Substrate versus inhibitor dynamics of P‐glycoprotein

Abstract

By far the most studied multidrug resistance protein is P-glycoprotein. Despite recent structural data, key questions about its function remain. P-glycoprotein (P-gp) is flexible and undergoes large conformational changes as part of its function and in this respect, details not only of the export cycle, but also the recognition stage are currently lacking. Given the flexibility, molecular dynamics (MD) simulations provide an ideal tool to examine this aspect in detail. We have performed MD simulations to examine the behaviour of P-gp. In agreement with previous reports, we found that P-gp undergoes large conformational changes which tended to result in the nucleotide-binding domains coming closer together. In all simulations, the approach of the NBDs was asymmetrical in agreement with previous observations for other ABC transporter proteins. To validate the simulations, we make extensive comparison to previous cross-linking data. Our results show very good agreement with the available data. We then went on to compare the influence of inhibitor compounds bound with simulations of a substrate (daunorubicin) bound. Our results suggest that inhibitors may work by keeping the NBDs apart, thus preventing ATP-hydrolysis. On the other hand, repeat simulations of daunorubicin (substrate) in one particular binding pose suggest that the approach of the NBDs is not impaired and that the structure would be still be competent to perform ATP hydrolysis, thus providing a model for inhibition or substrate transport. Finally we compare the latter to earlier QSAR data to provide a model for the first part of substrate transport within P-gp.

Analysis of the Free Energy Landscapes for the Opening–Closing Dynamics of the Maltose Transporter ATPase MalK2 Using Enhanced-Sampling Molecular Dynamics Simulation

“…In fact, many previous studies have also noted the asymmetric closing/opening pathway of NBDs, including P-gp, Sav1866, MalK 2 , FbpC, MsbA, and MJ0796, where one ABP site closes/opens first, followed by the other ABP site. 39,[41][42][43][44][45][46] Above all, the free energy maps could be roughly divided into three regions: (1) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Even though the Mg-ATP can trigger the closure of MalK 2 , the complete conformational transition from the open to the closed state could not be observed: the protein structure was trapped in a quasistable state with the mismatched interaction between the two D-loops, and thus ATP molecules were not sandwiched between the Walker A and signature motif. The PCA ( Figure 6-(b)) indicates a not-well-coupled movement between HSD and CSD in the right-hand side monomer (colored in cyan), which may be responsible for the mis-dimerizing.…”

Multiple Drug Transport Pathways through Human P-Glycoprotein

“…In recent work, molecular dynamics studies of daunorubicin and the QZ59 inhibitors have been reported 70 that suggest that inhibitors like QZ59-RRR and QZ59-SSS may inhibit P-gp by preventing NBD closure.…”

About P‐glycoprotein: a new drugable domain is emerging from structural data

“…Thus, the problem seems to probably reside elsewhere, namely in the polyspecificity of the drug‐binding pocket. From structural data, the high structural flexibility described for P‐gp suggested the existence of multiple redundant drug‐binding sites that recognize substrates through an induced‐fit mechanism . However, the specific mode by which efflux can be modulated (competitive, noncompetitive, or allosteric) is still controversial.…”