Intermolecular Interactions Between P-glycoprotein And Anti-tumor Drugs

Nowadays,P-glycoprotein(P-gp)has aroused great interest for researchers in chemotherapy.In clinical researches,the phenomenon that tumor cells show resistance to structurally unrelated anti-cancer drugs is called multidrug resistance(MDR).In the 1980s to 1990s,MDR has been related with the overexpress of ATP-binding cassette(ABC)family proteins in tumor cells.These family proteins are energy-dependent multidrug efflux membrane proteins that could pump drugs,xenobiotics out of cells.P-glycoprotein(P-gp)is a typical example of this kind of protein and it is a most studied ABC protein.Most anti-cancer drugs diffuse through a concentration gradient into the cells without any drug carriers.P-gp maintains relatively low concentrations in cells by transporting drugs out and protects the tumor cells.Hence,it is very important to study the interaction mechanism of P-gp with drugs,which could help elucidate the MDR and the failure of chemotherapy.Although experiments in vitro have investigated the interactions between P-gp and several substrates,the molecular mechanism of the promiscuity of P-gp remains unclear.Given this,molecular dynamics(MD)simulations were performed to study the interaction of P-gp with anti-tumor drugs.In this study,molecular dynamics(MD),random accelerated molecular dynamics(RAMD)simulation as well as Metadynamics method was used to explore the interaction of P-gp with structural and pharmacological different drugs.Detail analysis were conducted to elucidate the mechanism.1-palmitoyl-2-oleoyl-phospha-tidylcholine(POPC)membrane was used to build a sound P-gp-membrane system.Interactions of paclitaxel and doxorubicin were investigated with P-gp when placed them at the entrance of the cavity.Next,we explored the gates,portals and pathways in the binding process.Last,we studied the interaction of P-gp with different numbers and different kind of drugs.The main conclusions are listed below:1.It is found that drug(paclitaxel and doxorubicin)molecules spontaneously approached the binding sites of P-gp.The inner residues in the cavity dominate the processes.In their approaching processes,van der Waals(vdW)interaction played a significant role.The inner residues strongly interacted with the drugs and make them get deeper into the cavity.During the process,an obstacle-overcoming process was observed,showing that the inner residue side chains were quite fexible.Inner residues are found strongly interact with these two drugs and thus cause significant perturbation inside the cavity.The side chains of the inner residues fit both the shape and size of the drugs.The cavity possesses the adaptability to accommodate different drugs,which could help explain why P-gp has so many substrates.2.RAMD was used to study the egress process of drugs from P-gp.This could be seen as the revese process that drugs enter binding pocket.The interaction free energy along the chosen collective variable was calculated by metadynamics.The most possible portal of drugs to dissociate is TM4/TM6.It suggests an asymmetric binding process that TM4/TM6 may favor the drug entry and NBDs at the TM10/TM12 side favor the ATP-binding.The interactions there are found to be remarkably larger than that outside of the binding site.Both the RAMD and metadynamics simulations show the importance of flexibility of inner residues.Phe339 is found to gate the drug access to the binding site in the first step.The flexibility of side chains is concluded to allow the cavity to adapt to different drugs.Through the free energy calculations,it is found that before reaching the absolute minimum,there are several local minima which correlated with the inner residues' adaption process.3.Different numbers of drugs were placed inside the cavity.It is found that P-gp could stably bind two drugs,but when three drugs simultaneously placed into the binding pocket,things became different.The third paclitaxel obviously cannot stably bind inside the cavity,so is the third doxorubicin.For the sorafenib molecules,which is smaller than paclitaxel and doxorubicin,however,three sorafenibs were all able to stably binding inside the cavity.What's more,ten drugs with various logP values were also placed inside the cavity and the result shows the number of Phe and Tyr residues interact with drugs dominates the vdW percentage of interaction energy.The numbers of drugs atoms correlate well with the interaction energy.However,the logP values for each drug have been found no relations with the interaction energies.It is concluded that the Phe and Tyr residues inside the binding pocket is quite crucial for drug binding.