Molecular Dynamics simulation and Medicine

The future of molecular dynamics simulations in drug discovery

  • Understanding the mechanisms underlying the behavior of chemical and biological systems requires scrutiny at spatial and temporal resolutions that challenge current experimental techniques.
  • Molecular dynamics (MD) simulations being increasingly partnered with experiments in this because simulations can track system behavior across a vast spatiotemporal domain—length scales up to thousands of a˚ngstro¨ms, with atomic precision, and timescales up to milliseconds, at femtosecond resolution.
  • Continuum modeling accuracy is enriched by molecular dynamics (MD) simulations. These lower-scale simulations help us to unveil the behavior of drug molecules at the atomic scale (e.g. in lipid bilayers).
  • This power of simulations has been further increased by recent methodological advances. we predict what the next 25 years (2037) of MD simulations may bring, especially regarding their application to the search for new drugs.
  • Novel computational methods, including MD simulations, have assumed an ever growing role in drug discovery over the past quarter century. Yet, despite having learned and contributed much, we face many challenges ahead.
  • To take novel computational methods to the next level—such that they radically alter the very landscape of drug discovery—we must grapple with those challenges and rise above them.
  • One key empirical distinction helped aircraft designers become convinced decades ago of the correctness and value, and occasional limitations, of CFD simulations: simulations could capture the essential phenomena on timeframes overlapping with wind-tunnel tests. This overlap enabled CFD simulations to be validated by experiment, and experimental observations to be explained by, and then predicted by, CFD simulations. MD simulations of biological systems are now entering just such an overlapping timeframe regime—orders-of-magnitude extrapolations are rapidly becoming a thing of the past.
  • In the context of the problems now facing the pharmaceutical industry, we ask how we can best address drug discovery needs of the
    next quarter century using molecular dynamics simulations, and we suggest some possible approaches

David W. Borhani David E. Shaw , Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA

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