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Grasso_2024_ACS_JourChemTheoComp_Leveraging Machine Learning
Journal article

Leveraging machine learning-guided molecular simulations coupled with experimental data to decipher membrane binding mechanisms of aminosterols

  • Muscat, Stefano ORCID Istituto Dalle Molle di studi sull'intelligenza artificiale (IDSIA), Facoltà di scienze informatiche, Università della Svizzera italiana, Svizzera
  • Errico, Silvia ORCID Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Italy
  • Danani, Andrea ORCID Istituto Dalle Molle di studi sull'intelligenza artificiale (IDSIA), Facoltà di scienze informatiche, Università della Svizzera italiana, Svizzera
  • Chiti, Fabrizio ORCID Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence, Italy
  • Grasso, Gianvito ORCID Istituto Dalle Molle di studi sull'intelligenza artificiale (IDSIA), Facoltà di scienze informatiche, Università della Svizzera italiana, Svizzera
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  • 2024
Published in:
  • Journal of chemical theory and computation. - 2024, vol. 20, no. 18, p. 8279–8289
Computer simulations
Free energy
Membranes
Molecules
Vescicles
English Understanding the molecular mechanisms of the interactions between specific compounds and cellular membranes is essential for numerous biotechnological applications, including targeted drug delivery, elucidation of the drug mechanism of action, pathogen identification, and novel antibiotic development. However, estimation of the free energy landscape associated with solute binding to realistic biological systems is still a challenging task. In this work, we leverage the Time-lagged Independent Component Analysis (TICA) in combination with neural networks (NN) through the Deep-TICA approach for determining the free energy associated with the membrane insertion processes of two natural aminosterol compounds, trodusquemine (TRO), and squalamine (SQ). These compounds are particularly noteworthy because they interact with the outer layer of neuron membranes, protecting them from the toxic action of misfolded proteins involved in neurodegenerative disorders, in both their monomeric and oligomeric forms. We demonstrate how this strategy could be used to generate an effective collective variable for describing solute absorption in the membrane and for estimating free energy landscape of translocation via on-the-fly probability enhanced sampling (OPES) method. In this context, the computational protocol allowed an exhaustive characterization of the aminosterol entry pathway into a neuron-like lipid bilayer. Furthermore, it provided accurate prediction of membrane binding affinities, in close agreement with the experimental binding data obtained by using fluorescently labeled aminosterols and large unilamellar vesicles (LUVs). The findings contribute significantly to our understanding of aminosterol entry pathways and aminosterol-lipid membrane interactions. Finally, the computational methods deployed in this study further demonstrate considerable potential for investigating membrane binding processes.
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Language
  • English
Classification
Computer science and technology
License
CC BY
Open access status
hybrid
Identifiers
Persistent URL
https://n2t.net/ark:/12658/srd1330261
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