A Multistep Approach to Structure-Based Drug Design:  Studying Ligand Binding at the Human Neutrophil Elastase

Abstract

In this study we show that a combination of different theoretical methods is a viable approach to calculate the binding affinities of new ligands for the human neutrophile elastase. This protease degrades elastin and likely aids neutrophils in fulfilling their immunological functions. Abnormally high human neutrophil elastase (HNE) levels are involved in several diseases; therefore, inhibitors of HNE are of interest as targets for drug design. A recent study has revealed that cinnamic acid and bornyl ester derivatives bind to HNE, but DeltaG0 values from ligand docking results exhibited no correlation with those calculated from the IC50 values. To accurately compute binding affinities, we generated possible protein ligand complex structures by ligand docking calculations. For each of the ligands, the 30 most likely placements were used as starting points of nanosecond length molecular dynamics simulations. The binding free energies for these complex structures were estimated using a continuum solvent (MM-PBSA) approach. These results, along with structural data from the molecular dynamics runs, allowed the identification of a group of similar placements that serve as a model for the natural protein ligand complex structure. This structural model was used to perform thermodynamic integration (TI) calculations to obtain the relative binding free energies of similar ligands to HNE. The TI results were in quantitative agreement with the measured binding affinities. Thus, the presented approach can be used to generate a probable complex structure for known ligands to HNE and to use such a structure to calculate the effects of small ligand modifications on ligand binding, possibly leading to new inhibitors with improved binding affinities.

Perspective: Alchemical free energy calculations for drug discovery

“…15,64 Several other groups in academia have applied them in similar efforts. [65][66][67] Industry has also found some use for these techniques, [68][69][70] and several studies have FIG. 1.…”

“…19,70,89 In cases where the ligand binding mode is maintained as functional groups are modified, conventional relative free energy calculations may often work well without any special treatment of alternate potential binding modes. However, small modifications to ligands do on occasion yield big differences in ligand binding orientation, 65,88,[90][91][92][93][94][95][96][97] and there is currently no way to know when this will happen. For example, Stout et al developed a series of thymidylate synthase (TS) inhibitors based on phenolphthalein and phthalein derivatives.…”

“…Scaffold IFEs may be easier to obtain due to fewer steric hindrances (and in special cases such as a scaffold consisting of a symmetric ring, scaffold IFEs may be zero 128 ), though IFEs of a ligand can provide additional physical insight. These IFEs could be obtained a number of ways, including potential of mean force approaches, relative free energy calculations between different binding modes, 65,68,107,108 and even absolute binding free energy calculations to get relative free energies of binding modes. 106,124 Relative calculations between binding modes seem likely to work particularly well, and would probably best be implemented with a dual topology strategy, where the ligand is turned off in one binding mode while being turned on in another binding mode.…”

“…101,103,106 Others have had some success with a similar strategy. 65,124 However, in general the problem of identifying likely binding modes will be extremely challenging, especially in cases of dramatic receptor rearrangement on ligand binding, or where ligand modifications introduce unexpected and slow conformational rearrangement in the protein. In such cases, discovering candidate binding modes may be much more difficult.…”

Predicting Absolute Ligand Binding Free Energies to a Simple Model Site

“…Such methods perform poorly on some test sets. 9,10 At the highest level of rigor are various free energy methods, including the alchemical free energy calculations described below and potential of mean force-based methods 11,12 (for recent reviews of free energy methods, see works by Rodinger and Pomès, Kofke, and Shirts et al). [13][14][15] Here we focus on alchemical free energy methods, which evaluate ratios of partition functions to estimate binding free energies and thus include entropic and other contributions neglected at lower levels of theory.…”