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Sun JW, Thomas JS, Monkovic JM, Gibson H, Nagapurkar A, Frezzo JA, Katyal P, Punia K, Mahmoudinobar F, Renfrew PD, Montclare JK. Supercharged coiled-coil protein with N-terminal decahistidine tag boosts siRNA complexation and delivery efficiency of a lipoproteoplex. J Pept Sci 2024; 30:e3594. [PMID: 38499991 DOI: 10.1002/psc.3594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
Abstract
Short interfering RNA (siRNA) therapeutics have soared in popularity due to their highly selective and potent targeting of faulty genes, providing a non-palliative approach to address diseases. Despite their potential, effective transfection of siRNA into cells requires the assistance of an accompanying vector. Vectors constructed from non-viral materials, while offering safer and non-cytotoxic profiles, often grapple with lackluster loading and delivery efficiencies, necessitating substantial milligram quantities of expensive siRNA to confer the desired downstream effects. We detail the recombinant synthesis of a diverse series of coiled-coil supercharged protein (CSP) biomaterials systematically designed to investigate the impact of two arginine point mutations (Q39R and N61R) and decahistidine tags on liposomal siRNA delivery. The most efficacious variant, N8, exhibits a twofold increase in its affinity to siRNA and achieves a twofold enhancement in transfection activity with minimal cytotoxicity in vitro. Subsequent analysis unveils the destabilizing effect of the Q39R and N61R supercharging mutations and the incorporation of C-terminal decahistidine tags on α-helical secondary structure. Cross-correlational regression analyses reveal that the amount of helical character in these mutants is key in N8's enhanced siRNA complexation and downstream delivery efficiency.
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Affiliation(s)
- Jonathan W Sun
- Department of Chemistry, New York University, New York, New York, USA
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Joseph S Thomas
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Julia M Monkovic
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Halle Gibson
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Akash Nagapurkar
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Joseph A Frezzo
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Priya Katyal
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Kamia Punia
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Farbod Mahmoudinobar
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA
| | - P Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA
| | - Jin Kim Montclare
- Department of Chemistry, New York University, New York, New York, USA
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
- Department of Radiology, NYU Grossman School of Medicine, New York, New York, USA
- Department of Biomaterials, NYU College of Dentistry, New York, New York, USA
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Miguel Pereira Souza L, Camacho Lima M, Filipe Silva Bezerra L, Silva Pimentel A. Transposition of polymer-encapsulated small interfering RNA through lung surfactant models at the air-water interface. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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3
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Terteci-Popescu AE, Beu TA. Branched polyethyleneimine: CHARMM force field and molecular dynamics simulations. J Comput Chem 2022; 43:2072-2083. [PMID: 36169240 DOI: 10.1002/jcc.27005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/11/2022]
Abstract
Polyethyleneimine (PEI), one of the non-viral vectors of great interest for gene delivery, was investigated at all-atom level, with particular emphasis on its branched form. We report the extension of our previously published CHARMM force field (FF) for linear PEI, with parameters optimized specifically for branched configurations. A new residue type for the branch connector is introduced and the charges and bonded parameters are derived from ab initio calculations based on a model polymer. The new FF is validated by extensive molecular dynamics simulations of solvated branched PEIs of various protonation fractions and branch lengths. The gyration radii, end-to-end distances, and diffusion coefficients are compared with results for linear PEIs of similar molecular weights and protonation patterns. Solvated complexes of DNA with (linear/branched) PEI were also investigated to determine favorable attachment conformations. The parametrized atomistic force field is suitable for simulations of PEI with arbitrary branching pattern, protonation, and size, and is expected to provide relevant insights regarding optimal conditions for DNA-PEI complex formation.
