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Computational Fluorine Scanning Using Free-Energy Perturbation.

Alexander D Wade1, Andrea Rizzi2,3, Yuanqing Wang4

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We developed a computational method called perturbative fluorine scanning to predict the best drug binders among fluorinated molecules. This approach shows promise for medicinal chemistry, aiding in the design of improved therapeutics.

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Area of Science:

  • Computational chemistry
  • Medicinal chemistry
  • Drug discovery

Background:

  • Fluorine is widely used in medicinal chemistry to enhance drug binding affinity and pharmacokinetic properties.
  • Predicting the effects of fluorine substitution on binding affinity is crucial for rational drug design.
  • Existing computational methods for predicting binding affinity can be computationally expensive or lack accuracy.

Purpose of the Study:

  • To introduce and validate a novel computational approach, perturbative fluorine scanning, for predicting binding affinities of fluorinated drug analogues.
  • To assess the accuracy of perturbative fluorine scanning against rigorous alchemical free-energy calculations and experimental data.
  • To evaluate the utility of perturbative fluorine scanning in identifying optimal binders from a set of fluorinated compounds.

Main Methods:

  • Perturbative fluorine scanning utilizes free-energy perturbation calculations within molecular dynamics simulations of a single compound.
  • The method allows for the prediction of binding affinities for numerous fluorinated analogues based on simulations of a parent compound.
  • The approach was tested across nine diverse biological targets, including enzymes and receptors.

Main Results:

  • Perturbative fluorine scanning demonstrated excellent agreement with high-level alchemical free-energy calculations.
  • The method showed good agreement with experimental binding data for most of the nine test systems.
  • Discrepancies with experimental data in some systems underscore the need for improved force fields and accurate handling of tautomeric/protonation states.

Conclusions:

  • Perturbative fluorine scanning is a computationally efficient and promising method for predicting binding affinities of fluorinated molecules.
  • The technique can guide the selection of optimal fluorinated analogues in drug discovery programs.
  • Further refinements in force fields and protonation state treatment will enhance the predictive power of this valuable free-energy method.