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DREAM++: flexible docking program for virtual combinatorial libraries.

S Makino1, T J Ewing, I D Kuntz

  • 1Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco 94143-0446, USA.

Journal of Computer-Aided Molecular Design
|September 14, 1999
PubMed
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We developed DREAM++ software for docking ligands into protein binding sites. This computational tool aids in discovering novel HIV protease inhibitors by evaluating molecular interactions and complementarity.

Area of Science:

  • Computational Chemistry
  • Structural Biology
  • Drug Discovery

Background:

  • Accurate prediction of ligand-macromolecule interactions is crucial for drug design.
  • Existing computational methods may not fully capture the chemical and conformational flexibility of ligands.
  • Developing efficient tools for virtual screening and lead optimization is an ongoing challenge.

Purpose of the Study:

  • To introduce DREAM++ (Docking and Reaction programs using Efficient seArch Methods written in C++), a novel software suite for molecular docking and reaction simulation.
  • To enable the evaluation of computationally generated ligands and their reaction products for binding affinity and complementarity.
  • To propose novel HIV protease inhibitors using the DREAM++ suite.

Main Methods:

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  • DREAM++ integrates three programs: ORIENT++ for initial docking, REACT++ for simulating chemical reactions, and SEARCH++ for conformation searching.
  • The DOCK algorithm is employed by ORIENT++ for ligand positioning.
  • REACT++ allows for user-defined chemical modifications, and SEARCH++ utilizes a hybrid algorithm for efficient conformational analysis of reaction products.

    • Main Results:

    • The DREAM++ suite successfully differentiated high-affinity ligands for HIV protease-inhibitor complexes.
    • Key differentiating measures included interaction energies, protein subsite occupancy, and the number of docked conformations.
    • The software was used to propose novel HIV protease inhibitors synthesized from readily available reagents.

    Conclusions:

    • DREAM++ provides an effective computational framework for identifying potential drug candidates.
    • The ability to simulate chemical reactions and perform conformation searches enhances the evaluation of ligand-protein interactions.
    • The proposed novel inhibitors offer potential alternatives to existing treatments for HIV protease.