Exploring the binding features of estrogen receptor beta selective ligands with docking studies...

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Exploring the binding features of estrogen receptor beta selective ligands with docking studies incorporating protein flexibility Paweł Książek, Krzysztof Bryl University of Warmia and Mazury in Olsztyn, Chair of Physics and Biophysics Introduction Estrogen receptor β (ERβ) (Figure 1), a member of the nuclear receptor superfamily, is a recep- tor subtype with therapeutic potential for sever- al pathologies [1]. Nevertheless, ERβ remains a challenging target because its ligand-binding cav- ity is very similar to that present in ERα [2]. Fur- thermore, the receptor cavities of both ERα and ERβ are relatively flexible, and depending on the nature of the bound ligand, the shape of the cav- ity may change significantly. Binding pocket simi- latity and its plasticity make it difficult to develop ligands having sufficient levels of ERβ selectivity for therapeutic use. Nevertheless, considerable advances have re- cently been made in developing ERβ selective ag- onists [3]. The Katzenellenbogen group at the Uni- versity of Illinois developed several ERβ antago- nists which may constitute not only important tools to probe the biological effects of the selective stim- ulation of ERβ, but some of them appear to be agents with considerable therapeutic potential. Figure 1. Structure of estrogen receptor β (ERβ) ligand bind- ing domain (LBD) in complex with 17β-estradiol. Objectives In order to explore the binding features of nonsteroidal ERβselective agonists reported by Katzenellenbogen and co-workers selected com- pounds were analysed by molecular docking. While traditional rigid-receptor docking methods are useful when the receptor structure does not change substantially upon ligand binding, success for estrogen receptors is limited because of high flexibility of receptor molecules [4]. To overcome this issue we applied induced fit docking, a pro- tein-ligand docking method, which is reported to accurately account for both ligand and receptor flexibility [5]. Evaluation of molecular mechanisms of action of new selective ligands can give in- sights into ligand selectivity in estrogen receptor isoforms and help to design new molecules. Materials & Methods The coordinates for all protein–ligand complex- es were obtained from the RCSB Protein Da- ta Bank (PDB). Included in this study are the ERα (1ERE, 3ERD, 1X7R) and ERβ (2J7X, 1X7B, 1X7J). All protein structures were prepared us- ing the Schrödinger’s Protein Preparation Wizard module. Hydrogen atoms were added and the missing loops and sidechains fill in using Prime. All ligands (Figure 2) were drawn in Maestro 9.2 and prepared using Schrödinger's LigPrep mod- ule and were optimized with the OPLS force field. Figure 2. Ligands having either a bibenzyl- or stilbene core. All protein structures were applied with the in- duced-fit docking (IFD) method in the Schrödinger software suite [5]. The IFD protocol is depicted in Figure 3. Figure 3. Induced fit docking flowchart. ΔE is the energy gap from the lowest energy structure. Results Every ligand docking resulted with one protein-lig- and complex with the lowest IFD score. Pose com- parison strategy was adopted to identify ligand binding preferences. Docking of ten nonsteroidal antagonists demonstrates cavity plasticity allow- ing multiple ligand binding modes. Figure 4. The binding modes of 10 individual estrogen recep- tor β agonists after superposition of protein atoms. Conclusions Induced fit docking simulations revealed the conformational changes at the active site of the ERs and the difference in binding modes for selective ligands. Various nonsteroidal ERβselective agonists reported by Katzenellenbogen and co-work- ers can induce different conformations of the internal binding cavity that may be transmit- ted to the exterior of the protein. These ex- ternal changes in turn can result in differen- tial binding of various cofactors resulting in al- tered pharmacology. The plasticity of the binding cavity compli- cates structurebased design of ERβselective agonists. As modifications of ligands are made to improve affinity or selectivity, unex- pected changes in receptor conformation or ligand binding mode may occur. Medicinal and computational chemists are trying to hit a moving target. Ideally, addition- al crystallographic structures of newly syn- thesized ligands should be obtained to make sure that optimized ligands are still binding as predicted. References 1. Erin K. Shanle, Wei Xu, 2010, Selectively targeting estrogen receptors for cancer treatment, Advanced Drug Delivery Reviews. 2. Ashley C.W. Pike, Andrzej M. Brzozowski, Roderick E. Hubbard, 2000, A structural biologist’s view of the oestrogen receptor, Journal of Steroid Biochemistry & Molecular Biology. 3. Filippo Minutolo, Marco Macchia, Benita S. Katzenellenbogen, John A. Katzenellenbogen, 2009, Estrogen Receptor β Ligands: Recent Ad- vances and Biomedical Applications, Medicinal Research Reviews. 4. Francesca Spyrakis, Pietro Cozzini, 2009, How Computational Meth- ods Try to Disclose the Estrogen Receptor Secrecy - Modeling the Flexibility, Current Medicinal Chemistry. 5. Woody Sherman, Tyler Day, Matthew P. Jacobson, Richard A. Fries- ner, Ramy Farid, 2006, Novel Procedure for Modeling Ligand/Recep- tor Induced Fit Effects, Journal of Medicinal Chemistry.

