Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets

Abstract

Background: To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions.

Results: We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/.

Conclusions: SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.

Figure 1

Overview of SRPmotif using Isoleucyl-tRNA synthetase-Mupirocin complex as example. (A) Identify polypharmacological candidates with similar discontinuous binding segments by rapidly searching protein structure databases using 3D-BLAST. The proteins with 75% similar binding segments are considered as the candidates of the polypharmacological candidates. (B) These candidates with significantly similar interfaces (RMSD ≤ 2.0Å and average aligned ratio ≥ 0.85) are considered as polypharmacological proteins. (C) The polypharmacological proteins are used to recognize the conserved segments (pharma-motifs) which can be transformed into 1D sequence patterns based on the multiple structural alignments. These spatially discontinuous pharma-motifs are formed a pharma-interface for these polypharmacological proteins.

Figure 2

Conserved score (S_pi) of the residues in the pharma-motifs. The conserved scores (S_pi) of 56.5% interacting residues (red) and 41.9% other residues (blue) in the pharma-motifs are more than 7.0.

Figure 3

The pharma-interface and pharma-motifs of Isoleucyl-tRNA synthetase-Mupirocin complex. (A) The pharma-motif superimposition between Isoleucyl-tRNA synthetase and its polypharmacological target, Methionyl-tRNA synthetase, is well aligned. These two proteins are belonging to the different structure families and the pharma-motifs are the color segments. (B) Interacting residues are highly conserved in these pharma-motifs. The ligands are colored by magenta. (C) Pharma-motif 1 and the corresponding PROSITE motif, PS00178. (D) Pharma-motif 4 is the ATP binding motif and involves KMSKS loop with two conserved residues (G601 and N602). These two residues stabilize the KMSKS loop by using hydrogen bonds (green line) with residue K598.

Figure 4

The pharma-interface and pharma-motifs of the tyrosine-protein kinase KIT-Imatinib complex. (A) The four residues (E640, T670, C673 and D810) of KIT protein (cyan) form hydrogen bonds (green dashed lines) with Imatinib (magenta) and are conserved in this family. (B) The conserved residue K807 plays an important role to stabilize the kinase structures. (C) The conserved residues in these pharma-motifs are related to phosphorylation of KIT. Asterisks mark the residues interacting with the ATP with hydrogen bonds.