology, University of Pavia, Via Ferrata 9, 27100 Pavia (Italy)
| | - Simona Collina
- Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section, University of Pavia, Viale Taramelli 12, 27100 Pavia (Italy)
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45
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Tian WD, Ma YQ. Theoretical and computational studies of dendrimers as delivery vectors. Chem Soc Rev 2013; 42:705-27. [PMID: 23114420 DOI: 10.1039/c2cs35306g] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
It is a great challenge for nanomedicine to develop novel dendrimers with maximum therapeutic potential and minimum side-effects for drug and gene delivery. As delivery vectors, dendrimers must overcome lots of barriers before delivering the bio-agents to the target in the cell. Extensive experimental investigations have been carried out to elucidate the physical and chemical properties of dendrimers and explore their behaviors when interacting with biomolecules, such as gene materials, proteins, and lipid membranes. As a supplement of the experimental techniques, it has been proved that computer simulations could facilitate the progress in understanding the delivery process of bioactive molecules. The structures of dendrimers in dilute solutions have been intensively investigated by monomer-resolved simulations, coarse-grained simulations, and atom-resolved simulations. Atomistic simulations have manifested that the hydrophobic interactions, hydrogen-bond interactions, and electrostatic attraction play critical roles in the formation of dendrimer-drug complexes. Multiscale simulations and statistical field theories have uncovered some physical mechanisms involved in the dendrimer-based gene delivery systems. This review will focus on the current status and perspective of theoretical and computational contributions in this field in recent years. (275 references).
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Affiliation(s)
- Wen-de Tian
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
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46
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Rossi D, Marra A, Picconi P, Serra M, Catenacci L, Sorrenti M, Laurini E, Fermeglia M, Pricl S, Brambilla S, Almirante N, Peviani M, Curti D, Collina S. Identification of RC-33 as a potent and selective σ1 receptor agonist potentiating NGF-induced neurite outgrowth in PC12 cells. Part 2: g-scale synthesis, physicochemical characterization and in vitro metabolic stability. Bioorg Med Chem 2013; 21:2577-86. [PMID: 23498917 DOI: 10.1016/j.bmc.2013.02.029] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 02/14/2013] [Indexed: 11/18/2022]
Abstract
Strong pharmacological evidences indicate that σ1 receptors are implicated in the pathophysiology of all major CNS disorders. In the last years our research group has conducted extensive studies aimed at discovering novel σ1 ligands and we recently selected (R/S)-RC-33 as a novel potent and selective σ1 receptor agonist. As continuation of our work in this field, here we report our efforts in the development of this new σ1 receptor agonist. Initially, we investigated the binding of (R) and (S) enantiomers of RC-33 to the σ1 receptor by in silico experiments. The close values of the predicted affinity of (R)-RC-33 and (S)-RC-33 for the protein evidenced the non-stereoselective binding of RC-33 to the σ1 receptor; this, in turn, supported further development and characterization of RC-33 in its racemic form. Subsequently, we set-up a scaled-up, optimized synthesis of (R/S)-RC-33 along with some compound characterization data (e.g., solubility in different media and solid state characterization by thermal analysis techniques). Finally, metabolic studies of RC-33 in different biological matrices (e.g., plasma, blood, and hepatic S9 fraction) of different species (e.g., rat, mouse, dog, and human) were performed. (R/S)-RC-33 is generally stable in all examined biological matrices, with the only exception of rat and human liver S9 fractions in the presence of NADPH. In such conditions, the compound is subjected to a relevant oxidative metabolism, with a degradation of approximately 65% in rat and 69% in human. Taken together, our results demonstrated that (R/S)-RC-33 is a highly potent, selective, metabolically stable σ1 agonist, a promising novel neuroprotective drug candidate.
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Affiliation(s)
- Daniela Rossi
- Medicinal Chemistry Laboratory, Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section (MCPTS), University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
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47
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Visualizing the attack of RNase enzymes on dendriplexes and naked RNA using atomic force microscopy. PLoS One 2013; 8:e61710. [PMID: 23637890 PMCID: PMC3630113 DOI: 10.1371/journal.pone.0061710] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 03/14/2013] [Indexed: 12/22/2022] Open
Abstract
Cationic polymers such as poly(amidoamine), PAMAM, dendrimers have been used to electrostatically complex siRNA molecules forming dendriplexes for enhancing the cytoplasmic delivery of the encapsulated cargo. However, excess PAMAM dendrimers is typically used to protect the loaded siRNA against enzymatic attack, which results in systemic toxicity that hinders the in vivo use of these particles. In this paper, we evaluate the ability of G4 (flexible) and G5 (rigid) dendrimers to complex model siRNA molecules at low +/− ratio of 2/1 upon incubation for 20 minutes and 24 hours. We examine the ability of the formed G4 and G5 dendriplexes to shield the loaded siRNA molecules and protect them from degradation by RNase V1 enzymes using atomic force microscopy (AFM). Results show that G4 and G5 dendrimers form similar hexagonal complexes upon incubation with siRNA molecules for 20 minutes with average full width of 43±19.3 nm and 62±8.3 at half the maximum height, respectively. AFM images show that these G4 and G5 dendriplexes were attacked by RNase V1 enzyme leading to degradation of the exposed RNA molecules that increased with the increase in incubation time. In comparison, incubating G4 and G5 dendrimers with siRNA for 24 hours led to the formation of large particles with average full width of 263±60 nm and 48.3±2.5 nm at half the maximum height, respectively. Both G4 and G5 dendriplexes had a dense central core that proved to shield the loaded RNA molecules from enzymatic attack for up to 60 minutes. These results show the feasibility of formulating G4 and G5 dendriplexes at a low N/P (+/−) ratio that can resist degradation by RNase enzymes, which reduces the risk of inducing non-specific toxicity when used in vivo.
