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He S, Nader K, Abarrategi JS, Bediaga H, Nocedo-Mena D, Ascencio E, Casanola-Martin GM, Castellanos-Rubio I, Insausti M, Rasulev B, Arrasate S, González-Díaz H. NANO.PTML model for read-across prediction of nanosystems in neurosciences. computational model and experimental case of study. J Nanobiotechnology 2024; 22:435. [PMID: 39044265 PMCID: PMC11267683 DOI: 10.1186/s12951-024-02660-9] [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: 04/18/2024] [Accepted: 06/24/2024] [Indexed: 07/25/2024] Open
Abstract
Neurodegenerative diseases involve progressive neuronal death. Traditional treatments often struggle due to solubility, bioavailability, and crossing the Blood-Brain Barrier (BBB). Nanoparticles (NPs) in biomedical field are garnering growing attention as neurodegenerative disease drugs (NDDs) carrier to the central nervous system. Here, we introduced computational and experimental analysis. In the computational study, a specific IFPTML technique was used, which combined Information Fusion (IF) + Perturbation Theory (PT) + Machine Learning (ML) to select the most promising Nanoparticle Neuronal Disease Drug Delivery (N2D3) systems. For the application of IFPTML model in the nanoscience, NANO.PTML is used. IF-process was carried out between 4403 NDDs assays and 260 cytotoxicity NP assays conducting a dataset of 500,000 cases. The optimal IFPTML was the Decision Tree (DT) algorithm which shown satisfactory performance with specificity values of 96.4% and 96.2%, and sensitivity values of 79.3% and 75.7% in the training (375k/75%) and validation (125k/25%) set. Moreover, the DT model obtained Area Under Receiver Operating Characteristic (AUROC) scores of 0.97 and 0.96 in the training and validation series, highlighting its effectiveness in classification tasks. In the experimental part, two samples of NPs (Fe3O4_A and Fe3O4_B) were synthesized by thermal decomposition of an iron(III) oleate (FeOl) precursor and structurally characterized by different methods. Additionally, in order to make the as-synthesized hydrophobic NPs (Fe3O4_A and Fe3O4_B) soluble in water the amphiphilic CTAB (Cetyl Trimethyl Ammonium Bromide) molecule was employed. Therefore, to conduct a study with a wider range of NP system variants, an experimental illustrative simulation experiment was performed using the IFPTML-DT model. For this, a set of 500,000 prediction dataset was created. The outcome of this experiment highlighted certain NANO.PTML systems as promising candidates for further investigation. The NANO.PTML approach holds potential to accelerate experimental investigations and offer initial insights into various NP and NDDs compounds, serving as an efficient alternative to time-consuming trial-and-error procedures.
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Affiliation(s)
- Shan He
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, 58108, USA
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain
- IKERDATA S.L., ZITEK, UPV/EHU, Rectorate Building, nº 6, Leioa, 48940, Greater Bilbao, Basque Country, Spain
| | - Karam Nader
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain
| | - Julen Segura Abarrategi
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain
| | - Harbil Bediaga
- IKERDATA S.L., ZITEK, UPV/EHU, Rectorate Building, nº 6, Leioa, 48940, Greater Bilbao, Basque Country, Spain
| | - Deyani Nocedo-Mena
- Faculty of Physical Mathematical Sciences, Autonomous University of Nuevo León, San Nicolás de los Garza, 66455, Nuevo León, México
| | - Estefania Ascencio
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, 58108, USA
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain
- IKERDATA S.L., ZITEK, UPV/EHU, Rectorate Building, nº 6, Leioa, 48940, Greater Bilbao, Basque Country, Spain
| | - Gerardo M Casanola-Martin
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, 58108, USA
| | - Idoia Castellanos-Rubio
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain.
| | - Maite Insausti
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, Leioa, 48940, Spain
| | - Bakhtiyor Rasulev
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, 58108, USA
| | - Sonia Arrasate
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain.
| | - Humberto González-Díaz
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain
- BIOFISIKA: Basque Center for Biophysics CSIC, University of The Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Bizkaia, Basque Country, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, 48011, Biscay, Spain
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Dergunova LV, Filippenkov IB, Limborska SA, Myasoedov NF. Neuroprotective Peptides and New Strategies for Ischemic Stroke Drug Discoveries. Genes (Basel) 2023; 14:genes14050953. [PMID: 37239313 DOI: 10.3390/genes14050953] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/15/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Ischemic stroke continues to be one of the leading causes of death and disability in the adult population worldwide. The currently used pharmacological methods for the treatment of ischemic stroke are not effective enough and require the search for new tools and approaches to identify therapeutic targets and potential neuroprotectors. Today, in the development of neuroprotective drugs for the treatment of stroke, special attention is paid to peptides. Namely, peptide action is aimed at blocking the cascade of pathological processes caused by a decrease in blood flow to the brain tissues. Different groups of peptides have therapeutic potential in ischemia. Among them are small interfering peptides that block protein-protein interactions, cationic arginine-rich peptides with a combination of various neuroprotective properties, shuttle peptides that ensure the permeability of neuroprotectors through the blood-brain barrier, and synthetic peptides that mimic natural regulatory peptides and hormones. In this review, we consider the latest achievements and trends in the development of new biologically active peptides, as well as the role of transcriptomic analysis in identifying the molecular mechanisms of action of potential drugs aimed at the treatment of ischemic stroke.
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Affiliation(s)
- Lyudmila V Dergunova
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Kurchatov Sq. 2, 123182 Moscow, Russia
| | - Ivan B Filippenkov
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Kurchatov Sq. 2, 123182 Moscow, Russia
| | - Svetlana A Limborska
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Kurchatov Sq. 2, 123182 Moscow, Russia
| | - Nikolay F Myasoedov
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Kurchatov Sq. 2, 123182 Moscow, Russia
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Liu S, Mohri S, Manabe Y, Ejima A, Sato K, Sugawara T. Gly-Pro protects normal human dermal fibroblasts from UVA-induced damages via MAPK-NF-κB signaling pathway. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B: BIOLOGY 2022; 237:112601. [DOI: 10.1016/j.jphotobiol.2022.112601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/28/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022]
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Abramov AY, Bachurin SO. Neurodegenerative disorders-Searching for targets and new ways of diseases treatment. Med Res Rev 2021; 41:2603-2605. [PMID: 33645761 DOI: 10.1002/med.21794] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 02/05/2021] [Indexed: 02/01/2023]
Affiliation(s)
- Andrey Y Abramov
- Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Sergey O Bachurin
- Institute of Physiologically Active Compounds Russian Academy of Sciences Severny proezd, 1, Chernogolovka, 142432, Russia
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