Free energy screening of small ligands binding to an artificial protein cavity

Abstract

The λ-dynamics simulation method was used to study the binding of 10 five-member ring heterocycle derivatives to an artificial cavity created inside cytochrome C peroxidase by mutagenesis. Application of λ dynamics using a multiple topology approach resulted in trapping in local minima. To extend the method to these cases, a new restraining potential was devised and added to the extended Hamiltonian. Two approximations were introduced in order to estimate the binding free energy within small simulation times using this potential: (a) The entropy terms related to the restraining potential are assumed to cancel, due to the similarity of the ligands. (b) The restraining potential calculated from the coordinates of the environmental atoms during a λ-dynamics simulation is assumed to be equal to that of the average coordinates. Relatively short λ-dynamics simulations with this restraining potential successfully yielded reasonable estimates of the binding affinity of the ligands as compared with both experimental data and free energy perturbation calculations. Long time λ-dynamics simulations with a ten-ligand system revealed that better ligands tend to have small statistical errors, which is appropriate for screening out the plausible ligands from all candidates. Furthermore, short time λ-dynamics simulations with ten identical ligands demonstrated that sufficient precision was achieved for putative discovery of tight binding ligands or guests.

Probing Molecular Docking in a Charged Model Binding Site

“…A good example of this is thiophenylmethylamine (33), whose localized charge makes it harder to desolvate then thiopheneamidinium (21), a close analog with a delocalized charge. Nevertheless, the K d value of thiophenylmethylamine (33) is 0.05 mM, only slightly worse than that of thiopheneamidinium (21), which is 0.02 mM.…”

“…Brooks and colleagues tested their l-dynamics approach to predict binding affinities. 32,33 Olson and colleagues tested the ability of AutoDock 34 to reproduce crystallographically observed binding modes and to predict binding affinities of the known ligands. 31 Here, we use the CCP W191G pocket for studying charge-charge and charge-polar interactions in docking screens of large compound databases.…”

Perspective: Alchemical free energy calculations for drug discovery

“…109,[140][141][142] These are relatively simple binding sites which bind small, fragment-like ligands and yet are susceptible the binding mode sampling problems discussed here. Much of the work in these sites has been with absolute free energy calculations (with notable exceptions 105,109,128 ), but the available high quality data pave the way for a careful examination of relative free energy calculations in this context. These also should provide an excellent test case for new methodological innovations aimed at tackling binding mode sampling problems.…”

“…Other applications have highlighted similar issues. 18,[109][110][111][112] Water plays a thermodynamically significant role as well-slow water motions into and out of binding sites can yield errors in computed relative free energies in excess of 10 kcal/mol. 87 Thus, available computational data, though limited, suggest that issues relating to uncertain, incorrect, or changing ligand binding modes can introduce errors up to 7 kcal/mol in relative binding free energy calculations when these effects are ignored.…”

Separated topologies—A method for relative binding free energy calculations using orientational restraints

“…In the lambda dynamics approach, a restraint potential proportional to lambda is applied to the ligands, such that the fully coupled ligand feels no restraint potential, but the more decoupled ligands feel the restraint more strongly. 17,18 This restraint takes the form of a so-called ghost force in which the binding site non-bonded interactions create forces (of reduced magnitude, dependent on lambda) on the decoupled ligand, but the ligand does not create opposing forces on the binding site, creating non-Newtonian dynamics. In these works, the authors chose not to directly account for the effect of the restraint on the translational and rotational entropy of the ligands, instead arguing that these terms would be similar for different ligands in the same binding site and would not affect their relative binding free energies.…”