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Alchemical Enhanced Sampling with Optimized Phase Space Overlap.

Shi Zhang1, Timothy J Giese1, Tai-Sung Lee1

  • 1Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.

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The Alchemical Enhanced Sampling (ACES) method improves free energy simulations by enabling faster sampling of aromatic ring conformations. This new approach, utilizing optimized phase space overlap, enhances simulation efficiency for drug discovery.

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Area of Science:

  • Computational chemistry
  • Molecular dynamics simulations
  • Free energy calculations

Background:

  • Alchemical enhanced sampling (ACES) facilitates importance sampling in free energy simulations.
  • Hamiltonian replica exchange with dual topology and smoothstep softcore potentials are key components of ACES.
  • Aromatic ring functionalization in lead optimization presents sampling challenges due to slow ring flipping events.

Purpose of the Study:

  • To demonstrate the utility of the ACES method for overcoming conformational sampling issues in molecular simulations.
  • To investigate the impact of replica exchange and softcore selection on ring conformation distribution convergence.
  • To examine the influence of phase space overlap (PSO) and Hamiltonian replica exchange acceptance ratios on free energy accuracy.

Main Methods:

  • Utilizing the ACES method with a dual topology framework to model syn and anti ring conformations.
  • Employing Hamiltonian replica exchange to alchemically tunnel between states, bypassing high rotational barriers.
  • Introducing the optimized phase space overlap lambda-spacing method (Opt-PSO) for selecting lambda values based on nonlocal PSO analysis.

Main Results:

  • ACES effectively samples conformer distributions by alchemically tunneling between states.
  • The study demonstrates ACES's ability to address ring flipping conformational sampling issues in SARS-CoV-2 Mpro inhibitors.
  • The Opt-PSO method optimizes lambda spacing, improving phase space overlap and Hamiltonian replica exchange acceptance ratios.
  • Improved exchange statistics enhance the overall efficiency of the ACES method.

Conclusions:

  • The ACES method, combined with Opt-PSO, provides an efficient approach for conformational sampling in free energy simulations.
  • This method is particularly useful for challenging systems involving slow conformational changes, such as aromatic ring flipping.
  • The FE-ToolKit software package now includes the ACES method, making it freely available to researchers.