The Recognition of Unrelated Ligands by Identical Proteins

Abstract

Unrelated ligands, often found in drug discovery campaigns, can bind to the same receptor, even with the same protein residues. To investigate how this might occur, and whether it might be typically possible to find unrelated ligands for the same drug target, we sought examples of topologically unrelated ligands that bound to the same protein in the same site. Seventy-six pairs of ligands, each bound to the same protein (152 complexes total), were considered, classified into three groups. In the first (31 pairs of complexes), unrelated ligands interacted largely with the same pocket residues through different functional groups. In the second group (39 pairs), the unrelated ligand in each pair engaged different residues, though still within the same pocket. The smallest group (6 pairs) contained ligands with different scaffolds but with shared functional groups interacting with the same residues. We found that there are multiple chemically unrelated but physically similar functional groups that can complement any given local protein pocket; when these functional group substitutions are combined within a single molecule, they lead to topologically unrelated ligands that can each well-complement a site. It may be that many active and orthosteric sites can recognize topologically unrelated ligands.

Figure 1

Protein families represented in this study. (Left) Distribution of major drug-relevant protein families within the 76 proteins considered (count after the comma). (Right) Distribution of enzyme subfamilies. All family names are ChEMBL target classifications.

Figure 2

Statistics for binding site residue overlap, ligand volume overlap, and ligand similarity for the 76 complex pairs. (A) Binding site residue overlap (all heavy atoms) of complex pairs in each of the three classes and totaled overall. (B) Ligand volume overlap in each complex pair, separated by class and summed overall. Most pairs contain one ligand with 50% of its volume overlapped, indicating ligands are in the same binding pocket. (C) Dissimilarity of ligands in complex pairs for all three classes, by three different metrics: ECFP4 fingerprints, ROCS shape, and ROCS TanimotoCombo. Most are below common values used to distinguish chemically dissimilar scaffolds (dashed lines with corresponding colors).

Figure 3

Examples of class I complexes, where the same protein residues interact with different ligand functional groups (see Table SI-1 and Figure SI-4 in the Supporting Information). The structure overlap, binding site of each complex, 2D outline of protein−ligand interactions (blue dots are water, red dashed lines hydrogen bonds, orange lines represent hydrophobic contact; blue residue labels are common to both), and similarity metrics are shown. (A) Retinol-binding protein 4 bound to compound 6 and to compound 7. (B) M₂ muscarinic receptor bound to Iperoxo (8) and to QNB (9). (C) Tankyrase-1 bound to compounds 10 and 11.

Figure 4

Examples of class II complexes where different protein residues engage different ligand functional groups (see Table SI-2 and Figure SI-5 in the Supporting Information). The 3D crystal structure overlap, enlarged binding site of each complex, 2D outline of protein−ligand interactions (colored as in Figure 3), and similarity metrics are shown. (A) Coagulation factor Xa bound to DX-9056a (12) and to compound 13. (B) Progesterone receptor bound to ulipristal acetate (14) and to compound 15. (C) Glucose transporter bound to cytochalasin B (16) and to compound 17.

Figure 5

Examples of class III complexes where the same protein residues interact with similar functional groups on the ligands (also see Table SI-3 and SI-6). The structure overlap, enlarged binding site of each complex, 2D outline of protein−ligand interactions (colored as in Figure 3), and similarity metrics are shown: (A) β₂-adrenergic receptor bound to timolol (18) and to BI167107 (19); (B) FABP4 bound to compound 20 and to ibuprofen (21); and (C) adenosine receptor A2a bound to adenosine (22) and to compound 23.

Figure 6

Complex pairs where water mediates interactions with one ligand whereas the second ligand makes these interactions directly. The structure overlap, binding site of each complex, 2D outline of protein−ligand interactions (colored as in Figure 3), and similarity metrics are shown. (A) Pteridine reductase co-crystallized with compound 24 and with compound 25. (B) Renin co-crystallized with compound 26 and with compound 27.