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View of Srpmotif Using Isoleucyl-Trna Synthetase-Mupirocin Complex As Example Chiu et al. BMC Genomics 2012, 13(Suppl 7):S21 http://www.biomedcentral.com/1471-2164/13/S7/S21 PROCEEDINGS Open Access Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets Yi-Yuan Chiu1, Chun-Yu Lin1, Chih-Ta Lin1, Kai-Cheng Hsu1, Li-Zen Chang1, Jinn-Moon Yang1,2* From Asia Pacific Bioinformatics Network (APBioNet) Eleventh International Conference on Bioinformatics (InCoB2012) Bangkok, Thailand. 3-5 October 2012 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. Background design a drug inhibiting multiple target proteins (i.e. During the early drug discovery stage, discovering polypharmacological targets) builds a new paradigm for potential target proteins for a compound is important to diseases with complex mechanisms, such as cancers and drug design and to reduce cost and time by detecting diabetes. Therefore, discovering polypharmacological the potential harmful side effects. On the other hand, it targets, share similar interfaces and are often inhibited could provide the new usages for old drugs. Recently, to by the same compound, is a valuable issue in under- standing binding mechanisms and drug development. * Correspondence: [email protected] To identify the proteins with similar binding sites of a 1Institute of Bioinformatics and Systems Biology, National Chiao Tung given protein sequence or structure by searching the University, Hsinchu, 30050, Taiwan sequence or structure databases has usually used [1-4]. Full list of author information is available at the end of the article © 2012 Chiu et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Chiu et al. BMC Genomics 2012, 13(Suppl 7):S21 Page 2 of 11 http://www.biomedcentral.com/1471-2164/13/S7/S21 In general, the proteins (i.e. polypharmacological targets) (called polypharmacological targets) which share similar bound the same ligand should share similar binding interfaces and are often inhibited by the same com- environments, but they may not have significant evolu- pound; (2) A pharma-interface consists of a set of tionary relationship in both sequences and global struc- pharma-motifs; (3) A pharma-motif is a short conserved tures. As the exponential growth of the number of peptide forming a specific sub-interface with interacting protein structures, protein structures have been pro- residues and specific physico-chemical properties. Figure 1 posed to analyze the structural motifs and to describe shows the details of our method to identify a pharma- the binding environment [5,6]. Most of these studies interface and pharma-motifs from a given complex by the (e.g. SPASM [7], Superimpose [8], RASMOT-3D PRO following steps. [9], MultiBind [10], and Wu et al. [11]) search the simi- Step 1: Search candidates of polypharmacological targets lar local structures or binding sites (active sites) based To find the candidates of the polypharmacological tar- on only one structural motif. However, a protein-ligand gets of a query protein, we firstly transformed the 3D binding interface usually consists of a set of spatially dis- protein structure of a query complex (i.e. protein and its continuous structural motifs. For example, two motifs binding ligand) into a 1D sequence with 23 states of a (i.e. HxGH loop and KMSKS loop) catalyse the amino structural alphabet by using in-house tool 3D-BLAST acid activation with ATP in class-I aminoacyl-transfer (Figure 1A) [13,14]. We then identified the binding seg- RNA synthetases [12]. ments in the interface of the query complex. For each To address these issues, we proposed Space-Related segment, its corresponding 1D structural alphabet Pharmamotif (SRPmotif) method to identify the pharma- sequence was used for rapidly searching structural interfaces (≥ 2 structural motifs) sharing similar binding alphabet sequence database (SADB) by using 3D-BLAST environments from the polypharmacological targets. The and a list of similar protein structures of the query bind- pharma-interface consists of a set of spatially discontinu- ing segment was returned within several seconds. For ous peptide segments (i.e. pharma-motifs), which sur- the tolerance of the flexible binding environment, the round the ligand-binding site. By transforming the 3D proteins matching more than 75% query segments are structure segments into 1D structural alphabet sequences considered as the candidates. through in-house tool (called 3D-BLAST [13,14]), we can Here, we identified a binding segment (≥ 15 amino rapidly search the potential target proteins with similar acids) of a given complex by using a contact residue as a binding environment against Protein Data Bank (PDB) central point to extend seven amino acids forward and [15]. And then a structural alignment tool, such as DALI backward. An amino acid is considered as a contact resi- [16], was used to precisely locate the possible binding due if the distance between any atom of this residue and environment in these protein structures. Experimental the atoms of the binding ligand is less than 4Å. Any of results showed that around 56% interacting residues were two binding segments with at least one overlapped amino considered as highly conserved in our identified pharma- acid are merged into a single one. As a result, the binding motifs. These conserved residues involving in pharma- environment of a given complex is characterized by spa- motifs often play the key roles for biological functions tially discontinuous binding segments. and binding mechanisms. Furthermore, these pharma- Next, SRPmotif utilizes 3D-BLAST, a fast protein struc- motifs can be transferred into sequence-based motifs for ture database search, to detect the candidate proteins (i.e. searching similar proteins with local binding-site similar- polypharmacological targets) with similar binding seg- ity from protein sequence databases. We believe that ments. 3D-BLAST encodes the 3D structures into a serials SRPmotif is useful for studying protein functions and dis- of structural alphabets using and a angles defined in the covering the polypharmacological targets for drug design. DSSP program [17]. Based on the (, a) plot of 674 struc- The SRPmotif is available at http://gemdock.life.nctu.edu. tural pairs and a nearest neighbour clustering, a 23-state tw/SRP/. structural alphabet represents the profiles of most 3D frag- ments [14]. A BLOSUM-like substitution matrix, called Materials and methods structural alphabet substitution matrix (SASM) was devel- Pharma-motifs and pharma-interfaces oped by using a method similar to that used to construct Here, we proposed a new concept and a fast method BLOSUM62 [18] based on 674 structural protein pairs. (SRPmotif) to identify space-related pharma-motifs and 3D-BLAST searches the SADB using this SASM to quickly pharma-interfaces for discovering polypharmacological discover homologous structures of a query protein. targets. We considered a pharma-interface as a con- Step 2: Establishment of the pharma-interface served binding environment which consists of several In this step, the polypharmacological targets were deter- spatially discontinuous pharma-motifs. A pharma-inter- mined and used to construct pharma-interface. To deter- face can be described as follows: (1) A pharma-interface mine the polypharmacological targets through the is a conserved binding interface of multiple proteins
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