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. 2024 Mar 15;14(1):6296.
doi: 10.1038/s41598-024-56893-7.

VirtuousPocketome: a computational tool for screening protein-ligand complexes to identify similar binding sites

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VirtuousPocketome: a computational tool for screening protein-ligand complexes to identify similar binding sites

Lorenzo Pallante et al. Sci Rep. .

Abstract

Protein residues within binding pockets play a critical role in determining the range of ligands that can interact with a protein, influencing its structure and function. Identifying structural similarities in proteins offers valuable insights into their function and activation mechanisms, aiding in predicting protein-ligand interactions, anticipating off-target effects, and facilitating the development of therapeutic agents. Numerous computational methods assessing global or local similarity in protein cavities have emerged, but their utilization is impeded by complexity, impractical automation for amino acid pattern searches, and an inability to evaluate the dynamics of scrutinized protein-ligand systems. Here, we present a general, automatic and unbiased computational pipeline, named VirtuousPocketome, aimed at screening huge databases of proteins for similar binding pockets starting from an interested protein-ligand complex. We demonstrate the pipeline's potential by exploring a recently-solved human bitter taste receptor, i.e. the TAS2R46, complexed with strychnine. We pinpointed 145 proteins sharing similar binding sites compared to the analysed bitter taste receptor and the enrichment analysis highlighted the related biological processes, molecular functions and cellular components. This work represents the foundation for future studies aimed at understanding the effective role of tastants outside the gustatory system: this could pave the way towards the rationalization of the diet as a supplement to standard pharmacological treatments and the design of novel tastants-inspired compounds to target other proteins involved in specific diseases or disorders. The proposed pipeline is publicly accessible, can be applied to any protein-ligand complex, and could be expanded to screen any database of protein structures.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Main interactions defining the three motifs for the bitter taste receptor interacting with strychnine. (A) Representative snapshot of the bitter-ligand complex, (B) PLIP interaction analysis identifying Hydrophobic Interaction (HI) and Saltbridge Interaction (SB), (C, D, E) site views of the three motifs identified. The bitter taste receptor is represented in grey, the strychnine in blue and the interacting residues in green (hydrophobic interactions) and purple (salt bridges).
Figure 2
Figure 2
(A) Number of total structures in the original human proteome database and the number of selected hits from the similarity search and the subsequent multi-step filtering. (B) Binding site view of the strychnine bound to the best hit (PDB: 3A4S) according to the docking score at the end of the multi-step filtering process. Protein is rendered in grey, strychnine in blue, residues in the original motif of the bitter taste receptor in red and matching residues in the 3A4S structure in violet.
Figure 3
Figure 3
Bar plots representing the best 5 retrieved GO terms for each category in the third level of the GO hierarchy relative to Biological Processes (BP), Molecular Functions (MF) and Cellular Components (CC).
Figure 4
Figure 4
Flow Chart of the overall workflow of VirtuousPocketome.

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