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MoleGear: A Java-Based Platform for Evolutionary De Novo Molecular Design.

Yunhan Chu1, Xuezhong He2

  • 1Department of Chemical Engineering, Norwegian University of Science and Technology, N-7491 Trondheim, Norway. yunhan.chu@ntnu.no.

Molecules (Basel, Switzerland)
|April 14, 2019
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Summary

MoleGear is a new Java platform for de novo molecular design. It uses evolutionary algorithms to create novel drug candidates, demonstrating potential for HIV-1 protease inhibitor design.

Keywords:
de novo designdrug moleculesevolutionary algorithmfitnessmulti-objective function

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Area of Science:

  • Computational chemistry and drug discovery.
  • Development of novel computational platforms for molecular design.

Background:

  • De novo molecular design is crucial for identifying novel drug candidates.
  • Existing platforms may lack the flexibility or scalability for complex chemical space exploration.

Purpose of the Study:

  • To introduce MoleGear, a Java-based platform for de novo molecular design.
  • To demonstrate MoleGear's capability in generating potential drug candidates using evolutionary algorithms.

Main Methods:

  • Development of a Java-based platform, MoleGear, utilizing the Chemistry Development Kit (CDK).
  • Implementation of an evolutionary algorithm (EA) with fragment-based operators (growing, crossover, mutation).
  • Scoring molecules using predicted binding free energy and a multi-objective fitness function; parallel computation for scalability.

Main Results:

  • MoleGear successfully designed candidate molecules targeting human immunodeficiency virus 1 (HIV-1) protease.
  • The platform integrates utilities for fragment library design, chemical space analysis, and a graphical user interface.

Conclusions:

  • MoleGear provides a robust and scalable platform for de novo molecular design.
  • The successful design of HIV-1 protease inhibitors validates MoleGear's potential in drug discovery.