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For: Grasso G, Deriu MA, Patrulea V, Borchard G, Möller M, Danani A. Free energy landscape of siRNA-polycation complexation: Elucidating the effect of molecular geometry, polymer flexibility, and charge neutralization. PLoS One 2017;12:e0186816. [PMID: 29088239 PMCID: PMC5663398 DOI: 10.1371/journal.pone.0186816] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/09/2017] [Indexed: 12/16/2022]  Open
Number Cited by Other Article(s)
1
Steinegger KM, Merkel OM. How can simulations aid our understanding of nanoparticle-mediated siRNA delivery? Ther Deliv 2025:1-3. [PMID: 40357536 DOI: 10.1080/20415990.2025.2505397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2025] [Accepted: 05/09/2025] [Indexed: 05/15/2025]  Open
2
Ziebarth JD, Shadman H, Wang Y. Insights from Computational Studies of Polymeric Systems for Nucleic Acid Delivery. Mol Pharm 2025;22:1160-1173. [PMID: 39957182 DOI: 10.1021/acs.molpharmaceut.4c00994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2025]
3
Mohiuddin AKM, Ferdous N, Reza MN, Al Amin M, Khanam R, Hossain MU, Ahammad I, Mahmud S. Designing siRNA for silencing the human ERBB2 gene in cancer treatment: Evaluating intracellular delivery strategies. Comput Biol Med 2025;186:109663. [PMID: 39809083 DOI: 10.1016/j.compbiomed.2025.109663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 12/18/2024] [Accepted: 01/06/2025] [Indexed: 01/16/2025]
4
Dodaro A, Novello G, Menin S, Cavastracci Strascia C, Sturlese M, Salmaso V, Moro S. Post-Docking Refinement of Peptide or Protein-RNA Complexes Using Thermal Titration Molecular Dynamics (TTMD): A Stability Insight. J Chem Inf Model 2025;65:1441-1452. [PMID: 39818831 PMCID: PMC11815843 DOI: 10.1021/acs.jcim.4c01393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 11/09/2024] [Accepted: 12/06/2024] [Indexed: 01/19/2025]
5
Roy P, Kreofsky NW, Reineke TM. Quinine-Based Polymers Are Versatile and Effective Vehicles for Intracellular pDNA, mRNA, and Cas9 Protein Delivery. Biomacromolecules 2024;25:6693-6707. [PMID: 39324490 DOI: 10.1021/acs.biomac.4c00925] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
6
Ying ANJ, Tan YF, Wong YS, Venkatraman S. Sustained intra-cellular siRNA release from poly(L-arginine) multilayered nanoparticles for prolonged gene silencing. Expert Opin Drug Deliv 2024;21:1513-1522. [PMID: 39290161 DOI: 10.1080/17425247.2024.2405206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 09/07/2024] [Accepted: 09/10/2024] [Indexed: 09/19/2024]
7
Muscat S, Martino G, Manigrasso J, Marcia M, De Vivo M. On the Power and Challenges of Atomistic Molecular Dynamics to Investigate RNA Molecules. J Chem Theory Comput 2024. [PMID: 39150960 DOI: 10.1021/acs.jctc.4c00773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2024]
8
Binder J, Winkeljann J, Steinegger K, Trnovec L, Orekhova D, Zähringer J, Hörner A, Fell V, Tinnefeld P, Winkeljann B, Frieß W, Merkel OM. Closing the Gap between Experiment and Simulation─A Holistic Study on the Complexation of Small Interfering RNAs with Polyethylenimine. Mol Pharm 2024;21:2163-2175. [PMID: 38373164 PMCID: PMC7616749 DOI: 10.1021/acs.molpharmaceut.3c00747] [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] [Indexed: 02/21/2024]
9
Marquet F, Hagen H, Stanchieri M, Beinier VS, Grasso G, Danani A, Patrulea V, Borchard G. Clickable polyethyleneimine incorporated into triblock copolymeric micelles as an efficient platform in the delivery of siRNA to NSCLC cells. Int J Pharm 2024;649:123632. [PMID: 38000648 DOI: 10.1016/j.ijpharm.2023.123632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
10
Reza MN, Mahmud S, Ferdous N, Ahammad I, Hossain MU, Al Amin M, Mohiuddin AKM. Gene silencing of Helicobacter pylori through newly designed siRNA convenes the treatment of gastric cancer. Cancer Med 2023;12:22407-22419. [PMID: 38037736 PMCID: PMC10757103 DOI: 10.1002/cam4.6772] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/05/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023]  Open
11
Characterization of the Interaction of Polymeric Micelles with siRNA: A Combined Experimental and Molecular Dynamics Study. Polymers (Basel) 2022;14:polym14204409. [PMID: 36297986 PMCID: PMC9611052 DOI: 10.3390/polym14204409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022]  Open
12
Trofimenko E, Grasso G, Heulot M, Chevalier N, Deriu MA, Dubuis G, Arribat Y, Serulla M, Michel S, Vantomme G, Ory F, Dam LC, Puyal J, Amati F, Lüthi A, Danani A, Widmann C. Genetic, cellular, and structural characterization of the membrane potential-dependent cell-penetrating peptide translocation pore. eLife 2021;10:69832. [PMID: 34713805 PMCID: PMC8639150 DOI: 10.7554/elife.69832] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/28/2021] [Indexed: 12/11/2022]  Open
13
Marquet F, Patrulea V, Borchard G. Comparison of triblock copolymeric micelles based on α- and ε-poly(L-lysine): a Cornelian choice. Polym J 2021. [DOI: 10.1038/s41428-021-00552-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
14
