Limits...
Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase.

Mondal J, Friesner RA, Berne BJ - J Chem Theory Comput (2014)

Bottom Line: The simulations further show that the barrier is not a result of the reorganization free energy of the binding pocket.Chem.Soc.2011, 133, 9181-9183].

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States.

ABSTRACT

Computer simulations are used to determine the free energy landscape for the binding of the anticancer drug Dasatinib to its src kinase receptor and show that before settling into a free energy basin the ligand must surmount a free energy barrier. An analysis based on using both the ligand-pocket separation and the pocket-water occupancy as reaction coordinates shows that the free energy barrier is a result of the free energy cost for almost complete desolvation of the binding pocket. The simulations further show that the barrier is not a result of the reorganization free energy of the binding pocket. Although a continuum solvent model gives the location of free energy minima, it is not able to reproduce the intermediate free energy barrier. Finally, it is shown that a kinetic model for the on rate constant in which the ligand diffuses up to a doorway state and then surmounts the desolvation free energy barrier is consistent with published microsecond time-scale simulations of the ligand binding kinetics for this system [Shaw, D. E. et al. J. Am. Chem. Soc.2011, 133, 9181-9183].

No MeSH data available.


Related in: MedlinePlus

Top: Free energy G(N;d = ∞) in kcal/mol asa functionof number of pocket water (N) (which is effectivelysimilar to the case of a ligand-free pocket). (The free energy G(N;d = ∞) wasobtained from umbrella sampling simulation using water-number as thereaction coordinate as described in the Method section.) Bottom: The dependence of the freeenergy G(N;d) onthe number of pocket-waters, N, and on the ligand-pocketseparation d in the range of intermediate free energybarrier. The blue basins correspond to the free energy minima appearingon either side of the intermediate free-energy barrier. The averagenumbers of water molecules, N̅, at d = 0.75 nm (after overcoming the barrier) is ≈0and at N̅ at d = 0.95 nm (beforeovercoming the barrier) is ≈3. The two red lines provide thechanges in desolvation free energies for protein–ligand separationsrelative to the case when the ligand is outside the pocket just priorto and just after surmounting the intermediate free energy barrier.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4263462&req=5

fig5: Top: Free energy G(N;d = ∞) in kcal/mol asa functionof number of pocket water (N) (which is effectivelysimilar to the case of a ligand-free pocket). (The free energy G(N;d = ∞) wasobtained from umbrella sampling simulation using water-number as thereaction coordinate as described in the Method section.) Bottom: The dependence of the freeenergy G(N;d) onthe number of pocket-waters, N, and on the ligand-pocketseparation d in the range of intermediate free energybarrier. The blue basins correspond to the free energy minima appearingon either side of the intermediate free-energy barrier. The averagenumbers of water molecules, N̅, at d = 0.75 nm (after overcoming the barrier) is ≈0and at N̅ at d = 0.95 nm (beforeovercoming the barrier) is ≈3. The two red lines provide thechanges in desolvation free energies for protein–ligand separationsrelative to the case when the ligand is outside the pocket just priorto and just after surmounting the intermediate free energy barrier.

Mentions: We determine the contribution of desolvation to thefree energy barrier that the ligand must overcome in the process ofbinding to the pocket using the umbrella sampling strategy introducedby Hummer et al.41 The Gibbs free energy G(N;d = ∞) shownin the top panel of Figure 5 exhibits a strongmonotonic decrease with N between N = 0 and 8 water molecules. The minimum of G(N;d = ∞) gives the average numberof pocket-water molecules, N̅ in the ligand-freepocket. From this we can compute ΔG for thetransition from N̅ to N, correspondingto partial desolvation of the ligand-free pocket. The bottom plate of Figure 5 shows the freeenergy profile G+(N;d) as a function of N and d, in the neighborhood of the intermediate free energy barrier. Weclearly see the presence of two basins before and after the intermediatefree energy maximum. At d = 0.95 nm (just beforeovercoming the barrier) the average water occupation number is N̅ ≈ 3, and at d = 0.75 nm(just after overcoming the barrier) it is N̅ ≈ 0. Thus, for a given ligand-pocket distance, we can readfrom the graph in the bottom plate the average number of water moleculesin the pocket with the ligand present, and then from the top platethe corresponding value of ΔG for partial desolvationof the ligand-free pocket to that same number of water molecules.This allows us to estimate the desolvation free energy required forthe ligand to replace the water molecules in a ligand-free pocketupon binding. From Figure 3, we estimate thedesolvation free energy change accompanying the change in ligand-pocketdistance from d = 0.95 → d = 0.75 nm (which are the position before and after the intermediatefree-energy barrier respectively) to be ≈3.7 kcal/mol, a resultalmost equal to the total free energy cost (4 kcal/mol) for the ligandto surmount the barrier on going from d = 0.95 → d = 0.75 nm. This suggests that the intermediate free energybarrier encountered by the ligand is mainly due to pocket-desolvation,and that pocket-desolvation is thus a key step in the kinetics ofligand binding. Both these one-dimensional and two-dimensional freeenergetics of pocket-water are in reasonable agreement with an independentlyperformed pocket-water free energy analysis, using different initialconfiguration (Figures S2 and S3 in the SupportingInformation). We have also found that extending the simulationlength of each window from 2 to 5 ns does not change the result significantly.


Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase.

Mondal J, Friesner RA, Berne BJ - J Chem Theory Comput (2014)

Top: Free energy G(N;d = ∞) in kcal/mol asa functionof number of pocket water (N) (which is effectivelysimilar to the case of a ligand-free pocket). (The free energy G(N;d = ∞) wasobtained from umbrella sampling simulation using water-number as thereaction coordinate as described in the Method section.) Bottom: The dependence of the freeenergy G(N;d) onthe number of pocket-waters, N, and on the ligand-pocketseparation d in the range of intermediate free energybarrier. The blue basins correspond to the free energy minima appearingon either side of the intermediate free-energy barrier. The averagenumbers of water molecules, N̅, at d = 0.75 nm (after overcoming the barrier) is ≈0and at N̅ at d = 0.95 nm (beforeovercoming the barrier) is ≈3. The two red lines provide thechanges in desolvation free energies for protein–ligand separationsrelative to the case when the ligand is outside the pocket just priorto and just after surmounting the intermediate free energy barrier.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263462&req=5

fig5: Top: Free energy G(N;d = ∞) in kcal/mol asa functionof number of pocket water (N) (which is effectivelysimilar to the case of a ligand-free pocket). (The free energy G(N;d = ∞) wasobtained from umbrella sampling simulation using water-number as thereaction coordinate as described in the Method section.) Bottom: The dependence of the freeenergy G(N;d) onthe number of pocket-waters, N, and on the ligand-pocketseparation d in the range of intermediate free energybarrier. The blue basins correspond to the free energy minima appearingon either side of the intermediate free-energy barrier. The averagenumbers of water molecules, N̅, at d = 0.75 nm (after overcoming the barrier) is ≈0and at N̅ at d = 0.95 nm (beforeovercoming the barrier) is ≈3. The two red lines provide thechanges in desolvation free energies for protein–ligand separationsrelative to the case when the ligand is outside the pocket just priorto and just after surmounting the intermediate free energy barrier.
Mentions: We determine the contribution of desolvation to thefree energy barrier that the ligand must overcome in the process ofbinding to the pocket using the umbrella sampling strategy introducedby Hummer et al.41 The Gibbs free energy G(N;d = ∞) shownin the top panel of Figure 5 exhibits a strongmonotonic decrease with N between N = 0 and 8 water molecules. The minimum of G(N;d = ∞) gives the average numberof pocket-water molecules, N̅ in the ligand-freepocket. From this we can compute ΔG for thetransition from N̅ to N, correspondingto partial desolvation of the ligand-free pocket. The bottom plate of Figure 5 shows the freeenergy profile G+(N;d) as a function of N and d, in the neighborhood of the intermediate free energy barrier. Weclearly see the presence of two basins before and after the intermediatefree energy maximum. At d = 0.95 nm (just beforeovercoming the barrier) the average water occupation number is N̅ ≈ 3, and at d = 0.75 nm(just after overcoming the barrier) it is N̅ ≈ 0. Thus, for a given ligand-pocket distance, we can readfrom the graph in the bottom plate the average number of water moleculesin the pocket with the ligand present, and then from the top platethe corresponding value of ΔG for partial desolvationof the ligand-free pocket to that same number of water molecules.This allows us to estimate the desolvation free energy required forthe ligand to replace the water molecules in a ligand-free pocketupon binding. From Figure 3, we estimate thedesolvation free energy change accompanying the change in ligand-pocketdistance from d = 0.95 → d = 0.75 nm (which are the position before and after the intermediatefree-energy barrier respectively) to be ≈3.7 kcal/mol, a resultalmost equal to the total free energy cost (4 kcal/mol) for the ligandto surmount the barrier on going from d = 0.95 → d = 0.75 nm. This suggests that the intermediate free energybarrier encountered by the ligand is mainly due to pocket-desolvation,and that pocket-desolvation is thus a key step in the kinetics ofligand binding. Both these one-dimensional and two-dimensional freeenergetics of pocket-water are in reasonable agreement with an independentlyperformed pocket-water free energy analysis, using different initialconfiguration (Figures S2 and S3 in the SupportingInformation). We have also found that extending the simulationlength of each window from 2 to 5 ns does not change the result significantly.

Bottom Line: The simulations further show that the barrier is not a result of the reorganization free energy of the binding pocket.Chem.Soc.2011, 133, 9181-9183].

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States.

ABSTRACT

Computer simulations are used to determine the free energy landscape for the binding of the anticancer drug Dasatinib to its src kinase receptor and show that before settling into a free energy basin the ligand must surmount a free energy barrier. An analysis based on using both the ligand-pocket separation and the pocket-water occupancy as reaction coordinates shows that the free energy barrier is a result of the free energy cost for almost complete desolvation of the binding pocket. The simulations further show that the barrier is not a result of the reorganization free energy of the binding pocket. Although a continuum solvent model gives the location of free energy minima, it is not able to reproduce the intermediate free energy barrier. Finally, it is shown that a kinetic model for the on rate constant in which the ligand diffuses up to a doorway state and then surmounts the desolvation free energy barrier is consistent with published microsecond time-scale simulations of the ligand binding kinetics for this system [Shaw, D. E. et al. J. Am. Chem. Soc.2011, 133, 9181-9183].

No MeSH data available.


Related in: MedlinePlus