Docking-based identification of small-molecule binding sites at protein-protein interfaces

被引:10
作者
Rosell, Mireia [1 ,2 ]
Fernandez-Recio, Juan [1 ,2 ]
机构
[1] Barcelona Supercomp Ctr BSC, Barcelona, Spain
[2] Univ La Rioja, Inst Ciencias Vid & Vino ICVV, Gobierno La Rioja, CSIC, Logrono, Spain
关键词
Modulation of protein-protein interactions; Drug discovery; Interface hot-spot residues; Protein docking simulations; Cavity detection; Molecular dynamics; BCL-X-L; HOT-SPOT; DRUG DISCOVERY; SHAPE COMPLEMENTARITY; TRANSIENT POCKETS; CRYSTAL-STRUCTURE; LIGANDS; RECOGNITION; INHIBITORS; DOMAIN;
D O I
10.1016/j.csbj.2020.11.029
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Protein-protein interactions play an essential role in many biological processes, and their perturbation is a major cause of disease. The use of small molecules to modulate them is attracting increased attention, but protein interfaces generally do not have clear cavities for binding small compounds. A proposed strategy is to target interface hot-spot residues, but their identification through computational approaches usually require the complex structure, which is not often available. In this context, pyDock energy-based docking and scoring can predict hot-spots on the unbound proteins, thus not requiring the complex structure. Here, we have devised a new strategy to detect protein-protein inhibitor binding sites, based on the integration of molecular dynamics for the generation of transient cavities, and docking-based interface hot-spot prediction for the selection of the suitable cavities. This integrative approach has been validated on a test set formed by protein-protein complexes with known inhibitors for which complete structural data of unbound molecules and complexes is available. The results show that local conformational sampling with short molecular dynamics can generate transient cavities similar to the known inhibitor binding sites, and that docking simulations can identify the best cavities with similar predictive accuracy as when knowing the real interface. In a few cases, these predicted pockets are shown to be suitable for protein-ligand docking. The proposed strategy will be useful for many protein-protein complexes for which there is no available structure, as long as the the unbound proteins do not deviate dramatically from the bound conformations. (C) 2020 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.
引用
收藏
页码:3750 / 3761
页数:12
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