Enzyme ribonucleotide reductase: unraveling an enigmatic paradigm of enzyme inhibition by furanone derivatives

Inactivation of Lactobacillus leichmannii ribonucleotide reductase by 2',2'-difluoro-2'-deoxycytidine 5'-triphosphate: covalent modification

Ribonucleotide reductase (RNR) from Lactobacillus leichmannii, a 76 kDa monomer using adenosylcobalamin (AdoCbl) as a cofactor, catalyzes the conversion of nucleoside triphosphates to deoxynucleotides and is rapidly (<30 s) inactivated by 1 equiv of 2',2'-difluoro-2'-deoxycytidine 5'-triphosphate (F(2)CTP). [1'-(3)H]- and [5-(3)H]F(2)CTP were synthesized and used independently to inactivate RNR. Sephadex G-50 chromatography of the inactivation mixture revealed that 0.47 equiv of a sugar was covalently bound to RNR and that 0.71 equiv of cytosine was released. Alternatively, analysis of the inactivated RNR by SDS-PAGE without boiling resulted in 33% of RNR migrating as a 110 kDa protein. Inactivation of RNR with a mixture of [1'-(3)H]F(2)CTP and [1'-(2)H]F(2)CTP followed by reduction with NaBH(4), alkylation with iodoacetamide, trypsin digestion, and HPLC separation of the resulting peptides allowed isolation and identification by MALDI-TOF mass spectrometry (MS) of a (3)H/(2)H-labeled peptide containing C(731) and C(736) from the C-terminus of RNR accounting for 10% of the labeled protein. The MS analysis also revealed that the two cysteines were cross-linked to a furanone species derived from the sugar of F(2)CTP. Incubation of [1'-(3)H]F(2)CTP with C119S-RNR resulted in 0.3 equiv of sugar being covalently bound to the protein, and incubation with NaBH(4) subsequent to inactivation resulted in trapping of 2'-fluoro-2'-deoxycytidine. These studies and the ones in the preceding paper (DOI: 10.1021/bi9021318 ) allow proposal of a mechanism of inactivation of RNR by F(2)CTP involving multiple reaction pathways. The proposed mechanisms share many common features with F(2)CDP inactivation of the class I RNRs.

Computational enzymatic catalysis

Computational methodologies are playing increasingly important roles in elucidating and presenting the complete and detailed mechanisms of enzymatic reactions because of their capacity to determine and characterize intermediates and transition states from both structural and energetics points of view, independent of their reduced lifetimes and without interfering with the natural reactional flux. These features are turning the field into an active and interesting area of research, involving a diverse range of studies, mostly directed at understanding the ways in which enzymes function under certain circumstances and predicting how they will behave under others. The accuracy of the computational data obtained for a given mechanistic hypothesis depends essentially on three mutually exclusive factors: the accuracy of the Hamiltonian of the reaction mechanism, consideration of the modulating aspect of the enzyme's structure in the energetics of the active center, and consideration of the enzyme's conformational fluctuations and dynamics. Although, unfortunately, it is impossible at present to optimize these crucial factors simultaneously, the success of any enzymatic mechanistic study depends on the level of equilibrium achieved among them. Different authors adopt different solutions, and this Account summarizes the most favored, with emphasis placed on our own preferences. Another crucial aspect in computational enzymatic catalysis is the model used in the calculations. Our aim is to build the simplest model that captures the essence of the catalytic power of an enzyme, allowing us to apply the highest possible theoretical level and minimize accidental errors. The choice is, however, far from obvious, ranging from simple models containing tens of atoms up to models of full enzymes plus solvent. Many factors underlie the choice of an appropriate model; here, examples are presented of very different modeling strategies that have been employed to obtain meaningful results. One particular case study, that of enzyme ribonucleotide reductase (RNR), a radical enzyme that catalyzes the reduction of ribonucleotides into deoxyribonucleotides, is one of the examples illustrating how the successive increase of the system's size does not dramatically change the thermodynamics and kinetics of the reaction. The values obtained and presented speak for themselves in that the only ones that are distinctly different are those calculated using an exceedingly small model, which omitted the amino acids that establish hydrogen bonds with the reactive unit of the substrate. This Account also describes our computational analysis of the mechanism of farnesyltransferase, a heterodimeric zinc metalloenzyme that is currently one of the most fascinating targets in cancer research. We focus on the present methodologies that we have been using, our models and understanding of the problem, and the accuracy of results and associated problems within this area of research.

Understanding Ribonucleotide Reductase Inactivation by Gemcitabine

This paper focuses on the inhibition of ribonucleotide reductase (RNR) by gemcitabine, 2',2'-difluoro-2'-deoxycytidine (dFdC), a deoxycytidine analogue that is a very active drug against solid tumors and is currently commercialized as gemzar. RNR inactivation is reductant-dependent and occurs in a very different way from that of other known substrate analogues. In the presence of reductants monomer R1 of RNR is inhibited, whereas in the absence of reductants the radical is lost and monomer R2 is inhibited. As inside the cell reductants are available, it is likely that R1 inactivation is the most favorable mechanism responsible for drug cytotoxicity. This inhibition pathway has been unknown to date, but we have conducted a theoretical study that has led us to the first proposal of a mechanism for RNR inhibition by dFdC in the presence of reductants.