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PySmash: Python package and individual executable program for representative substructure generation and application.

Zi-Yi Yang1, Zhi-Jiang Yang2, Yue Zhao3

  • 1Department of Pharmacy, Xiangya Hospital, Central South University and the Xiangya School of Pharmaceutical Sciences, Central South University, Sichuan, China.

Briefings in Bioinformatics
|March 12, 2021
PubMed
Summary

PySmash is a new tool for generating representative substructures, aiding drug discovery by evaluating molecular properties and interpreting models. It offers user-friendly algorithms for efficient compound design and optimization.

Keywords:
ADMETPython packageQSARsoftwaresubstructure screening

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Area of Science:

  • Computational chemistry
  • cheminformatics
  • drug discovery

Background:

  • Substructure screening is crucial for assessing molecular potency and ADMET properties in drug discovery.
  • It aids in interpreting quantitative structure-activity relationship (QSAR) models for designing new compounds.
  • Data-driven systems for deriving substructures from large chemical libraries are increasingly important.

Purpose of the Study:

  • To develop PySmash, a user-friendly and powerful tool for generating and implementing representative substructures.
  • To provide a versatile solution for various cheminformatics tasks in drug discovery pipelines.

Main Methods:

  • PySmash offers three substructure generation algorithms: circular, path-based, and functional group-based.
  • Users can customize substructure size, accuracy, coverage, statistical significance, and parallel computation.
  • The tool includes functionality for external data screening.

Main Results:

  • PySmash is available as both a Python package and an individual executable program for ease of use and pipeline integration.
  • The tool successfully demonstrates its utility in toxicophore derivation, privileged motif detection, and integration with machine learning models.
  • These applications highlight PySmash's value in safety evaluation, therapeutic activity exploration, and molecular optimization.

Conclusions:

  • PySmash is presented as a user-friendly and integrated tool for automatic substructure generation and implementation.
  • Its applications in safety, efficacy, and optimization showcase its broad utility in drug discovery.
  • The software is publicly available, encouraging wider adoption and research.