A kinetic, modeling and mechanistic re-analysis of thymidine phosphorylase and some related enzymes

Abstract

Thymidine phosphorylase (TP) is an important target enzyme for cancer chemotherapy but currently available inhibitors lack in vivo potency. Related enzymes also are therapeutic targets. A greater understanding of enzyme structure and mechanism may help in the design of improved drugs and this work assists in that regard. Also important is the correct identification of the ionization states and tautomeric forms of substrates and products when bound to the enzyme and during the course of the reaction. Approximate methods for estimating some ΔpK_as between aqueous and protein-bound substrates are exemplified for nucleobases and nucleosides. The estimates demonstrate that carbonyl-protonated thymidine and hydroxy tautomers of thymine are not involved in TP's actions. Other estimates indicate that purine nucleoside phosphorylase binds inosine and guanosine as zwitterionic tautomers and that phosphorolysis proceeds through these forms. Extensive molecular modeling based on an X-ray structure of human TP indicates that TP is likely to be mechanistically similar to all other natural members of the class in proceeding through a α-oxacarbenium-like transition state or states.

Keywords::

• Thymidine phosphorylase
• enzyme-bound substrate pK_as
• anomalous tautomerism
• purine nucleoside phosphorylase
• isotope effects
• arsenate esters
• molecular modeling
• kinetics
• inhibition

Notes

^† The second pK_a of α‐D-ribose 1-phosphate in water at 25°C is 6.28 [53], ∼8-fold more acidic than dihydrogen-phosphate (pK_a = 7.2); α‐D‐2-deoxyribose 1-phosphate is expected to be about 3-fold more acidic (aqueous pK_a = ∼6.7).

^‡ Poulter and Federick [26] report the aqueous pK_a of O^C2 protonated uracil as − 4.46, (not − 2.98 as misquoted in reference 38) which then has to be adjusted for attachment of the electron withdrawing sugar ring and then ‘site-effects’ similar to those discussed in the main text for protonation of the anion.

^¶ Substrate/‘TP’ and ‘TS’/‘TP’ structure coordinate files are available, in pdb or mol2 format, by email from the author.

Appendices are available as supplementary online material by accessing the article on the journal webpage.