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

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Presentation on theme: "Uses and Abuses of Experimental pKa Data Tony Slater pKaData Limited CUP XII Santa Fe March 2011 www.pkadata.com."— Presentation transcript:

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

2 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 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 pKa measurements for almost 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 What’s special about the IUPAC set? "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 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 Range of Chemistry and Applicability with applicability to :- Pharmaceutical industry Agrochemical industry Specialty Chemicals industry pKa prediction software companies Nb. quality assessment of particular relevance here

6 Types of Search Substructure Search for basic pKa 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 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, ). 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 In what areas are pKas used? 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) continued

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

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

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

12 What causes the variation? ionic strength variations continued pKa log 10 (ionic strength) physiological range (plasma, cytoplasm...)

13 What causes the variation? 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” continued estimated uncertainty in the value of K estimated uncertainty in the value of ΔpK Considering only reliable data and ones measured between °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 – (1.38) to 9.78 – 9.91 (0.13) for the base.

14 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 – 10.9 but which is which? Initial literature suggested lower pKa due to OH, but subsequent literature disagrees

15 Other considerations hydration continued 3 pKas given: “anhydrous" species equilibrium pK, partial covalent hydration covalently hydrated species

16 Other considerations stability continued pKa = 5.49 neutral molecule slowly ring-closes to give 4-methylpteridine

17 Summary of IUPAC Databases Contacts Website : 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


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