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

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.

Binding mode analysis of ABCA7 for the prediction of novel Alzheimer's disease therapeutics

“…Thus, we conducted blind docking studies considering the entire MSDs of the ABCA7 homology model using AutoDock [129] . The MSDs as docking space were particularly chosen because they cover the suggested/outlined binding sites in other ABCA transporters [96] , [97] , [98] , which is generally supported by the structural information of other ABC transporters subfamilies [100] , [101] , [102] , [103] , [104] , [105] , [106] , [107] , [108] , [109] , [110] , [111] , [112] , [113] , [114] . Fig.…”

“…The present study aimed for the development of an ABCA7 homology model and subsequent blind docking analysis of the membrane-spanning domains (MDDs) with the pan-ABC transporter inhibitors 6 – 28 , as the multitarget biding site that is supposed to be shared amongst several subfamily members of ABC transporters was postulated to be located in the proximity of the MSDs [4] . This postulation is supported by cryo-EM (ABCB1 [102] , ABCB2 [103] , ABCB4 [104] , ABCC8 [105] , and ABCG2 [106] ) and homology model data (ABCB1 [107] , ABCB2 [108] , ABCB5 [109] , ABCC1 [110] , ABCC4 [111] , ABCC5 [100] , ABCC6 [112] , ABCC7 [113] , ABCC11 [114] , and ABCG2 [101] ) of other ABC transporters which had their primary substrate/inhibitor binding sites within the transmembrane regions.…”

The Important Role of Transporter Structures in Drug Disposition, Efficacy, and Toxicity

“…The ADMET properties can also be predicted based on the computational structure of ABC transporters and others to assess the pharmacokinetic properties of lead compounds or candidates (Demel et al, 2009;Yalcin-Ozkat, 2021;Yin et al, 2021). Moreover, there are several studies based on computational structures for mutation studies of transporters (Becerra et al, 2021;Onnee et al, 2021). To elucidate the transport mechanisms of ABC transporters, their different intermediate conformations must be linked to the dynamic transition process (Thomas and Tampe, 2020).…”

Specific MRP4 Inhibitor Ceefourin-1 Enhances Apoptosis Induced by 6-Mercaptopurine in Jurkat Leukemic Cells, but Not in Normal Lymphoblast Cell Line CRL-1991

“…To study the binding site and the intermolecular interactions of 6-MP and ceefourin-1 in MRP4, molecular docking studies were carried out using the AUTODOCK 4.2.6 software (The Scripps Research Institute, San Diego, CA, USA) [17]. The MRP4 structure, previously modeled [18], was used as an input for the AUTOGRID 4.2.6. The maps were calculated with 0.375 Å spacing between grid points.…”

“…In order to determine the binding energy of ceefourin-1 and 6-MP into MRP4, umbrella sampling simulations were performed by using the MRP4 C1 of the previous 25 ns AA-MD trajectory [18], the system was built under the previously mentioned conditions. Once the system was obtained and relaxed using the AA-MD relaxation protocol, a 10 ns (100 frames) MD simulation was performed in the Metadynamics module of Desmond using the protein and ligand center of mass distance as the collective variable, with 0.3 kcal/mol height and 0.1 kcal/mol width as the Gaussian parameters for the umbrella protocol, on an NPT ensemble at 310.15 K and 1.01325 bar.…”