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Affiliation(s)
| | - Titus Adrian Beu
- Faculty of Physics, Department of Biomolecular Physics, University Babeş-Bolyai, Cluj-Napoca, Romania
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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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Mahajan S, Tang T. Polyethylenimine-DNA Nanoparticles under Endosomal Acidification and Implication to Gene Delivery. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8382-8397. [PMID: 35759612 DOI: 10.1021/acs.langmuir.2c00952] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Non-viral gene delivery using polyethylenimine (PEI) has shown tremendous promise as a therapeutic technique. Through the formation of nanoparticles (NPs), PEIs protect genetic material such as DNA from degradation. Escape of the NPs from endosomes and lysosomes is facilitated by PEI's buffering capacity over a wide range of pH. However, little is known about the effects of endosomal acidification on the morphology of the NPs. In this work, large-scale coarse-grained simulations performed to mimic endosomal acidification reveal that NPs undergo a resizing process that is highly dependent on the N/P ratio (ratio of PEI nitrogen to DNA phosphate) at which they are prepared. With a low N/P ratio, NPs further aggregate after endosomal acidification, whereas with a high N/P ratio they dissociate. The mechanisms behind such NP resizing and its consequences on endosomal escape and nuclear trafficking are discussed. Based on the findings, suggestions are made on the PEI architecture that may enhance NP dissociation driven by endosomal acidification.
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Affiliation(s)
- Subhamoy Mahajan
- Department of Mechanical Engineering, University of Alberta, Edmonton T6G 2R3, Alberta, Canada
| | - Tian Tang
- Department of Mechanical Engineering, University of Alberta, Edmonton T6G 2R3, Alberta, Canada
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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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Coarse-Grained Models of RNA Nanotubes for Large Time Scale Studies in Biomedical Applications. Biomedicines 2020; 8:biomedicines8070195. [PMID: 32640509 PMCID: PMC7400038 DOI: 10.3390/biomedicines8070195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/16/2020] [Accepted: 07/04/2020] [Indexed: 01/13/2023] Open
Abstract
In order to describe the physical properties of large time scale biological systems, coarse-grained models play an increasingly important role. In this paper we develop Coarse-Grained (CG) models for RNA nanotubes and then, by using Molecular Dynamics (MD) simulation, we study their physical properties. Our exemplifications include RNA nanotubes of 40 nm long, equivalent to 10 RNA nanorings connected in series. The developed methodology is based on a coarse-grained representation of RNA nanotubes, where each coarse bead represents a group of atoms. By decreasing computation cost, this allows us to make computations feasible for realistic structures of interest. In particular, for the developed coarse-grained models with three bead approximations, we calculate the histograms for the bond angles and the dihedral angles. From the dihedral angle histograms, we analyze the characteristics of the links used to build the nanotubes. Furthermore, we also calculate the bead distances along the chains of RNA strands in the nanoclusters. The variations in these features with the size of the nanotube are discussed in detail. Finally, we present the results on the calculation of the root mean square deviations for a developed RNA nanotube to demonstrate the equilibration of the systems for drug delivery and other biomedical applications such as medical imaging and tissue engineering.
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Beu TA, Ailenei AE, Costinaş RI. Martini Force Field for Protonated Polyethyleneimine. J Comput Chem 2020; 41:349-361. [PMID: 31762047 DOI: 10.1002/jcc.26110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 01/02/2023]
Abstract
Polyethyleneimine (PEI), one of the most widely used nonviral gene carriers, was investigated in the presented work at coarse-grained (CG) level. The main focus was on elaborating a realistic CG force field (FF) aimed to reproduce dynamic structural features of protonated PEI chains and, furthermore, to enable massive simulations of DNA-PEI complex formation and condensation. We parametrized CG Martini FF models for PEI in polarizable and nonpolarizable water by applying Boltzmann inversion techniques to all-atom (AA) probability distributions for distances, angles, and dihedrals of entire monomers. The fine-tuning of the FFs was achieved by fitting simulated CG gyration radii and end-to-end distances to their AA counterparts. The developed Martini FF models are shown to be well suited for realistic large-scale simulations of size/protonation-dependent behavior of solvated PEI chains, either individually or as part of DNA-PEI systems. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Titus Adrian Beu
- Faculty of Physics, Department of Biomolecular Physics, University Babeş-Bolyai, Mihail Kogălniceanu Street 1, Cluj-Napoca, 400084, Romania
| | - Andrada-Elena Ailenei
- Faculty of Physics, Department of Biomolecular Physics, University Babeş-Bolyai, Mihail Kogălniceanu Street 1, Cluj-Napoca, 400084, Romania
| | - Răzvan-Ioan Costinaş
- Faculty of Physics, Department of Biomolecular Physics, University Babeş-Bolyai, Mihail Kogălniceanu Street 1, Cluj-Napoca, 400084, Romania
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9
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Li S, Xu Q, Li K, Yu C, Zhou Y. High-χ alternating copolymers for accessing sub-5 nm domains via simulations. Phys Chem Chem Phys 2020; 22:5577-5583. [DOI: 10.1039/d0cp00383b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on molecular dynamics simulations, we designed novel high-χ alternating copolymers (ACPs) for fabricating sub-5 nm domains.
