NANO.PTML model for read-across prediction of nanosystems in neurosciences. computational model and experimental case of study.

Shan He, Karam Nader, Julen Segura Abarrategi, Harbil Bediaga, Deyani Nocedo-Mena, Estefania Ascencio, Gerardo M Casanola-Martin, Idoia Castellanos-Rubio, Maite Insausti, Bakhtiyor Rasulev, Sonia Arrasate, Humberto González-Díaz
Author Information
  1. Shan He: Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, 58108, USA.
  2. Karam Nader: Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain.
  3. Julen Segura Abarrategi: Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain.
  4. Harbil Bediaga: IKERDATA S.L., ZITEK, UPV/EHU, Rectorate Building, nº 6, Leioa, 48940, Greater Bilbao, Basque Country, Spain.
  5. Deyani Nocedo-Mena: Faculty of Physical Mathematical Sciences, Autonomous University of Nuevo León, San Nicolás de los Garza, 66455, Nuevo León, México.
  6. Estefania Ascencio: Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, 58108, USA.
  7. Gerardo M Casanola-Martin: Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, 58108, USA.
  8. Idoia Castellanos-Rubio: Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain. idoia.castellanos@ehu.eus.
  9. Maite Insausti: Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain.
  10. Bakhtiyor Rasulev: Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, 58108, USA.
  11. Sonia Arrasate: Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain. sonia.arrasate@ehu.eus.
  12. Humberto González-Díaz: Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain.

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 (FeO_A and FeO_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 (FeO_A and FeO_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.

Keywords

References

  1. Neuropharmacology. 2016 Apr;103:270-8 [PMID: 26721628]
  2. Metabolism. 2017 Apr;69S:S36-S40 [PMID: 28126242]
  3. Nat Mater. 2006 Feb;5(2):118-22 [PMID: 16444262]
  4. Bioinformatics. 2010 Mar 15;26(6):822-30 [PMID: 20130029]
  5. Methods Mol Biol. 2019;2000:125-182 [PMID: 31148014]
  6. Chem Rev. 2019 Mar 13;119(5):3296-3348 [PMID: 30758194]
  7. Sensors (Basel). 2012;12(2):1657-87 [PMID: 22438731]
  8. Nanoscale. 2021 Nov 4;13(42):17854-17870 [PMID: 34671801]
  9. Nat Rev Dis Primers. 2021 May 13;7(1):33 [PMID: 33986301]
  10. Nanotoxicology. 2015;9(5):636-42 [PMID: 25211549]
  11. Curr Pharm Des. 2017;23(13):1916-1926 [PMID: 28056734]
  12. Nanoscale. 2021 Jan 21;13(2):1318-1330 [PMID: 33410431]
  13. BMC Genomics. 2020 Jan 2;21(1):6 [PMID: 31898477]
  14. Small. 2008 Jan;4(1):26-49 [PMID: 18165959]
  15. Environ Sci Technol. 2014 Dec 16;48(24):14686-94 [PMID: 25384130]
  16. Ecotoxicology. 2008 Jul;17(5):315-25 [PMID: 18408994]
  17. Crit Rev Anal Chem. 2015;45(4):289-99 [PMID: 25831472]
  18. ACS Chem Neurosci. 2018 Nov 21;9(11):2572-2587 [PMID: 29791132]
  19. Int J Mol Sci. 2022 Oct 25;23(21): [PMID: 36361643]
  20. Nucleic Acids Res. 2014 Jan;42(Database issue):D1083-90 [PMID: 24214965]
  21. Nucleic Acids Res. 2015 Jul 1;43(W1):W612-20 [PMID: 25883136]
  22. Nat Rev Drug Discov. 2019 Jan;18(1):41-58 [PMID: 30310233]
  23. Polymers (Basel). 2011 Sep 1;3(3):1377-1397 [PMID: 22577513]
  24. Comput Methods Programs Biomed. 2016 Aug;132:93-103 [PMID: 27282231]
  25. Med Res Rev. 2021 Sep;41(5):2804-2822 [PMID: 32815157]
  26. Toxicol Appl Pharmacol. 2016 May 15;299:78-89 [PMID: 26739622]
  27. Chem Mater. 2021 Nov 23;33(22):8693-8704 [PMID: 34853492]
  28. Korean J Anesthesiol. 2022 Feb;75(1):25-36 [PMID: 35124947]
  29. Adv Drug Deliv Rev. 2012 Dec;64(15):1663-93 [PMID: 22664229]
  30. J Nanopart Res. 2016;18(9):256 [PMID: 27642255]
  31. Biochem Soc Trans. 2017 Jul 21;45(4):1025-1033 [PMID: 28733489]
  32. Mol Pharm. 2020 Jul 6;17(7):2612-2627 [PMID: 32459098]
  33. Cold Spring Harb Perspect Biol. 2015 Jan 05;7(1):a020412 [PMID: 25561720]
  34. Nanoscale. 2014 Sep 21;6(18):10623-30 [PMID: 25083742]
  35. Parkinsonism Relat Disord. 2018 Jan;46 Suppl 1:S1-S5 [PMID: 28784297]
  36. Biology (Basel). 2020 Jul 30;9(8): [PMID: 32751710]
  37. Nanoscale. 2019 Nov 21;11(45):21811-21823 [PMID: 31691701]
  38. BioData Min. 2023 Feb 17;16(1):4 [PMID: 36800973]
  39. Iran J Basic Med Sci. 2023;26(10):1107-1119 [PMID: 37736505]
  40. Nucleic Acids Res. 2019 Jan 8;47(D1):D930-D940 [PMID: 30398643]
  41. Mol Divers. 2011 May;15(2):561-7 [PMID: 20931280]
  42. Ecotoxicol Environ Saf. 2014 Sep;107:162-9 [PMID: 24949897]
  43. Drug Discov Today. 2016 Jul;21(7):1076-113 [PMID: 27080147]
  44. Nanoscale. 2018 Nov 29;10(46):21879-21892 [PMID: 30457620]
  45. Biochim Biophys Acta. 2002 Jun 12;1590(1-3):131-9 [PMID: 12063176]
  46. Nucleic Acids Res. 2012 Jan;40(Database issue):D1100-7 [PMID: 21948594]
  47. Med Res Rev. 2021 Sep;41(5):2823-2840 [PMID: 33155318]
  48. Bioorg Med Chem. 2013 Apr 1;21(7):1870-9 [PMID: 23415089]
  49. Nucleic Acids Res. 2017 Jan 4;45(D1):D945-D954 [PMID: 27899562]
  50. Risk Anal. 2010 Nov;30(11):1723-34 [PMID: 20561263]
  51. Nanotoxicology. 2017 Sep;11(7):891-906 [PMID: 28937298]
  52. Environ Int. 2014 Dec;73:288-94 [PMID: 25173945]
  53. ACS Appl Mater Interfaces. 2020 Jun 24;12(25):27917-27929 [PMID: 32464047]
  54. Adv Exp Med Biol. 2017;947:103-142 [PMID: 28168667]
  55. J Cheminform. 2018 Feb 06;10(1):4 [PMID: 29411163]
  56. Nanoscale. 2020 Jul 2;12(25):13471-13483 [PMID: 32613998]
  57. Nanoscale. 2017 Jun 22;9(24):8435-8448 [PMID: 28604902]
  58. Med Res Rev. 2021 Sep;41(5):2746-2774 [PMID: 32808322]
  59. Neurol Sci. 2021 Jul;42(7):2653-2660 [PMID: 33846881]
  60. Toxicology. 2013 Nov 8;313(1):15-23 [PMID: 23165187]
  61. Med Res Rev. 2021 Sep;41(5):2634-2655 [PMID: 32638429]
  62. Beilstein J Nanotechnol. 2024 May 15;15:535-555 [PMID: 38774585]

