Precision spatiotemporal analysis of large-scale compound–protein interactions through molecular dynamics simulation

Biological systems are composed of and regulated by intricate and diverse biomolecular interactions. Experimental and computational approaches have been developed to elucidate the mechanisms of these interactions; however, owing to cost, time, and accuracy issues, large-scale spatiotemporal analyses of molecular pairs remain challenging. Thus, the molecular recognition mechanisms underlying these diverse interactions remain unclear. We successfully simulated the large-scale molecular dynamics (MD) of 4,275 protein-compound pairs by combining a method to accelerate the MD simulations with the supercomputer Fugaku. Our spatiotemporal analysis of generated big MD data revealed universal features underlying molecular recognition and binding processes. This study expands our understanding of the concept of MD simulations from a technique to investigate the dynamic properties of individual protein-drug pairs to an approach to perform large-scale spatiotemporal analysis and compound screening. This study opens an avenue in biological research for subsequent drug discovery.

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Publication Details

Journal
PNAS Nexus
Published
2025-02-27
DOI
https://doi.org/10.1093/pnasnexus/pgaf094
Citations
2
Primary Topic
Metabolomics and Mass Spectrometry Studies
Type
article
Field-Weighted Citation Impact
1.61
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Precision spatiotemporal analysis of large-scale compound–protein interactions through molecular dynamics simulation

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Metabolomics and Mass Spectrometry Studies
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Precision spatiotemporal analysis of large-scale compound–protein interactions through molecular dynamics simulation

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article en
2 citations

Abstract

Biological systems are composed of and regulated by intricate and diverse biomolecular interactions. Experimental and computational approaches have been developed to elucidate the mechanisms of these interactions; however, owing to cost, time, and accuracy issues, large-scale spatiotemporal analyses of molecular pairs remain challenging. Thus, the molecular recognition mechanisms underlying these diverse interactions remain unclear. We successfully simulated the large-scale molecular dynamics (MD) of 4,275 protein-compound pairs by combining a method to accelerate the MD simulations with the supercomputer Fugaku. Our spatiotemporal analysis of generated big MD data revealed universal features underlying molecular recognition and binding processes. This study expands our understanding of the concept of MD simulations from a technique to investigate the dynamic properties of individual protein-drug pairs to an approach to perform large-scale spatiotemporal analysis and compound screening. This study opens an avenue in biological research for subsequent drug discovery.

PNAS NexusVol. 4(3)
Tokyo Institute of Technology (JP), Kyoto University (JP), RIKEN Center for Computational Science (JP), Kyoto University Hospital (JP), RIKEN Center for Integrative Medical Sciences (JP), Yokohama City University (JP)
Openalex Percentile: Top 18%
Metabolomics and Mass Spectrometry Studies
1.61
DOIOpen Access PDFOpenAlex
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