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Affiliation(s)
- Shanlong Li
- School of Chemistry & Chemical Engineering
- Frontiers Science Center for Transformative Molecules
- Shanghai Key Laboratory of Electrical Insulation and Thermal Aging
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Qingsong Xu
- School of Chemistry & Chemical Engineering
- Frontiers Science Center for Transformative Molecules
- Shanghai Key Laboratory of Electrical Insulation and Thermal Aging
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Ke Li
- School of Chemistry & Chemical Engineering
- Frontiers Science Center for Transformative Molecules
- Shanghai Key Laboratory of Electrical Insulation and Thermal Aging
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Chunyang Yu
- School of Chemistry & Chemical Engineering
- Frontiers Science Center for Transformative Molecules
- Shanghai Key Laboratory of Electrical Insulation and Thermal Aging
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Yongfeng Zhou
- School of Chemistry & Chemical Engineering
- Frontiers Science Center for Transformative Molecules
- Shanghai Key Laboratory of Electrical Insulation and Thermal Aging
- Shanghai Jiao Tong University
- Shanghai 200240
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Mahajan S, Tang T. Polyethylenimine–DNA Ratio Strongly Affects Their Nanoparticle Formation: A Large-Scale Coarse-Grained Molecular Dynamics Study. J Phys Chem B 2019; 123:9629-9640. [DOI: 10.1021/acs.jpcb.9b07031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Subhamoy Mahajan
- Department of Mechanical Engineering, University of Alberta, Edmonton, AB, Canada
| | - Tian Tang
- Department of Mechanical Engineering, University of Alberta, Edmonton, AB, Canada
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11
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Ke X, Wei Z, Wang Y, Shen S, Ren Y, Williford JM, Luijten E, Mao HQ. Subtle changes in surface-tethered groups on PEGylated DNA nanoparticles significantly influence gene transfection and cellular uptake. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2019; 19:126-135. [PMID: 31048082 DOI: 10.1016/j.nano.2019.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 04/03/2019] [Accepted: 04/09/2019] [Indexed: 12/18/2022]
Abstract
PEGylation strategy has been widely used to enhance colloidal stability of polycation/DNA nanoparticles (NPs) for gene delivery. To investigate the effect of polyethylene glycol (PEG) terminal groups on the transfection properties of these NPs, we synthesized DNA NPs using PEG-g-linear polyethyleneimine (lPEI) with PEG terminal groups containing alkyl chains of various lengths with or without a hydroxyl terminal group. For both alkyl- and hydroxyalkyl-decorated NPs with PEG grafting densities of 1.5, 3, or 5% on lPEI, the highest levels of transfection and uptake were consistently achieved at intermediate alkyl chain lengths of 3 to 6 carbons, where the transfection efficiency is significantly higher than that of nonfunctionalized lPEI/DNA NPs. Molecular dynamics simulations revealed that both alkyl- and hydroxyalkyl-decorated NPs with intermediate alkyl chain length exhibited more rapid engulfment than NPs with shorter or longer alkyl chains. This study identifies a new parameter for the engineering design of PEGylated DNA NPs.
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Affiliation(s)
- Xiyu Ke
- Department of Materials Science and Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States; Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, United States
| | - Zonghui Wei
- Graduate Program in Applied Physics, Northwestern University, Evanston, IL, United States
| | - Ying Wang
- Department of Materials Science and Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States; Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, United States
| | - Sabrina Shen
- Department of Materials Science and Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Yong Ren
- Department of Materials Science and Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States; Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, United States
| | | | - Erik Luijten
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States; Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, United States; Department of Physics and Astronomy, Northwestern University, Evanston, IL, United States.
| | - Hai-Quan Mao
- Department of Materials Science and Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States; Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, United States; Translational Tissue Engineering Center and Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, United States.
