Abstract
Modulating protein–protein interactions (PPIs) with small drug-like molecules targeting it exhibits great promise in modern drug discovery. G protein-coupled receptors (GPCRs) are the largest family of targeted proteins and could form dimers in living biological cells through PPIs. However, compared to drug development of the orthosteric site, there has been lack of investigations on the druggability of the PPI interface for GPCRs and its functional implication on experiments. Thus, in order to address these issues, we constructed a novel computational strategy, which involved in molecular dynamics simulation, virtual screening and protein structure network (PSN), to study one representative GPCR homodimer (CXCR4). One druggable pocket was identified in the PPI interface and one small molecule targeting it was screened, which could strengthen PPI mainly through hydrophobic interaction between the benzene rings of the PPI molecule and TM4 of the receptor. The PSN results further reveals that the PPI molecule could increase the number of the allosteric regulation pathways between the druggable pocket of the dimer interface to the orthostatic site for the subunit A but only play minor role for the other subunit B, leading to the asymmetric change in the volume of the binding pockets for the two subunits (increase for the subunit A and minor change for the subunit B). Consequently, the screening performance of the subunit A to the antagonists is enhanced while the subunit B is unchanged nearly, implying that the PPI molecule may be beneficial to enhance the drug efficacies of the antagonists. In addition, one main regulation pathway with the highest frequency was identified for the subunit A, which consists of Trp1955.34–Tyr190ECL2–Val1965.35–Gln2005.39–Asp2626.58–Cys28N-term, revealing their importance in the allosteric regulation from the PPI molecule. The observations from the work could provide valuable information for the development of the PPI drug-like molecule for GPCRs.
Highlights
In living cells, only a few proteins perform their biological functions independently, and the vast majority of proteins function through interacting with other molecules (Keskin et al, 2016; Wang et al, 2018b)
The druggable pockets in the dimer interfaces are highly similar for the four classes, which are mainly involved in Trp1955.34, Val1985.37, Phe1995.38 of the subunit A, Val1975.36, Gln2005.39, Phe2015.40, Ile2596.55, Ser2606.56, Ser2636.59, and Leu2676.63 of subunit B
As the largest family of drug-targeted proteins, it was evidenced that G protein-coupled receptors (GPCRs) could form the dimers through the protein–protein interaction
Summary
Only a few proteins perform their biological functions independently, and the vast majority (more than 80%) of proteins function through interacting with other molecules (Keskin et al, 2016; Wang et al, 2018b). If drugs could strengthen the PPI interaction or damage it, the function of PPI will be inevitably influenced. Small molecule LEDGINs could block the interaction between HIV-1 integrase and human LEDGF/p75 so that it could inhibit HIV replication(Reddy et al, 2014). Researches on strengthening PPI interaction are very limited with respect to inhibiting one, it is highly valuable for some specific proteins. ISD could strengthen the interaction between Neph and ZO-1 so that it could prevent podocyte injury and preserve glomerular filtration function (Sagar et al, 2017)
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