In Silico Simulation of Impacts of Metal Nano-Oxides on Cell Viability in THP-1 Cells Based on the Correlation Weights of the Fragments of Molecular Structures and Codes of Experimental Conditions Represented by Means of Quasi-SMILES

Int J Mol Sci. 2023 Jan 20;24(3):2058. doi: 10.3390/ijms24032058.

Abstract

A simulation of the effect of metal nano-oxides at various concentrations (25, 50, 100, and 200 milligrams per millilitre) on cell viability in THP-1 cells (%) based on data on the molecular structure of the oxide and its concentration is proposed. We used a simplified molecular input-line entry system (SMILES) to represent the molecular structure. So-called quasi-SMILES extends usual SMILES with special codes for experimental conditions (concentration). The approach based on building up models using quasi-SMILES is self-consistent, i.e., the predictive potential of the model group obtained by random splits into training and validation sets is stable. The Monte Carlo method was used as a basis for building up the above groups of models. The CORAL software was applied to building the Monte Carlo calculations. The average determination coefficient for the five different validation sets was R2 = 0.806 ± 0.061.

Keywords: Monte Carlo method; Quasi-SMILES; cell viability in THP-1 cells; in silico; nano-oxides.

MeSH terms

  • Cell Survival
  • Computer Simulation
  • Humans
  • Molecular Structure
  • Monte Carlo Method
  • Oxides
  • Quantitative Structure-Activity Relationship*
  • Software*
  • THP-1 Cells

Substances

  • Oxides

Grants and funding

This work was supported by CONCERT REACH, grant agreement LIFE17 GIE/IT/000461.