pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments

• Published in: Journal of computer-aided molecular design Vol. 32; no. 10; pp. 1117 - 1138
• Main Authors: Işık, 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.
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 01.10.2018
• Subjects: Animal Anatomy; Chemistry; Chemistry and Materials Science; Computer Applications in Chemistry; Histology; Morphology; Physical Chemistry; Blind prediction challenge; Microscopic p; Spectrophotometric p; Macroscopic p; SAMPL; Acid dissociation constants; Macroscopic protonation state; Microscopic protonation state; measurement
• ISSN: 0920-654X; 1573-4951
• DOI: 10.1007/s10822-018-0168-0

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 (p K a ) 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 p K a prediction component to assess the accuracy with which contemporary p K a 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 p K a values currently exist, predicting the p K a s 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 p K a measurements to construct a high-quality experimental reference dataset of macroscopic p K a s for the evaluation of computational p K a prediction methodologies that was utilized in the SAMPL6 p K a challenge. For several compounds in which the microscopic protonation states associated with macroscopic p K a s 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 p K a prediction methodologies on kinase inhibitor-like compounds.