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Beu TA, Ailenei AE, Farcaş A. CHARMM force field for protonated polyethyleneimine. J Comput Chem 2018; 39:2564-2575. [PMID: 30365171 DOI: 10.1002/jcc.25637] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/14/2018] [Accepted: 09/14/2018] [Indexed: 01/25/2023]
Abstract
We present a revised version of our previously published atomistic Chemistry at Harvard Macromolecular Mechanics (CHARMM) force field for polyethyleneimine (PEI). It is based on new residue types (with symmetric CNC backbone), whose integer charges and bonded parameters are derived from ab initio calculations on an enlarged set of model polymers. The force field is validated by extensive molecular dynamics simulations on solvated PEI chains of various lengths and protonation patterns. The profiles of the gyration radius, end-to-end distance, and diffusion coefficient fine-tune our previous results, while the simulated diffusion coefficients excellently reproduce experimental findings. The developed CHARMM force field is suitable for realistic atomistic simulations of size/protonation-dependent behavior of PEI chains, either individually or composing polyplexes, but also provides reliable all-atom distributions for deriving coarse-grained force fields for PEI. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Titus Adrian Beu
- University Babeş-Bolyai, Faculty of Physics, Department of Biomolecular Physics, 1 Mihail Kogălniceanu Street, Cluj-Napoca 400084, Romania
| | - Andrada-Elena Ailenei
- University Babeş-Bolyai, Faculty of Physics, Department of Biomolecular Physics, 1 Mihail Kogălniceanu Street, Cluj-Napoca 400084, Romania
| | - Alexandra Farcaş
- University Babeş-Bolyai, Faculty of Physics, Department of Biomolecular Physics, 1 Mihail Kogălniceanu Street, Cluj-Napoca 400084, Romania
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14
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Mahajan S, Tang T. Martini coarse-grained model for polyethylenimine. J Comput Chem 2018; 40:607-618. [DOI: 10.1002/jcc.25747] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 10/10/2018] [Accepted: 10/13/2018] [Indexed: 01/16/2023]
Affiliation(s)
- Subhamoy Mahajan
- Department of Mechanical Engineering; University of Alberta; Edmonton Alberta Canada
| | - Tian Tang
- Department of Mechanical Engineering; University of Alberta; Edmonton Alberta Canada
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Ferracini R, Martínez Herreros I, Russo A, Casalini T, Rossi F, Perale G. Scaffolds as Structural Tools for Bone-Targeted Drug Delivery. Pharmaceutics 2018; 10:pharmaceutics10030122. [PMID: 30096765 PMCID: PMC6161191 DOI: 10.3390/pharmaceutics10030122] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/02/2018] [Accepted: 08/03/2018] [Indexed: 12/19/2022] Open
Abstract
Although bone has a high potential to regenerate itself after damage and injury, the efficacious repair of large bone defects resulting from resection, trauma or non-union fractures still requires the implantation of bone grafts. Materials science, in conjunction with biotechnology, can satisfy these needs by developing artificial bones, synthetic substitutes and organ implants. In particular, recent advances in materials science have provided several innovations, underlying the increasing importance of biomaterials in this field. To address the increasing need for improved bone substitutes, tissue engineering seeks to create synthetic, three-dimensional scaffolds made from organic or inorganic materials, incorporating drugs and growth factors, to induce new bone tissue formation. This review emphasizes recent progress in materials science that allows reliable scaffolds to be synthesized for targeted drug delivery in bone regeneration, also with respect to past directions no longer considered promising. A general overview concerning modeling approaches suitable for the discussed systems is also provided.
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Affiliation(s)
- Riccardo Ferracini
- Department of Surgical Sciences, Orthopaedic Clinic-IRCCS A.O.U. San Martino, 16132 Genova, Italy.
| | - Isabel Martínez Herreros
- Department of Surgical Sciences, Orthopaedic Clinic-IRCCS A.O.U. San Martino, 16132 Genova, Italy.
| | - Antonio Russo
- Department of Surgical Sciences, Orthopaedic Clinic-IRCCS A.O.U. San Martino, 16132 Genova, Italy.
| | - Tommaso Casalini
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland.
- Biomaterials Laboratory, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland, Via Cantonale 2C, Galleria, 26928 Manno, Switzerland.
| | - Filippo Rossi
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, 20131 Milano, Italy.
| | - Giuseppe Perale
- Department of Surgical Sciences, Orthopaedic Clinic-IRCCS A.O.U. San Martino, 16132 Genova, Italy.
