Conformational changes in the nucleotide‐binding domains of P‐glycoprotein induced by ATP hydrolysis

Dehghani-Ghahnaviyeh, Sepehr; Kapoor, Karan; Tajkhorshid, Emad

doi:10.1002/1873-3468.13992

Cited by 18 publications

(21 citation statements)

References 66 publications

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“…18,19 Hydrolysis of ATP, on the other hand, releases the dimerized NBDs, allowing the transporter to reset to the IF state. [24][25][26] Through these general couplings, ATP binding and hydrolysis in the NBDs mechanically control the interconversion between the IF and OF, and therefore, the accessibility of the substrate between the two sides of the membrane.…”

Section: Introductionmentioning

confidence: 99%

Active participation of membrane lipids in inhibition of multidrug transporter P-glycoprotein

2021

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Section: Introductionmentioning

confidence: 99%

Active participation of membrane lipids in inhibition of multidrug transporter P-glycoprotein

2021

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“…As an active transporter, Pgp has to follow the general ‘alternating-access’ model 30, 31 for its function, thus alternating between the inward-facing (IF) and outward-facing (OF) states, alternatively exposing the DBP (and the bound substrate) to the intracellular and extracellular sides of the membrane. The large-scale structural transitions of the transporter are fueled by and coupled to ATP-driven dimerization and opening of its two nucleotide binding domains (NBDs) connected to the TMDs 32–34 (Fig. S1).…”

Section: Introductionmentioning

confidence: 99%

Extended-Ensemble Docking to Probe Evolution of Ligand Binding Sites During Large-Scale Structural Changes of Proteins

Kapoor

Thangapandian

Tajkhorshid

2021

Preprint

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Proteins can sample a broad energetic landscape as they undergo conformational transition between different functional states. As key players in almost all cellular processes, proteins are important drug targets. Considering the different conformational states of proteins is therefore central for a successful drug-design strategy. Here we introduce a novel docking protocol, termed as extended-ensemble docking, pertaining to proteins that undergo large-scale (global) conformational changes during their function. In its application to multidrug ABC-transporter P-glycoprotein (Pgp), extensive non-equilibrium molecular dynamics simulations employing system-specific collective variables capturing the alternate access mechanism of Pgp, are first used to construct the transition cycle of the transporter. An extended set of conformational states representing the full transition between the inward- and the outward-facing states of Pgp, is then used to seed high-throughput docking calculations of a set of known substrates, non-substrates, and modulators of the transporter. Large differences are observed in the predicted binding affinities in the conformational ensemble, with compounds showing stronger binding affinities in intermediate conformations compared to the starting crystal structure. Hierarchical clustering of the individual binding modes of the different compounds shows all ligands preferably bind to the large central cavity of the protein, formed at the apex of the transmembrane domain (TMD), whereas only small binding populations are observed in the previously described R and H sites present in the individual TMD leaflets. The central cavity is further clustered into two major subsites: first subsite preferably binds transported substrates and high-affinity inhibitors, whereas the second subsite shows preference for larger substrates and low-affinity modulators. These central sites along with the low-affinity interaction sites present in the individual TMD leaflets may respectively correspond to the proposed high- and low-affinity binding sites in Pgp. We propose further optimization strategy for developing more potent inhibitor of Pgp, based on increasing its specificity to the extended-ensemble of the protein instead of using a single protein structure, as well as its selectivity for the high-affinity binding site. In contrast to earlier in-silico studies using single static structures of Pgp, our results show good correlation with other experimental studies, pointing to the importance of incorporating the global conformational flexibility of proteins in future drug-discovery endeavors.

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“…18,19 Hydrolysis of ATP, on the other hand, releases the dimerized NBDs, allowing the transporter to reset to the IF state. 24–26 Through these general couplings, ATP binding and hydrolysis in the NBDs mechanically control the inter-conversion between the IF and OF, and therefore, the accessibility of the substrate between the two sides of the membrane.…”

Section: Introductionmentioning

confidence: 99%

Active Participation of Membrane Lipids in Inhibition of Multidrug Transporter P-Glycoprotein

Kapoor

Pant

Tajkhorshid

2020

Preprint

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P-glycoprotein (Pgp) is a major efflux pump in humans, overexpressed in a variety of cancers and associated with the development of multi-drug resistance. Allosteric modulation induced by binding of various ligands (e.g., transport substrates, inhibitors, and ATP) has been bio-chemically shown to directly influence the function of Pgp. However, the molecular details of such effects are not well established. In particular, the role and involvement of the surrounding lipid environment on ligand-induced modulation of the conformational dynamics of the transporter have not been investigated at any level. Here, we employ all-atom molecular dynamics (MD) simulations to study the conformational landscape of Pgp in the presence of a high-affinity, third-generation inhibitor, tariquidar, in comparison to the nucleotide-free (APO) and the ATP-bound states, in order to shed light on and to characterize how the inhibitor blocks the function of the transporter. Simulations in a multi-component lipid bilayer show a dynamic equilibrium between open and closed inward-facing (IF) conformations in the APO-state, with binding of ATP shifting the equilibrium towards conformations feasible for ATP hydrolysis and subsequent completion of the transport cycle. In the presence of the inhibitor bound to the drug-binding pocket in the transmembrane domain (TMD), the transporter samples more open IF conformations, and the nucleotide binding domains (NBDs) are observed to become highly dynamic. Interestingly, and reproduced in multiple independent simulations, the inhibitor is observed to recruit lipid molecules into the Pgp lumen through the two proposed drug-entry portals, where the lipid head groups from the lower leaflet translocate inside the TMD, while the lipids tails remain extended into the bulk lipid environment. These “wedge-lipid” molecules likely enhance the inhibitor-induced conformational changes in the TMD leading to the differential modulation of coupling pathways observed with the NBDs downstream. We suggest a novel inhibitory mechanism for tariquidar, and for related third-generation Pgp inhibitors, where lipids are seen to enhance the inhibitory role in the catalytic cycle of membrane transporters.

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Conformational changes in the nucleotide‐binding domains of P‐glycoprotein induced by ATP hydrolysis

Cited by 18 publications

References 66 publications

Active participation of membrane lipids in inhibition of multidrug transporter P-glycoprotein

Active participation of membrane lipids in inhibition of multidrug transporter P-glycoprotein

Extended-Ensemble Docking to Probe Evolution of Ligand Binding Sites During Large-Scale Structural Changes of Proteins

Active Participation of Membrane Lipids in Inhibition of Multidrug Transporter P-Glycoprotein

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