Grants

  1. IT1558-22/grants Basque Government / Eusko Jaurlaritza
  2. IT1558-22/grants Basque Government / Eusko Jaurlaritza
  3. IT1558-22/grants Basque Government / Eusko Jaurlaritza
  4. IT1558-22/grants Basque Government / Eusko Jaurlaritza
  5. IT1558-22/grants Basque Government / Eusko Jaurlaritza
  6. IT1558-22/grants Basque Government / Eusko Jaurlaritza
  7. PID2022-137365NB-I00/Ministry of Science and Innovation
  8. PID2022-137365NB-I00/Ministry of Science and Innovation
  9. PID2022-137365NB-I00/Ministry of Science and Innovation
  10. PID2022-137365NB-I00/Ministry of Science and Innovation
  11. PID2022-137365NB-I00/Ministry of Science and Innovation
  12. PID2022-137365NB-I00/Ministry of Science and Innovation
  13. PID2022-137365NB-I00/Ministry of Science and Innovation
  14. 2022/IKER/000040/NextGenerationEU INVESTIGO
  15. 2022/IKER/000040/NextGenerationEU INVESTIGO
  16. PID2022- 136993OB-I00/Spanish Ministry of Science and Innovation
  17. PID2022- 136993OB-I00/Spanish Ministry of Science and Innovation
  18. PID2022- 136993OB-I00/Spanish Ministry of Science and Innovation
  19. DE-SC0022239/U.S. Department of Energy (DOE)
  20. DE-SC0022239/U.S. Department of Energy (DOE)
  21. 2019077/Center for Computationally-Assisted Science and Technology (CCAST) at North Dakota State University
  22. 2019077/Center for Computationally-Assisted Science and Technology (CCAST) at North Dakota State University
  23. KK-2022/00032/SPRI ELKARTEK grants AIMOFGIF
  24. KK-2022/00032/SPRI ELKARTEK grants AIMOFGIF

MeSH Term

Nanoparticles
Machine Learning
Algorithms
Animals
Neurodegenerative Diseases
Neurosciences
Computer Simulation
Humans
Blood-Brain Barrier
Drug Delivery Systems
Drug Carriers

Chemicals

Drug Carriers

Word Cloud

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