- Biomaterials Laboratory, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland, Via Cantonale 2C, Galleria, 26928 Manno, Switzerland.
- Industrie Biomediche Insubri SA, Via Cantonale 67, 6805 Mezzovico-Vira, Switzerland.
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16
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Beu TA, Farcaş A. CHARMM force field and molecular dynamics simulations of protonated polyethylenimine. J Comput Chem 2017; 38:2335-2348. [DOI: 10.1002/jcc.24890] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/16/2017] [Accepted: 06/30/2017] [Indexed: 01/16/2023]
Affiliation(s)
- Titus Adrian Beu
- Faculty of Physics; Department of Biomolecular Physics, University Babeş-Bolyai; Mihail Kogălniceanu Street 1 Cluj-Napoca 400084 Romania
| | - Alexandra Farcaş
- Faculty of Physics; Department of Biomolecular Physics, University Babeş-Bolyai; Mihail Kogălniceanu Street 1 Cluj-Napoca 400084 Romania
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17
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Uusitalo JJ, Ingólfsson HI, Marrink SJ, Faustino I. Martini Coarse-Grained Force Field: Extension to RNA. Biophys J 2017. [PMID: 28633759 DOI: 10.1016/j.bpj.2017.05.043] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
RNA has an important role not only as the messenger of genetic information but also as a regulator of gene expression. Given its central role in cell biology, there is significant interest in studying the structural and dynamic behavior of RNA in relation to other biomolecules. Coarse-grain molecular dynamics simulations are a key tool to that end. Here, we have extended the coarse-grain Martini force field to include RNA after our recent extension to DNA. In the same way DNA was modeled, the tertiary structure of RNA is constrained using an elastic network. This model, therefore, is not designed for applications involving RNA folding but rather offers a stable RNA structure for studying RNA interactions with other (bio)molecules. The RNA model is compatible with all other Martini models and opens the way to large-scale explicit-solvent molecular dynamics simulations of complex systems involving RNA.
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Affiliation(s)
- Jaakko J Uusitalo
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Helgi I Ingólfsson
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.
| | - Ignacio Faustino
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
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18
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Ziebarth JD, Kennetz DR, Walker NJ, Wang Y. Structural Comparisons of PEI/DNA and PEI/siRNA Complexes Revealed with Molecular Dynamics Simulations. J Phys Chem B 2017; 121:1941-1952. [PMID: 28145711 PMCID: PMC5677264 DOI: 10.1021/acs.jpcb.6b10775] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Polyplexes composed of polyethyleneimine (PEI) and DNA or siRNA have attracted great attention for their use in gene therapy. Although many physicochemical characteristics of these polyplexes remain unknown, PEI/DNA complexes have been repeatedly shown to be more stable than their PEI/siRNA counterparts. Here, we examine potential causes for this difference using atomistic molecular dynamics simulations of complexation between linear PEI and DNA or siRNA duplexes containing the same number of bases. The two types of polyplexes are stabilized by similar interactions, as PEI amines primarily interact with nucleic acid phosphate groups but also occasionally interact with groove atoms of both nucleic acids. However, the number of interactions in PEI/DNA complexes is greater than in comparable PEI/siRNA complexes, with interactions between protonated PEI amines and DNA being particularly enhanced. These results indicate that structural differences between DNA and siRNA may play a role in the increased stability of PEI/DNA complexes. In addition, we investigate the binding of PEI chains to polyplexes that have a net positive charge. The binding of PEI to these overcharged complexes involves interactions between PEI and areas on the nucleic acid surface that have maintained a negative electrostatic potential and is facilitated by the release of water from the nucleic acid.
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Affiliation(s)
- Jesse D Ziebarth
- Department of Chemistry, The University of Memphis , Memphis, Tennessee 38152, United States
| | - Dennis R Kennetz
- Department of Chemistry, The University of Memphis , Memphis, Tennessee 38152, United States
| | - Nyles J Walker
- Department of Chemistry, The University of Memphis , Memphis, Tennessee 38152, United States
| | - Yongmei Wang
- Department of Chemistry, The University of Memphis , Memphis, Tennessee 38152, United States
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