Regulation of the Mitochondrial Functions by the Ubiquitin Protéasome System: Molecular Bases and Physiopathological Relevance

In this work we report extensive DFT study of sydnone-alkyne cyclization which included investigation of the reaction mechanism, analysis of different factors affecting sydnone and alkyne reactivity as well as attempt to reproduce quantitatively experimental activation free energy. The calculations were performed for a set of 18 sydnone-alkyne reactions with a help of a semi-automatized workflow involving reagent preparation and generation of starting structures for a plausible transition state. Reconstructed reaction path supported two-step mechanism: cycloaddition followed by retro-Diels-Alder reaction. Since the latter had a tiny barrier, the cycloaddition step was predicted to be the rate-limiting. For the ensemble of reactions, calculations reproduce activation free energies extracted from experimental reaction rates (k) with the accuracy of 2 kcal/mol. Accounting for solvation effects didn't change the overall trend of activation free energies as a function of substituents. A series of statistical model linking logk and sydnones structure was built using Support Vector Regression and Multiple Linear Regression machine-learning methods coupled with different types of molecular descriptors; none of them demonstrated a good performance at cross-validation stage. Detailed analysis of different factors affecting reaction rate variation as a function of substituents revealed particular role of the charge on C3 atom in the sydnone moiety as well as of the size of the substituent at C3.