Relative Binding Free Energies of Peptide Inhibitors of HIV-1 Protease: The Influence of the Active Site Protonation State

Abstract

Hydrogen bonding plays an important role in the stabilization of complexes between HIV-1 protease (HIV-1 PR) and its inhibitors. The adequate treatment of the protease active site protonation state is important for accurate molecular simulations of the protonation state is important for accurate molecular simulations of the protease-inhibitor complexes. We have applied the free energy simulation/thermodynamic cycle approach to evaluate the relative binding affinities of the S vs R isomers of the U85548E inhibitor of the protease. Several mono- and diprotonation states of the catalytic aspartic acid residues of the protease active site were considered in the course of molecular simulations. The calculated difference in binding free energy of the S vs R isomers strongly depended on the location of proton(s), but in all cases the binding free energy of the S inhibitor was higher. On the basis of our calculations, we propose that in the HIV-1 PR-inhibitor complex only one catalytic aspartic acid residue is protonated and that the binding free energy of the S isomer is ca. 2.8 kcal/mol higher than that of the R isomer. The accuracy of these predictions shall be evaluated when binding affinities of both isomers become available.

A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design

“…Such methods can be quite successful in identifying lead compounds (Lam et al, 1994). More sophisticated and expensive calculations have applied the free energy perturbation method in order to evaluate changes in binding energy upon substitution of small molecular fragments (Reddy et al, 1994;Chen & Tropsha, 1995). The current state of the art in molecular simulations of HIV-I-PR inhibitor binding was reviewed by McCarrick and Kollman (1994).…”

“…These interactions result in an almost complete burial of most HIV-I-PR inhibitors. Conclusions about the energetic contributions to the total binding strength of these inhibitors, based largely on applications of conventional modeling tools (Hutchins & Greer, 1991;Appelt, 1993;Guida, 1994;Chen & Tropsha, 1995;Holloway et al, 1995), find that hydrogen bonding patterns and hydrophobic interactions are frequent components of inhibitor binding (Appelt, 1993;Wlodawer & Erickson, 1993;Gustchina et al, 1994). The extent and importance of these interactions have, however, been difficult to characterize.…”

Computationally accessible method for estimating free energy changes resulting from site-specific mutations of biomolecules: Systematic model building and structural/hydropathic analysis of deoxy and oxy hemoglobins

“…A number of research groups, using a variety of techniques-including solution NMR, have concluded that one of the two aspartate residues located in the catalytic domain of HIV protease is protonated, while the other is negatively charged. [52][53][54] Similarly, the determination of pK a values for all carboxyl groups in ribonuclease HI indicated that for two aspartate residues in close proximity, one has an elevated pK a , while the other has a depressed pK a ; i.e., one of the residues is protonated. 55 Other studies have demonstrated that the desolvation of acidic residues can result in pK a shifts toward or past the environmental pH, occurring most often with acidic residues found in areas of proteins that insufficiently stabilized their negative charge, and/or were hydrophobic in nature.…”

Identification of HIV Inhibitors Guided by Free Energy Perturbation Calculations

“…Additional successful applications of the FEP method for the calculation of HIV-1 PR inhibition, including non-peptide inhibitors, have been reported by McCarrick and Kollman [86], Rao and Murcko [87], Varney et al [88], Chen and Tropsha [89], and Wang et al [90] and has laid the path for more recent accomplishments in FEP guided design of HIV-1 reverse transcriptase inhibitors.…”