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Barraza GA, Castro-Guijarro AC, de la Fuente Hoffmann V, Bolívar Ávila SJ, Flamini MI, Sanchez AM. Drug repositioning for rosacea disease: Biological TARGET identification, molecular docking, pharmacophore mapping, and molecular dynamics analysis. Comput Biol Med 2024; 181:108988. [PMID: 39168013 DOI: 10.1016/j.compbiomed.2024.108988] [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: 04/18/2024] [Revised: 07/16/2024] [Accepted: 08/02/2024] [Indexed: 08/23/2024]
Abstract
Rosacea is a chronic dermatological condition that currently lacks a clear treatment approach due to an uncomprehensive knowledge of its pathogenesis. The main obstacle lies in understanding its etiology and the mode of action of the different drugs used. This study aims to clarify these aspects by employing drug repositioning. Using an in silico approach, we performed a transcriptomic analysis comparing samples from individuals with diverse types of rosacea to those from healthy controls to identify genes deregulated in this disease. Subsequently, we realized molecular docking and molecular dynamics studies to assess the binding affinity of drugs currently used to treat rosacea and drugs that target proteins interacting with, and thus affecting, proteins deregulated in rosacea. Our findings revealed that the downregulation of SKAP2 and upregulation of S100A7A in rosacea, could be involved in the pathogenesis of the disease. Furthermore, considering the drugs currently used for rosacea management, we demonstrated stable interactions between isotretinoin and BFH772 with SKAP2, and permethrin and PAC-14028 with S100A7A. Similarly, considering drugs targeting SKAP2 and S100A7A interactome proteins, we found that pitavastatin and dasatinib exert stable interactions with SKAP2, and lovastatin and tirbanibulin with S100A7A. In addition, we determine that the types of bonds involved in the interactions were different in SKAP2 from S100A7A. The drug-SKAP2 interactions are hydrogen bonds, whereas the drug-S100A7A interactions are of the hydrophobic type. In conclusion, our study provides evidence for the possible contribution of SKAP2 and S100A7A to rosacea pathology. Furthermore, it provides significant information on the molecular interactions between drugs and these proteins, highlighting the importance of considering structural features and binding interactions in the design of targeted therapies for skin disorders such as rosacea.
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Affiliation(s)
- Gustavo Adolfo Barraza
- Laboratorio de Transducción de Señales y Movimiento Celular, Instituto de Medicina y Biología Experimental de Cuyo (IMBECU), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Ana Carla Castro-Guijarro
- Laboratorio de Biología Tumoral, Instituto de Medicina y Biología Experimental de Cuyo (IMBECU), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Valentina de la Fuente Hoffmann
- Laboratorio de Transducción de Señales y Movimiento Celular, Instituto de Medicina y Biología Experimental de Cuyo (IMBECU), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Santiago Junior Bolívar Ávila
- Instituto de Química Rosario (IQUIR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Santa Fe, Argentina
| | - Marina Inés Flamini
- Laboratorio de Biología Tumoral, Instituto de Medicina y Biología Experimental de Cuyo (IMBECU), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, Mendoza, Argentina.
| | - Angel Matias Sanchez
- Laboratorio de Transducción de Señales y Movimiento Celular, Instituto de Medicina y Biología Experimental de Cuyo (IMBECU), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, Mendoza, Argentina.
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Hilburg SL, Jin T, Alexander-Katz A. Dynamic transformation of bio-inspired single-chain nanoparticles at interfaces. J Chem Phys 2023; 159:114902. [PMID: 37712796 DOI: 10.1063/5.0164475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/24/2023] [Indexed: 09/16/2023] Open
Abstract
The interfacial behavior of macromolecules dictates their intermolecular interactions, which can impact the processing and application of polymers for pharmaceutical and synthetic use. Using molecular dynamics simulations, we observe the evolution of a random heteropolymer in the presence of liquid-liquid interfaces. The system of interest forms single-chain nanoparticles through hydrophobic collapse in water, lacking permanent crosslinks and making their morphology mutable in new environments. Complex amphiphilic polymers are shown to be capable of stabilizing high interfacial tension water-hexane interfaces, often unfolding to maximize surface coverage. Despite drastic changes to polymer conformation, monomer presence in the water phase is generally maintained and most changes are due to increased hydrophobic solvent exposure toward the oil phase. These results are then compared to the behavior at the water-graphene interface, where the macromolecules adsorb but do not remodel. The polymer's behavior is shown to depend significantly on both its own amphiphilic character and the deformability of the interface.
