Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques

Abstract

Motivation: The binding sites of proteins generally contain smaller regions that provide major contributions to the binding free energy and hence are the prime targets in drug design. Screening libraries of fragment-sized compounds by NMR or X-ray crystallography demonstrates that such 'hot spot' regions bind a large variety of small organic molecules, and that a relatively high 'hit rate' is predictive of target sites that are likely to bind drug-like ligands with high affinity. Our goal is to determine the 'hot spots' computationally rather than experimentally.

Results: We have developed the FTMAP algorithm that performs global search of the entire protein surface for regions that bind a number of small organic probe molecules. The search is based on the extremely efficient fast Fourier transform (FFT) correlation approach which can sample billions of probe positions on dense translational and rotational grids, but can use only sums of correlation functions for scoring and hence is generally restricted to very simple energy expressions. The novelty of FTMAP is that we were able to incorporate and represent on grids a detailed energy expression, resulting in a very accurate identification of low-energy probe clusters. Overlapping clusters of different probes are defined as consensus sites (CSs). We show that the largest CS is generally located at the most important subsite of the protein binding site, and the nearby smaller CSs identify other important subsites. Mapping results are presented for elastase whose structure has been solved in aqueous solutions of eight organic solvents, and we show that FTMAP provides very similar information. The second application is to renin, a long-standing pharmaceutical target for the treatment of hypertension, and we show that the major CSs trace out the shape of the first approved renin inhibitor, aliskiren.

Availability: FTMAP is available as a server at http://ftmap.bu.edu/.

Fig. 1.

Binding of organic solvents to elastase, determined by X-ray crystallography (Allen et al., ; Mattos et al., 2006) and computational mapping. (A) Probe molecules in the S₁ pocket of elastase, based on superimposing elastase structures solved in acetone, dimethylformamide, 5-hexene-1,2-diol, isopropanol, ethanol and trifluoroethanol. Probes are color-coded to distinguish between different molecules. (B) Probe molecules in the active site of elastase, based on superimposing the structures listed in (A). The probes are color-coded to distinguish between the different subsites. (C) Centers of probe clusters in the largest CS of elastase, located in the S₁ pocket, from mapping the protein using the 16 probes. Probes are color-coded to distinguish between different molecules. (D) Centers of probe clusters in the five CSs located in the active site of elastase as determined by the mapping. The probes are color-coded to distinguish between the different CSs: CS1, cyan; CS4, salmon; CS5, sky blue; CS7, orange; and CS8, pale green.

Fig. 2.

(A) Intermolecular non-bonded interactions between probes and elastase residues, determined by X-ray crystallography (Mattos et al., 2006) and computational mapping. The experimental and computational results are based on the interactions found between various elastase residues and the probes in the clusters shown in Figure 1B and D, respectively. (B) The same as panel (A), but for hydrogen bonds rather than non-bonded interactions.

Fig. 3.

Mapping results for renin. (A) Superposition of aliskiren (magenta) and a peptidomimetic inhibitor (orange) in the binding site of renin. The important subsites are labeled. (B) Mapping of the aliskiren-bound structure (PDB code 2v0z). Shown are the clusters centers in the CSs located in the renin-active site, superimposed on the inhibitor structures shown in panel (A). (C) Mapping of the ligand-free renin structure (PDB code 2ren). Cluster centers as in panel (B). (D) Mapping of renin co-crystallized with a peptidomimetic inhibitor (PDB code 1rne). Cluster centers as in panel (B).

Fig. 4.

(A) Intermolecular non-bonded interactions between inhibitors, probes and renin residues. The interactions are shown for the peptidomimetic inhibitor, aliskiren and the probes. The probe interactions are based on mapping the structure co-crystallized with the peptidomimetic inhibitor (PDB code 1rne). Two atoms are considered to interact if located within 5 Å from each other. (B) Same as in panel (A), but hydrogen bonds rather than non-bonded interactions.