pKa-Prediction Challenge timeframe: Oct 25, 2017 to Jan 23, 2018

This challenge consists of predicting microscopic and macroscopic pKas of 24 small molecules. These fragment-like small molecules are selected for their similarity to kinase inhibitors and for experimental tractability. Our aim is to evaluate how well current pKa prediction methods perform with drug fragment-like molecules.

In molecules with multiple titratable groups, the protonation state of one group can affect the proton dissociation propensity of another functional group. The microscopic pKa refers to the pKa of deprotonation of a single titratable group while all the other titratable and tautomerizable functional groups of the same molecule are held fixed. The macroscopic pKa defines the acid dissociation constant related to the loss of a proton from a molecule regardless of which functional group the proton is dissociating from, so it doesn't necessarily convey structural information [1].

pKa measurements were collected using spectrophotometric pKa measurements with a Sirius T3 instrument by Mehtap Isik from the Chodera Lab at Memorial Sloan Kettering with the support of the Merck Rahway Preformulation Department, especially Dorothy Levorse, Timothy Rhodes, and Brad Sherborne.

Complete details on the SAMPL6 pKa challenge are available in the SAMPL6 Github repository, where all information related to input structures and submission directions can be found:

https://github.com/MobleyLab/SAMPL6

Experimental details

Small molecules were purchased in powder form. 10 mg/ml DMSO solutions were prepared and used as stock solutions for the preparation of samples, where 1-5 uL of 10 mg/ml DMSO stock solution is diluted in 1.5 mL ionic-strength adjusted water (0.15 M KCl).  

The UV-metric pKa measurement protocol of the Sirius T3 [http://www.sirius-analytical.com/science/pka] measures the change in multiwavelength absorbance in the 250-450 nm UV region of the spectrum while the pH is titrated between pH 1.8 and 12.2 to evaluate pKas [2,3]. A protonation state change of titratable sites near chromophores will modulate the UV absorbance spectra of these chromophores, allowing populations of distinct UV-active species to be resolved as a function of pH. To do this, basis spectra are identified and populations extracted via analysis of the pH-dependent multi-wavelength absorbance. This method is capable of measuring pKas between 2 and 12.

pKa measurements of soluble compounds were performed in ionic-strength adjusted water with 0.15 M KCl. For compounds with insufficient solubility, a cosolvent protocol was used where 3 UV-metric pKa measurements were performed at different cosolvent:water ratios (typically 30%, 40%, and 50% methanol) and  the Yasuda-Shedlovsky extrapolation method [4] was used to estimate the pKa at 0% cosolvent.

Three replicate measurements were made for all compounds at room temperature (25°C). Multiwavelength absorbance analysis on the Sirius T3 allows for very good resolution of pKas, but it is important to note that this method produces estimates of macroscopic pKas. If multiple microscopic pKas have close pKa values and overlapping changes in UV absorbance associated with protonation/deprotonaton events, the spectral analysis could produce a single macroscopic pKa that represents an aggregation of multiple microscopic pKas.

Prediction challenge

Three submission types for pKa predictions will be accepted. Participants are encouraged to submit their results in all or multiple submission types as it fits to their prediction methods.

Type I - microscopic pKas and related microstates

Predicting microscopic pKa values and related microstate structures. Different protonation states and tautomer combinations constitute different microstates.

Type II - microstate populations as a function of pH

Predicting (logarithmic) fractional microstate populations between pH interval 2 to 12 in 0.1 pH increments.

Type III - macroscopic pKas

Predicting the value of  macroscopic pKas between 2 and 12.

References

[1] Bodner, G.M. (1986). Assigning the pKa’s of polyprotic acids. J. Chem. Educ 63, 246.

[2] Tam, K.Y., and Takács-Novák, K. (2001). Multi-wavelength spectrophotometric determination of acid dissociation constants: a validation study. Analytica Chimica Acta 434, 157–167.

[3] Allen, R.I., Box, K.J., Comer, J.E.A., Peake, C., and Tam, K.Y. (1998). Multiwavelength spectrophotometric determination of acid dissociation constants of ionizable drugs. Journal of Pharmaceutical and Biomedical Analysis 17, 699–712.

[4] Avdeef, A., Box, K.J., Comer, J.E.A., Gilges, M., Hadley, M., Hibbert, C., Patterson, W., and Tam, K.Y. (1999). PH-metric logP 11. pKa determination of water-insoluble drugs in organic solvent–water mixtures. Journal of Pharmaceutical and Biomedical Analysis 20, 631–641.