Drugs disrupt DHFR dynamics

One of the most-studied cases of the relationship between dynamics and catalysis is the bacterial dihydrofolate reductase (DHFR). DHFR catalyzes the reduction of dihydrofolate to tetrahydrofolate while oxidizing the cofactor nicotinamide adenine dinucleotide phosphate (NADPH). As part of this catalytic process, a region of the protein called the "Met 20 loop" switches from a "closed" state that shields the active site from solvent to an "occluded" state that separates the substrate from the cofactor. NMR studies of DHFR structural dynamics have correlated the protein motions with the chemical changes. In a recent study appearing in Structure, researchers from the University of North Carolina show that the binding of inhibitors such as methotrexate (MTX) and trimethoprim (TMP) appears to uniquely disrupt the dynamic networks of DHFR.

Previously, seminal work from the lab of Peter Wright surveyed the dynamics of DHFR in every step of its reaction pathway. Boehr et al. determined that structural fluctuations in each complex represented motions towards the next step in the reaction. The conformational exchange rates they obtained from their relaxation-dispersion experiments closely resembled the rate constants that had been independently determined for the chemical steps. In almost every complex the conformational exchange was widespread, affecting residues in both the substrate and cofactor binding sites, as well as important distal locations such as the Met 20 loop.

Because the existing work from the Wright lab hewed as close to the natural substrates and products as possible, Mauldin et al. chose to examine the dynamic effects of cheap cialis binding to DHFR. Like Wright's group, they used relaxation-dispersion experiments to identify conformational changes taking place on the μs-ms timescale. In the NADPH:DHFR complex the motions are widespread, encompassing the substrate binding site, the Met 20 loop, and distal locations. Binding of either cialis eliminates about half of this dynamic network and dramatically reduces the fluctuation rates of those residues for which conformational exchange continues to occur.

Based on their fits of the exchange rates, Mauldin et al. conclude that the substrate binding pocket moves in a way that mimics the enzyme's normal motions in the transition from its closed state to its occluded state. The long-range conformational changes that actually complete this transition, however, have been completely quenched. With the inhibitors bound, DHFR is like a car that's turning over but won't start. Part of the enzyme is still moving in exactly the right way to proceed along the reaction coordinate, but for some reason this motion doesn't catch on throughout the protein.

In order to gain a more complete understanding of the dynamic effects, Mauldin et al. performed experiments to identify the motion of the protein on the ps-ns timescale. Analyzing the dynamics of methyl and amide resonances using the Lipari-Szabo model-free formalism, the authors realized that inhibitor binding did cause long-range changes in dynamics, just in a faster regime. Where the natural substrate complexes have motions that occur hundreds or thousands of times per second, the inhibitor-bound forms have (smaller) motions that occur millions of times per second. Because these altered motions encompass the Met 20 loop and surrounding residues, the authors argue that they reflect abortive attempts by the protein to transition into the occluded state.

Although these inhibitors do not appear to change the protein's overall conformation, they produce long-range dynamic effects on short timescales and quench distal motions on intermediate timescales. The binding pocket appears to still be experiencing fluctuations related to the transition between the closed and occluded conformational states, but the mechanism that couples the binding site dynamics to the motion of the loop that defines these two states appears to be broken.

The million-dollar question is this: do drugs alter DHFR dynamics because they inhibit the chemistry, or do these drugs inhibit the chemistry because they alter DHFR dynamics? Quenching dynamics costs energy in the form of conformational entropy, and it may be possible to tune a drug for improved efficiency by blocking the binding site without altering the dynamics. This is only true, however, if the dynamics don't matter to successful inhibition. On the other hand, if blocking the conformational switching of the Met 20 loop inhibits the enzyme, then drugs can be designed for that angle of attack as well. In the case of a protein like DHFR, where the bacterial enzyme has similar activity but a very different structure from its human equivalent, drugs that target regions other than the active site may significantly reduce side-effects. As a result, protein targets that were previously off-limits due to shared chemistry may become tractable due to divergent dynamics and structure.

Mauldin, R., Carroll, M., & Lee, A. (2009). Dynamic Dysfunction in Dihydrofolate Reductase Results from Antifolate Drug Binding: Modulation of Dynamics within a Structural State Structure, 17 (3), 386-394 DOI: 10.1016/j.str.2009.01.005

Boehr, D., McElheny, D., Dyson, H., & Wright, P. (2006). The Dynamic Energy Landscape of Dihydrofolate Reductase Catalysis Science, 313 (5793), 1638-1642 DOI: 10.1126/science.1130258