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48
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Laurini E, Da Col V, Wünsch B, Pricl S. Analysis of the molecular interactions of the potent analgesic S1RA with the σ1 receptor. Bioorg Med Chem Lett 2013; 23:2868-71. [PMID: 23582276 DOI: 10.1016/j.bmcl.2013.03.087] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 03/18/2013] [Accepted: 03/22/2013] [Indexed: 10/27/2022]
Abstract
The highly selective σ1 receptor antagonist S1RA is endowed with a surprisingly high affinity for its target protein given a missing fundamental hydrophobic pharmacophoric requirement. Here we show that, with respect to other potent σ1 ligands, S1RA is able to compensate this loss by fulfilling all other pharmacophoric requirements and by gaining in solvation energy.
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Affiliation(s)
- Erik Laurini
- Molecular Simulation Engineering (MOSE) Laboratory - DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy
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49
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Li G, Hu Z, Yin H, Zhang Y, Huang X, Wang S, Li W. A novel dendritic nanocarrier of polyamidoamine-polyethylene glycol-cyclic RGD for "smart" small interfering RNA delivery and in vitro antitumor effects by human ether-à-go-go-related gene silencing in anaplastic thyroid carcinoma cells. Int J Nanomedicine 2013; 8:1293-306. [PMID: 23569377 PMCID: PMC3615931 DOI: 10.2147/ijn.s41555] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The application of RNA interference techniques is promising in gene therapeutic approaches, especially for cancers. To improve safety and efficiency of small interfering RNA (siRNA) delivery, a triblock dendritic nanocarrier, polyamidoamine-polyethylene glycol-cyclic RGD (PAMAM-PEG-cRGD), was developed and studied as an siRNA vector targeting the human ether-à-go-go-related gene (hERG) in human anaplastic thyroid carcinoma cells. Structure characterization, particle size, zeta potential, and gel retardation assay confirmed that complete triblock components were successfully synthesized with effective binding capacity of siRNA in this triblock nanocarrier. Cytotoxicity data indicated that conjugation of PEG significantly alleviated cytotoxicity when compared with unmodified PAMAM. PAMAM-PEG-cRGD exerted potent siRNA cellular internalization in which transfection efficiency measured by flow cytometry was up to 68% when the charge ratio (N/P ratio) was 3.5. Ligand-receptor affinity together with electrostatic interaction should be involved in the nano-siRNA endocytosis mechanism and we then proved that attachment of cRGD enhanced cellular uptake via RGD-integrin recognition. Gene silencing was evaluated by reverse transcription polymerase chain reaction and PAMAM-PEG-cRGD-siRNA complex downregulated the expression of hERG to 26.3% of the control value. Furthermore, gene knockdown of hERG elicited growth suppression as well as activated apoptosis by means of abolishing vascular endothelial growth factor secretion and triggering caspase-3 cascade in anaplastic thyroid carcinoma cells. Our study demonstrates that this novel triblock polymer, PAMAM-PEG-cRGD, exhibits negligible cytotoxicity, effective transfection, “smart” cancer targeting, and therefore is a promising siRNA nanocarrier.
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Affiliation(s)
- Guanhua Li
- Department of Vascular and Thyroid Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
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Laurini E, Marson D, Dal Col V, Fermeglia M, Mamolo MG, Zampieri D, Vio L, Pricl S. Another brick in the wall. Validation of the σ1 receptor 3D model by computer-assisted design, synthesis, and activity of new σ1 ligands. Mol Pharm 2012; 9:3107-26. [PMID: 23020867 DOI: 10.1021/mp300233y] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Originally considered an enigmatic polypeptide, the σ(1) receptor has recently been identified as a unique ligand-regulated protein. Many studies have shown the potential of σ(1) receptor ligands for the treatment of various diseases of the central nervous system (CNS); nevertheless, almost no information about the 3D structure of the receptor and/or the possible modes of interaction of the σ(1) protein with its ligands have been unveiled so far. With the present work we validated our σ(1) 3D homology model and assessed its reliability as a platform for σ(1) ligand structure-based drug design. To this purpose, the 3D σ(1) model was exploited in the design of 33 new σ(1) ligands and in their ranking for receptor affinity by extensive molecular dynamics simulation-based free energy calculations. Also, the main interactions involved in receptor/ligand binding were analyzed by applying a per residue free energy deconvolution and in silico alanine scanning mutagenesis calculations. Subsequently, all compounds were synthesized in our laboratory and tested for σ(1) binding activity in vitro. The agreement between in silico and in vitro results confirms the reliability of the proposed σ(1) 3D model in the a priori prediction of the affinity of new σ(1) ligands. Moreover, it also supports and corroborates the currently available biochemical data concerning the σ(1) protein residues considered essential for σ(1) ligand binding and activity.
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Affiliation(s)
- Erik Laurini
- Molecular Simulation Engineering Laboratory, Department of Industrial Engineering and Information Technology, University of Trieste, Via Valerio 10, 34127 Trieste, Italy
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