Uses and Abuses of Experimental pKa Data

1. www.pkadata.com Uses and Abuses of Experimental pKa Data Tony Slater pKaData Limited CUP XII Santa Fe March 2011

2. www.pkadata.com Sources of experimental pKa data • pharmaceutical and agrochemical company in-house data • not available externally • literature compilations • for a critical list, see Profiles of Drug Substances, Excipients and Related Methodology Volume 33, 2007, by Richard J. Prankerd, ed Harry G. Brittain • pKa data sets used in comparing pKa prediction programs, eg. • Manchester, J.; Walkup, G.; Rivin, O.; You, Z. Evaluation of pKa estimation methods on 211 druglike compounds. J. Chem. Inf. Model. 2010, 50, 565–571. • Liao, C.; Nicklaus, M. Comparison of Nine Programs Predicting pKa Values of Pharmaceutical Substances. J. Chem. Inf. Model. 2009, 49, 2801–2812. • the IUPAC pKa compilations nb. to be of most use, these compilations need to be in computer-readable form

3. www.pkadata.com The IUPAC compilations Four books containing pKa data for organic acids and bases in aqueous solution :- • Dissociation Constants of Organic Bases in Aqueous Solution, by D. D. Perrin • Dissociation Constants of Organic Bases in Aqueous Solution, Supplement 1972, by D. D. Perrin • Dissociation Constants of Organic Acids in Aqueous Solution, by G. Kortum, W. Vogel, and K. Andrussow • Ionisation Constants of Organic Acids in Aqueous Solution, by E. P. Serjeant and Boyd Dempsey One book containing pKa data for organic acids and bases in non-aqueous solution :- • Acid-Base Dissociation Constants in Dipolar Aprotic Solvents (1990); K. Izutsu

4. www.pkadata.com What’s special about the IUPAC set? • pKa measurements for almost 12000 compounds in aqueous solution • number of measurements considerably higher (eg. some compounds have had their pKa(s) measured at different temperatures/ionic strengths and by different authors) • fully referenced • measurement method recorded • temperature recorded • remarks field provides more details such as ionic strength, buffer composition etc • assessment of data quality is made "The critical assessment of data quality is one of the major features of this seminal group of pKa compilations for weak organic acids and bases sponsored by the International Union of Pure and Applied Chemistry (IUPAC)“ from Profiles of Drug Substances, Excipients and Related Methodology Volume 33, 2007, by Richard J. Prankerd, ed Harry G. Brittain • In addition, we have added more value:- • ionisation assignments added • tautomers predicted

5. www.pkadata.com Range of Chemistry and Applicability Range of organic chemistry includes :- BASES aliphatic alicyclic aromatic heterocyclic natural products dyes and indicators • ACIDS • aliphatic carboxylic acids • alicyclic carboxylic acids • aromatic carboxylic acids • phenolic acids • other acids • dyes and indicators • unclassified organic acids • with applicability to :- • Pharmaceutical industry • Agrochemical industry • Specialty Chemicals industry • pKa prediction software companies • Nb. quality assessment of particular relevance here

6. www.pkadata.com Types of Search • Substructure • Search for basicpKa with 6.5 < pKa < 7.5 • Search for only highest quality data • Search for data where 35°C ≤ temperature ≤ 40°C • Any combination of the above • Etc................. We only supply the data, in suitable format, not the search software, so the types of search possible will depend on your in-house software. However, OpenEye are writing software around these data................ IUPAC pKa data can be merged with your existing in-house data, with the IUPAC-sourced data clearly identified.

7. www.pkadata.com In what areas are pKas used? • strength of interaction with receptor, eg. • will required charges and proton donor/acceptor pattern be presented to the receptor? • protein binding, eg. • correlation between pKa and human serum albumin binding constant for a set of anthranilic acid analogs (Stiff, C.; Zhong, M. et. al. Correlation of carboxylic acid pKa to protein binding and antibacterial activity of a novel class of bacterial translation inhibitors. Bioorg. Med. Chem. Lett. 2007, 17, 5479-82). • absorption, eg. • will the drug be orally absorbed? • use of prodrugs or heterocyclic guanidines to remove positive charge or reduce basicity of oral inhibitors of the blood coagulation cascade • distribution, eg. • knowing type of ionisation, pKa, and logP, can calculate logD for a given pH

8. www.pkadata.com In what areas are pKas used? continued • metabolism, eg. • affect strength of interaction with metabolising enzymes • elimination, eg. • elimination increases with increasing amounts of ionised form • solubility, eg. • weak acids and bases are more soluble in their ionised forms • dissolution rate, eg. • the ionised form of the drug will have greater solubility in the diffusion layer than the unionised weak acid or weak base (e.g. penicillin V potassium dissolves faster than penicillin V itself)

9. www.pkadata.com Data Variation • how much variation is there? • which pKa values should I use? glycine 2.24 – 2.47 (49 measurements) 8.98 – 10.36 (38 measurements)

10. www.pkadata.com What causes the variation? • temperature variations frequently measured at room temperature, but in pharmaceutical context, normally interested in 37°C pKa 78% of the variation temperature (°C)

11. www.pkadata.com What causes the variation? continued pKa 62% of the variation temperature (°C)

12. www.pkadata.com What causes the variation? continued • ionic strength variations pKa log10(ionic strength) physiological range (plasma, cytoplasm...)

13. www.pkadata.com What causes the variation? continued • errors / data quality • which values to have more confidence in? • IUPAC assessment of data quality reliable≤ 1% ≤ ±0.005 approximate > 1%, ≤ 10% > ±0.005, ≤ ±0.04 uncertain > 10% > ±0.04 very uncertain “cannot be estimated but is likely to be very great” estimated uncertainty in the value of ΔpK estimated uncertainty in the value of K Considering only reliable data and ones measured between 20 - 25°C, the variation for glycine reduces from 2.24 – 2.47 (0.23) to 2.35 – 2.37 (0.02) for the acid, and from 8.98 – 10.36 (1.38) to 9.78 – 9.91 (0.13) for the base.

14. www.pkadata.com Other considerations • pH of effect compartment (when known) • eg. from stomach (very acid) to plasma (approx. neutral) • acidic or basic ionisation • frequently obvious, but not always, eg. Tyramine 2 pKas in the ranges 9.22 – 9.77 and 10.78 – 10.9 but which is which? Initial literature suggested lower pKa due to OH, but subsequent literature disagrees

15. www.pkadata.com Other considerations continued • hydration 3 pKas given:- 6.52 9.00 9.72 “anhydrous" species equilibrium pK, partial covalent hydration covalently hydrated species

16. www.pkadata.com Other considerations continued • stability neutral molecule slowly ring-closes to give 4-methylpteridine pKa = 5.49

17. www.pkadata.com Summary of IUPAC Databases • IUPAC pKa compilations as computer-readable data • pKa data for ~12000 organic acids and bases in aqueous solution • Good range of organic chemistry with applicability to pharmaceutical, • agrochemical and specialty chemicals research • IUPAC assignment of data quality • Very useful data set for pKa prediction software • Fully referenced with method, temperature, ionic strength etc recorded • Ionisation assignment for logD calculations and greater search capability • Ability to merge with existing in-house data, with IUPAC-sourced data • clearly identified • All data given in this presentation were taken from the IUPAC databases Contacts Email : tony@pkadata.com Website : www.pkadata.com