Study of Endogen Substrates, Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics.

Edgardo Becerra,Giovanny Aguilera-Durán,Guadalupe García-Alcocer,Laura Berumen,Antonio Romo-Mancillas

doi:10.3390/molecules26041051

Edgardo Becerra, Giovanny Aguilera-Durán + Show 3 more

Open Access

https://doi.org/10.3390/molecules26041051

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Abstract

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.

Highlights

Multidrug resistance protein-4 (MRP4) plays a critical role in the distribution of different xenobiotics and endogen substrates, which can lead to different effects in the organism
X-ray, protein threading was performed in this study and relaxing the structures was performed by coarse-grained molecular dynamics simulations (CG-MDS) to carry out the molecular docking, while MDS and umbrella sampling studies were performed to yield relevant information regarding the residues involved in the binding of the studied molecules groups and changes in the ∆G of Folic acid (FA) and cyclic adenosine monophosphate (cAMP) in the presence or the absence of ATP, which allowed us to observe the relevance of the mutations in the binding and movement of MRP4 and its variants
The non-synonymous single nucleotide polymorphisms (nsSNPs) G187W and Y556C led to changes in the ligand binding site, docking score (DS), and binding energy (∆G)

Summary

Introduction

The transport of xenobiotics out of the cell across membranes is a mechanism used by cells to detoxify. This mechanism is mediated by ATP-binding cassette (ABC) transporters [1]. Multidrug resistance protein-4 (MRP4) is a member of the ABCC subfamily and mediates the transport of xenobiotics such as cardiovascular, antiviral, and anticancer drugs. The substrates for MRP4 are mainly glucuronide conjugates and organic anions [2]

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