Figure 1.
Overview of pathway-based screening strategy for identifying conserved binding environments and multitarget inhibitors of multiple proteins.
(A) The proteins in the shikimate pathway. (B) Chemical reactions of shikimate dehydrogenase (SDH) and shikimate kinase (SK). SDH converts 3-dehydroshikimate into shikimate using NAPDH and then SK converts shikimate into shikimate 3-phosphate by ATP. These three compounds share the same substructure (blue region). (C) Establishment of site-moiety maps of SDH and SK. A site-moiety map represents the binding environments of a protein binding site by anchors. (D) The site-moiety map alignment of SDH and SK for identifying the conserved binding environments (pathway anchors). (E) Pathway anchors of SDH and SK. Hydrogen-bonding and van der Waals anchors are colored in green and gray, respectively. (F) Pathway inhibitors identified by the pathway anchors.
Figure 2.
Pathway site-moiety map of SDH (yellow) and SK (purple).
(A) Superimposed binding sites of SDH and SK by the anchor-based alignment method. Four pathway anchors were identified despite low sequence and structure similarities of SDH and SK. Hydrogen-bonding and van der Waals anchors are colored in green and gray, respectively. (B) Common moiety preferences of four pathway anchors.
Figure 3.
Relationship between the pathway anchors and biological functions.
(A) Ligands of SDH and SK in the pathway site-moiety map. The ligands include shikimate and NADPH of SDH (PDB code 3PHI), and shikimate and ACP (ATP analog) of SK (PDB code 1ZUH [39], a shikimate kinase structure of Mycobacterium tuberculosis). (B) Pathway anchors for biological functions. Diagrams of the ligands and the pathway anchors for (C) SDH and (D) SK. Residues are colored in red if their mutations lead to loss of enzyme activity [14], [19], [30], [31].
Figure 4.
New multitarget inhibitors identified by the pathway-based screening strategy.
(A) The compound structures and IC50 values of the multitarget inhibitors. The relationships between the inhibitors and the pathway anchors are represented by green (hydrogen-bonding interactions) and gray (van der Waals interactions) circles. Docking poses of these inhibitors and anchor residues of (B–D) SDH and (E–G) SK.
Figure 5.
Comparison of conservation scores.
(A) Conservation-score distribution of pathway anchor residues, anchor residues, binding site residues, and other residues. The scores are from 1 (least conserved) to 9 (most conserved). (B) Conservation-score distribution of pathway anchors and anchors. A conservation score of a pathway anchor or an anchor is derived by averaging the conservation scores of pathway anchor residues or anchor residues.
Figure 6.
Specific anchors and selective inhibitors of shikimate dehydrogenase (SDH).
(A) Specific anchors of SDH. The specific site includes these anchors H3, V1, and V3. (B) Compound structures and IC50 values of two selective inhibitors. Docking poses of these two selective inhibitors (C) NRB03174 and (D) HTS02873.
Figure 7.
Performance of the PathSiMMap compared with site-moiety map-based and energy-based methods for (A) SDH and (B) SK.
The PathSiMMap (blue line) is the best and significantly outperforms the site-moiety map (red line) and the energy-based method (green line) for identifying SDH and SK inhibitors.