Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies

04 March 2021, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


In silico screening of drug target interactions is a key part of the drug discovery process. Changes in the drug scaffold via contraction or expansion of rings, the breaking of rings and the introduction of cyclic structures from acyclic structures are commonly applied by medicinal chemists to improve binding affinity and enhance favorable properties of candidate compounds. These processes, commonly referred to as scaffold hopping, are challenging to model computationally. Although relative binding free energy (RBFE) calculations have shown success in predicting binding affinity changes caused by perturbing R-groups attached to a common scaffold, applications of RBFE calculations to modeling scaffold hopping are relatively limited. Scaffold hopping inevitably involves breaking and forming bond interactions of quadratic functional forms, which is highly challenging. A novel method for handling ring opening/closure/contraction/expansion and linker contraction/expansion is presented here. To the best of our knowledge, RBFE calculations on linker contraction/expansion have not been previously reported. The method uses auxiliary restraints to hold the atoms at the ends of a bond in place during the breaking and forming of the bonds. The broad applicability of the method was demonstrated by examining perturbations involving small molecule macrocycles and mutations of proline in proteins. High accuracy was obtained using the method for most of the perturbations studied. Unlike other methods that rely on λ-dependent functional forms for bond interactions, the method presented here can be employed using modern MD software without modification of codes or force field functions.


Free Energy Calculations
Scaffold Hopping
alchemical simulation methods
molecular dynamics
Amber MD package
ligand design strategies

Supplementary materials

scaffold-hopping SI final


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