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Affiliation(s)
- Shayna L Hilburg
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tianyi Jin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Qian Z, Zhu YL, Lu ZY, Qian HJ. Unexpected Solvent Effect Leading to Interface Segregation of Single-Chain Nanoparticles in All-Polymer Nanocomposite Films upon Solvent Evaporation. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c02061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Zhao Qian
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - You-Liang Zhu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Zhong-Yuan Lu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Hu-Jun Qian
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
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Zhang P, Wang Z, Wang ZG. Conformation Transition of a Homopolymer Chain in Binary Mixed Solvents. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Pengfei Zhang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-Dimension Materials, College of Material Science and Engineering, Donghua University, Shanghai 201620, China
| | - Zheng Wang
- School of Physics, Nankai University, Tianjin 300071, China
| | - Zhen-Gang Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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Hilburg SL, Alexander-Katz A. Solvent Remodeling in Single-Chain Amphiphilic Heteropolymer Systems. Macromol Rapid Commun 2022; 43:e2200142. [PMID: 35298063 DOI: 10.1002/marc.202200142] [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: 02/15/2022] [Revised: 03/08/2022] [Indexed: 11/08/2022]
Abstract
This work demonstrates the remodeling of single-chain nanoparticles (SCNPs) upon a transition to organic solvent through molecular dynamics simulations. Methacrylate-based random heteropolymers (RHPs), assembled via transient non-covalent linkages in water, have shown promise in an assortment of applications that harness their bio-inspired properties. While their molecular behavior has been broadly characterized in aqueous environments, many newer applications include the use of organic solvent rather than bio-mimetic conditions. The polymer assemblies, typically driven by the hydrophobic effect in water, are less well understood in non-aqueous solution. Here, a specific RHP system is examined which forms compact globular morphologies in highly polar or highly non-polar environments while adopting extended conformations in solvents of intermediate polarity. The pivotal role of electrostatic interactions between charge groups in low dielectric mediums is also observed. Finally, high temperature anneal cycles are compared to room temperature transformations to illuminate barriers to remodeling upon environmental changes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shayna L Hilburg
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
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Liao S, Wei L, Abriata LA, Stellacci F. Control and Characterization of the Compactness of Single-Chain Nanoparticles. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c02071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suiyang Liao
- Institute of Materials, École Polytechnique Fédérale de Lausanne, Station 12, 1015 Lausanne, Switzerland
| | - Lixia Wei
- Institute of Materials, École Polytechnique Fédérale de Lausanne, Station 12, 1015 Lausanne, Switzerland
| | - Luciano A. Abriata
- Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Francesco Stellacci
- Institute of Materials, École Polytechnique Fédérale de Lausanne, Station 12, 1015 Lausanne, Switzerland
- Interfaculty Bioengineering Institute, École Polytechnique Fédérale de Lausanne, Station 12, 1015 Lausanne, Switzerland
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Luo J, Zhu Y, Ruan Y, Wu W, Ouyang X, Du Z, Liu G. Diameter and Elasticity Governing the Relaxation of Soft-Nanoparticle Melts. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jintian Luo
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-dimension Materials, College of Material Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yihui Zhu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-dimension Materials, College of Material Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yifu Ruan
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-dimension Materials, College of Material Science and Engineering, Donghua University, Shanghai 201620, China
| | - Weiwei Wu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-dimension Materials, College of Material Science and Engineering, Donghua University, Shanghai 201620, China
| | - Xikai Ouyang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-dimension Materials, College of Material Science and Engineering, Donghua University, Shanghai 201620, China
| | - Zhukang Du
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - GengXin Liu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-dimension Materials, College of Material Science and Engineering, Donghua University, Shanghai 201620, China
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Blazquez-Martín A, Verde-Sesto E, Moreno AJ, Arbe A, Colmenero J, Pomposo JA. Advances in the Multi-Orthogonal Folding of Single Polymer Chains into Single-Chain Nanoparticles. Polymers (Basel) 2021; 13:293. [PMID: 33477597 PMCID: PMC7831314 DOI: 10.3390/polym13020293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 11/16/2022] Open
Abstract
The folding of certain proteins (e.g., enzymes) into perfectly defined 3D conformations via multi-orthogonal interactions is critical to their function. Concerning synthetic polymers chains, the "folding" of individual polymer chains at high dilution via intra-chain interactions leads to so-called single-chain nanoparticles (SCNPs). This review article describes the advances carried out in recent years in the folding of single polymer chains into discrete SCNPs via multi-orthogonal interactions using different reactive chemical species where intra-chain bonding only occurs between groups of the same species. First, we summarize results from computer simulations of multi-orthogonally folded SCNPs. Next, we comprehensively review multi-orthogonally folded SCNPs synthesized via either non-covalent bonds or covalent interactions. Finally, we conclude by summarizing recent research about multi-orthogonally folded SCNPs prepared through both reversible (dynamic) and permanent bonds.
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Affiliation(s)
- Agustín Blazquez-Martín
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; (A.B.-M.); (E.V.-S.); (A.J.M.); (A.A.); (J.C.)
| | - Ester Verde-Sesto
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; (A.B.-M.); (E.V.-S.); (A.J.M.); (A.A.); (J.C.)
| | - Angel J. Moreno
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; (A.B.-M.); (E.V.-S.); (A.J.M.); (A.A.); (J.C.)
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, E-20018 San Sebastián, Spain
| | - Arantxa Arbe
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; (A.B.-M.); (E.V.-S.); (A.J.M.); (A.A.); (J.C.)
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, E-20018 San Sebastián, Spain
| | - Juan Colmenero
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; (A.B.-M.); (E.V.-S.); (A.J.M.); (A.A.); (J.C.)
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, E-20018 San Sebastián, Spain
- Departamento de Polímeros y Materiales Avanzados: Física, Química y Tecnología, University of the Basque Country (UPV/EHU), PO Box 1072, E-20800 San Sebastián, Spain
| | - José A. Pomposo
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; (A.B.-M.); (E.V.-S.); (A.J.M.); (A.A.); (J.C.)
- Departamento de Polímeros y Materiales Avanzados: Física, Química y Tecnología, University of the Basque Country (UPV/EHU), PO Box 1072, E-20800 San Sebastián, Spain
- IKERBASQUE—Basque Foundation for Science, Plaza Euskadi 5, E-48009 Bilbao, Spain
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