Probing the Pharmacological Binding Sites of P-Glycoprotein Using Umbrella Sampling Simulations

Subramanian, Nandhitha; Schumann-Gillett, Alexandra; Mark, Alan E.; O’Mara, Megan L.

doi:10.1021/acs.jcim.8b00624

Cited by 20 publications

(20 citation statements)

References 88 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…51, 94, 95 Potential of mean force calculations using umbrella sampling also identified multiple overlapping binding locations for different substrates inside the TMDs of Pgp. 96, 97 The results of our extended-ensemble docking provide further evidence for this proposal, where the M1 and M2 subsites serve as binding sites for the high-affinity modulators/small substrates and large, low-affinity modulators/substrates, respectively (Fig. 11A).…”

Section: Discussionsupporting

confidence: 59%

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

Kapoor

Thangapandian

Tajkhorshid

2021

Preprint

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionsupporting

confidence: 59%

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

Kapoor

Thangapandian

Tajkhorshid

2021

Preprint

View full text Add to dashboard Cite

show abstract

“…53,110,111 Potential of mean force calculations using umbrella sampling also identified multiple overlapping binding locations for different substrates in Pgp. 112,113 The results of our extended-ensemble docking provide further support for this proposal, where the M1 and M2 subsites serve as the main binding sites for the high-affinity modulators/small substrates and large, low-affinity modulators/substrates, respectively (Fig. 11A).…”

Section: Discussionsupporting

confidence: 66%

Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins

2022

View full text Add to dashboard Cite

show abstract

“…The technical possibilities of molecular dynamics simulations mean that MD simulations of P-gp have been conducted with a variety of simulation conditions. To date, independent simulation studies of P-gp structures have used a range of different force fields, including several from the AMBER, ,,− CHARMM, ,− GROMOS, ,,,,,− OPLS, , and MARTINI , families of force fields. In many cases, the choice of force field is governed by the familiarity of the researcher with the particular force field or its associated MD package.…”

Section: Introductionmentioning

confidence: 99%

Effect of the Force Field on Molecular Dynamics Simulations of the Multidrug Efflux Protein P-Glycoprotein

Wang

O’Mara

2021

J. Chem. Theory Comput.

Self Cite

View full text Add to dashboard Cite

Molecular dynamics (MD) simulations have been used extensively to study P-glycoprotein (P-gp), a flexible multidrug transporter that is a key player in the development of multidrug resistance to chemotherapeutics. A substantial body of literature has grown from simulation studies that have employed various simulation conditions and parameters, including AMBER, CHARMM, OPLS, GROMOS, and coarsegrained force fields, drawing conclusions from simulations spanning hundreds of nanoseconds. Each force field is typically parametrized and validated on different data and observables, usually of small molecules and peptides; there have been few comparisons of force field performance on large protein− membrane systems. Here we compare the conformational ensembles of P-gp embedded in a POPC/cholesterol bilayer generated over 500 ns of replicate simulation with five force fields from popular biomolecular families: AMBER 99SB-ILDN, CHARMM 36, OPLS-AA/L, GROMOS 54A7, and MARTINI. We find considerable differences among the ensembles with little conformational overlap, although they correspond to similar extents to structural data obtained from electron paramagnetic resonance and crosslinking studies. Moreover, each trajectory was still sampling new conformations at a high rate after 500 ns of simulation, suggesting the need for more sampling. This work highlights the need to consider known limitations of the force field used (e.g., biases toward certain secondary structures) and the simulation itself (e.g., whether sufficient sampling has been achieved) when interpreting accumulated results of simulation studies of P-gp and other transport proteins.

show abstract

Probing the Pharmacological Binding Sites of P-Glycoprotein Using Umbrella Sampling Simulations

Cited by 20 publications

References 88 publications

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

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

Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins

Effect of the Force Field on Molecular Dynamics Simulations of the Multidrug Efflux Protein P-Glycoprotein

Contact Info

Product

Resources

About