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Identification of Optimal Ligand Growth Vectors Using an Alchemical Free-Energy Method.

Accepted version
Peer-reviewed

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Article

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Abstract

In this work, a novel method to rationally design inhibitors with improved steric contacts and enhanced binding free energies is presented. This new method uses alchemical single step perturbation calculations to rapidly optimize the van der Waals interactions of a small molecule in a protein-ligand complex in order to maximize its binding affinity. The results of the optimizer are used to predict beneficial growth vectors on the ligand, and good agreement is found between the predictions from the optimizer and a more rigorous free energy calculation, with a Spearman's rank order correlation of 0.59. The advantage of the method presented here is the significant speed up of over 10-fold compared to traditional free energy calculations and sublinear scaling with the number of growth vectors assessed. Where experimental data were available, mutations from hydrogen to a methyl group at sites highlighted by the optimizer were calculated with MBAR, and the mean unsigned error between experimental and calculated values of the binding free energy was 0.83 kcal/mol.

Description

Keywords

Entropy, Ligands, Protein Binding, Thermodynamics

Journal Title

J Chem Inf Model

Conference Name

Journal ISSN

1549-9596
1549-960X

Volume Title

60

Publisher

American Chemical Society (ACS)

Rights

All rights reserved
Sponsorship
EPSRC (1819407)
Engineering and Physical Sciences Research Council (EP/L015552/1)
Engineering and Physical Sciences Research Council (EP/P020259/1)