Computational Drug Discovery and Design

the definition of the path that connects the two end states of

interest. Since the free energy is a state function, the nature of the

path is unimportant, and we can choose to use a thermodynamic

cycle that connects the bound and unbound states through several

nonphysical intermediate ones, as shown in Fig.1. The nonphysical

nature of the cycle used is the reason why this type of calculations is

typically referred to asalchemical. The cycle depicted in Fig.1 can

be discretized inNstates, which are independently simulated.

These independent simulations are also often referred to aswin-

dows. Then, the free energy difference between each stateiand its

+

+

+

ΔG°b

ΔGsolvelec+vdw

ΔGsolvrestr

ΔGprotrestr

ΔGprotelec+vdw

ΔG=0

Protein (P) Ligand (L) Complex (PL)

Lelec+vdw

L

Lrestr

PLelec+vdw

PLrestr

PLrestr+elec+vdw

A) F)

E)

C) D)

B)

Fig. 1Thermodynamic cycle used in absolute binding free energy calculations. The fully interacting ligand
(orange) in solution at the top left (A) is transformed into a noninteracting solute (B, white) during a series of
equilibrium simulations where its electrostatic and van der Waals interactions are scaled to zero, providing the
termΔGsolvelecþvdW. The ligand is then restrained while still noninteracting with the environment (C), calculating

ΔGsolvrestr. This state is equivalent to having the noninteracting ligand restrained within the protein cavity (D).
The restrained and noninteracting ligand in complex with the protein has its electrostatic and vdW interactions
turned back on again (E), givingΔGprotelecþvdW. The restraints between ligand and protein are then removed
(ΔGprotrestr), closing the cycle, and the final state is the unrestrained and fully interacting ligand in complex with
the protein (F). Reproduced from Aldeghi et al. [7] with permission from The Royal Society of Chemistry

206 Matteo Aldeghi et al.