pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments
Authors: Işik Mehtap , Levorse Dorothy , Rustenburg Ariën S. , Ndukwe Ikenna E. , Wang Heather , Wang Xiao , Reibarkh Mikhail , Martin Gary E. , Makarov Alexey A. , Mobley David L. , Rhodes Timothy , Chodera John D. 
Published: July 2018

Determining the net charge and protonation states populated by a small molecule in an environment of interest or the cost of altering those protonation states upon transfer to another environment is a prerequisite for predicting its physicochemical and pharmaceutical properties. The environment of interest can be aqueous, an organic solvent, a protein binding site, or a lipid bilayer. Predicting the protonation state of a small molecule is essential to predicting its interactions with biological macromolecules using computational models. Incorrectly modeling the dominant protonation state, shifts in dominant protonation state, or the population of significant mixtures of protonation states can lead to large modeling errors that degrade the accuracy of physical modeling. Low accuracy hinders the use of physical modeling approaches for molecular design. For small molecules, the acid dissociation constant (pKa) is the primary quantity needed to determine the ionic states populated by a molecule in an aqueous solution at a given pH. As a part of SAMPL6 community challenge, we organized a blind pKa prediction component to assess the accuracy with which contemporary pKa prediction methods can predict this quantity, with the ultimate aim of assessing the expected impact on modeling errors this would induce. While a multitude of approaches for predicting pKa values currently exist, predicting the pKas of drug-like molecules can be difficult due to challenging properties such as multiple titratable sites, heterocycles, and tautomerization. For this challenge, we focused on set of 24 small molecules selected to resemble selective kinase inhibitors—an important class of therapeutics replete with titratable moieties. Using a Sirius T3 instrument that performs automated acid-base titrations, we used UV absorbance-based pKa measurements to construct a high-quality experimental reference dataset of macroscopic pKas for the evaluation of computational pKa prediction methodologies that was utilized in the SAMPL6 pKa challenge. For several compounds in which the microscopic protonation states associated with macroscopic pKas were ambiguous, we performed follow-up NMR experiments to disambiguate the microstates involved in the transition. This dataset provides a useful standard benchmark dataset for the evaluation of pKa prediction methodologies on kinase inhibitor-like compounds.

Abbreviations

SAMPL

Statistical Assessment of the Modeling of Proteins and Ligands

pKa

-log10 acid dissociation equilibrium constant

psKa

-log10 apparent acid dissociation equilibrium constant in cosolvent

DMSO

Dimethyl sulfoxide

ISA

lonic-strength adjusted

SEM

Standard error of the mean

TFA

Target factor analysis

LC-MS

Liquid chromatography - mass spectrometry

NMR

Nuclear magnetic resonance spectroscopy

HMBC

Heteronuclear Multiple-Bond Correlation

TFA-d

deutero-trifluoroacetic acid