Kumar R, Santa Chalarca CF, Bockman MR, Bruggen CV, Grimme CJ, Dalal RJ, Hanson MG, Hexum JK, Reineke TM. Polymeric Delivery of Therapeutic Nucleic Acids. Chem Rev 2021;121:11527-11652. [PMID: 33939409 DOI: 10.1021/acs.chemrev.0c00997] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
15
Sperti M, Malavolta M, Ciniero G, Borrelli S, Cavaglià M, Muscat S, Tuszynski JA, Afeltra A, Margiotta DPE, Navarini L. JAK inhibitors in immune-mediated rheumatic diseases: From a molecular perspective to clinical studies. J Mol Graph Model 2021;104:107789. [DOI: 10.1016/j.jmgm.2020.107789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 09/21/2020] [Accepted: 10/20/2020] [Indexed: 12/11/2022]
16
Rapallo A, Gaspari R, Grasso G, Danani A. Extended diffusion theory: Recovering dynamics from biased/accelerated molecular simulations. J Comput Chem 2020;42:586-599. [PMID: 33351966 DOI: 10.1002/jcc.26474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/09/2020] [Accepted: 12/02/2020] [Indexed: 11/08/2022]
17
Miyazaki T, Uchida S, Hatano H, Miyahara Y, Matsumoto A, Cabral H. Guanidine-phosphate interactions stabilize polyion complex micelles based on flexible catiomers to improve mRNA delivery. Eur Polym J 2020. [DOI: 10.1016/j.eurpolymj.2020.110028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
18
Uchida S, Perche F, Pichon C, Cabral H. Nanomedicine-Based Approaches for mRNA Delivery. Mol Pharm 2020;17:3654-3684. [PMID: 32845639 DOI: 10.1021/acs.molpharmaceut.0c00618] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
19
Miyazaki T, Uchida S, Nagatoishi S, Koji K, Hong T, Fukushima S, Tsumoto K, Ishihara K, Kataoka K, Cabral H. Polymeric Nanocarriers with Controlled Chain Flexibility Boost mRNA Delivery In Vivo through Enhanced Structural Fastening. Adv Healthc Mater 2020;9:e2000538. [PMID: 32583633 DOI: 10.1002/adhm.202000538] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/29/2020] [Indexed: 12/20/2022]
20
Batys P, Morga M, Bonarek P, Sammalkorpi M. pH-Induced Changes in Polypeptide Conformation: Force-Field Comparison with Experimental Validation. J Phys Chem B 2020;124:2961-2972. [PMID: 32182068 PMCID: PMC7590956 DOI: 10.1021/acs.jpcb.0c01475] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Indexed: 12/17/2022]
21
Stojceski F, Grasso G, Pallante L, Danani A. Molecular and Coarse-Grained Modeling to Characterize and Optimize Dendrimer-Based Nanocarriers for Short Interfering RNA Delivery. ACS OMEGA 2020;5:2978-2986. [PMID: 32095720 PMCID: PMC7033960 DOI: 10.1021/acsomega.9b03908] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
22
Grasso G, Mercuri S, Danani A, Deriu MA. Biofunctionalization of Silica Nanoparticles with Cell-Penetrating Peptides: Adsorption Mechanism and Binding Energy Estimation. J Phys Chem B 2019;123:10622-10630. [DOI: 10.1021/acs.jpcb.9b08106] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
23
Gurtovenko AA. Molecular-Level Insight into the Interactions of DNA/Polycation Complexes with Model Cell Membranes. J Phys Chem B 2019;123:6505-6514. [DOI: 10.1021/acs.jpcb.9b05110] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
24
Grasso G, Morbiducci U, Massai D, Tuszynski JA, Danani A, Deriu MA. Destabilizing the AXH Tetramer by Mutations: Mechanisms and Potential Antiaggregation Strategies. Biophys J 2019;114:323-330. [PMID: 29401430 DOI: 10.1016/j.bpj.2017.11.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/03/2017] [Accepted: 11/20/2017] [Indexed: 01/12/2023]  Open
25
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: 46] [Impact Index Per Article: 6.6] [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
26
Deriu MA, Tsapis N, Noiray M, Grasso G, El Brahmi N, Mignani S, Majoral JP, Fattal E, Danani A. Elucidating the role of surface chemistry on cationic phosphorus dendrimer-siRNA complexation. NANOSCALE 2018;10:10952-10962. [PMID: 29850714 DOI: 10.1039/c8nr01928b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
27
Grasso G, Muscat S, Rebella M, Morbiducci U, Audenino A, Danani A, Deriu MA. Cell penetrating peptide modulation of membrane biomechanics by Molecular dynamics. J Biomech 2018;73:137-144. [PMID: 29631749 DOI: 10.1016/j.jbiomech.2018.03.036] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/14/2018] [Accepted: 03/21/2018] [Indexed: 11/17/2022]
28
Supramolecular complexes of DNA with cationic polymers: The effect of polymer concentration. POLYMER 2018. [DOI: 10.1016/j.polymer.2018.03.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
29
Grasso G, Rebella M, Muscat S, Morbiducci U, Tuszynski J, Danani A, Deriu MA. Conformational Dynamics and Stability of U-Shaped and S-Shaped Amyloid β Assemblies. Int J Mol Sci 2018;19:ijms19020571. [PMID: 29443891 PMCID: PMC5855793 DOI: 10.3390/ijms19020571] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/04/2018] [Accepted: 02/10/2018] [Indexed: 11/16/2022]  Open
30
Mlýnský V, Bussi G. Exploring RNA structure and dynamics through enhanced sampling simulations. Curr Opin Struct Biol 2018;49:63-71. [PMID: 29414513 DOI: 10.1016/j.sbi.2018.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/20/2017] [Accepted: 01/02/2018] [Indexed: 01/23/2023]
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