Transcript of Exploring the binding features of estrogen receptor beta selective ligands with docking studies...

Page 1: Exploring the binding features of estrogen receptor beta selective ligands with docking studies incorporating protein flexibility

Exploring the binding features of estrogen receptor beta selectiveligands with docking studies incorporating protein flexibility

Paweł Książek, Krzysztof BrylUniversity of Warmia and Mazury in Olsztyn, Chair of Physics and Biophysics

IntroductionEstrogen receptor β (ERβ) (Figure 1), a memberof the nuclear receptor superfamily, is a recep-tor subtype with therapeutic potential for sever-al pathologies [1]. Nevertheless, ERβ remains achallenging target because its ligand-binding cav-ity is very similar to that present in ERα [2]. Fur-thermore, the receptor cavities of both ERα andERβ are relatively flexible, and depending on thenature of the bound ligand, the shape of the cav-ity may change significantly. Binding pocket simi-latity and its plasticity make it difficult to developligands having sufficient levels of ERβ selectivityfor therapeutic use.

Nevertheless, considerable advances have re-cently been made in developing ERβ selective ag-onists [3]. The Katzenellenbogen group at the Uni-versity of Illinois developed several ERβ antago-nists which may constitute not only important toolsto probe the biological effects of the selective stim-ulation of ERβ, but some of them appear to beagents with considerable therapeutic potential.

Figure 1. Structure of estrogen receptor β (ERβ) ligand bind-ing domain (LBD) in complex with 17β-estradiol.

ObjectivesIn order to explore the binding features ofnonsteroidal ERβselective agonists reported byKatzenellenbogen and co-workers selected com-pounds were analysed by molecular docking.While traditional rigid-receptor docking methodsare useful when the receptor structure does notchange substantially upon ligand binding, successfor estrogen receptors is limited because of highflexibility of receptor molecules [4]. To overcomethis issue we applied induced fit docking, a pro-tein-ligand docking method, which is reported toaccurately account for both ligand and receptorflexibility [5]. Evaluation of molecular mechanismsof action of new selective ligands can give in-sights into ligand selectivity in estrogen receptorisoforms and help to design new molecules.

Materials & MethodsThe coordinates for all protein–ligand complex-es were obtained from the RCSB Protein Da-

ta Bank (PDB). Included in this study are theERα (1ERE, 3ERD, 1X7R) and ERβ (2J7X, 1X7B,1X7J). All protein structures were prepared us-ing the Schrödinger’s Protein Preparation Wizardmodule. Hydrogen atoms were added and themissing loops and sidechains fill in using Prime.All ligands (Figure 2) were drawn in Maestro 9.2and prepared using Schrödinger's LigPrep mod-ule and were optimized with the OPLS force field.

Figure 2. Ligands having either a bibenzyl- or stilbene core.

All protein structures were applied with the in-duced-fit docking (IFD) method in the Schrödingersoftware suite [5]. The IFD protocol is depicted inFigure 3.

Figure 3. Induced fit docking flowchart. ΔE is the energy gapfrom the lowest energy structure.

ResultsEvery ligand docking resulted with one protein-lig-and complex with the lowest IFD score. Pose com-parison strategy was adopted to identify ligandbinding preferences. Docking of ten nonsteroidalantagonists demonstrates cavity plasticity allow-ing multiple ligand binding modes.

Figure 4. The binding modes of 10 individual estrogen recep-tor β agonists after superposition of protein atoms.

Conclusions● Induced fit docking simulations revealed the

conformational changes at the active site ofthe ERs and the difference in binding modesfor selective ligands.

● Various nonsteroidal ERβselective agonistsreported by Katzenellenbogen and co-work-ers can induce different conformations of theinternal binding cavity that may be transmit-ted to the exterior of the protein. These ex-ternal changes in turn can result in differen-tial binding of various cofactors resulting in al-tered pharmacology.

● The plasticity of the binding cavity compli-cates structurebased design of ERβselectiveagonists. As modifications of ligands aremade to improve affinity or selectivity, unex-pected changes in receptor conformation orligand binding mode may occur.

● Medicinal and computational chemists aretrying to hit a moving target. Ideally, addition-al crystallographic structures of newly syn-thesized ligands should be obtained to makesure that optimized ligands are still binding aspredicted.

References1. Erin K. Shanle, Wei Xu, 2010, Selectively targeting estrogen receptors

for cancer treatment, Advanced Drug Delivery Reviews.2. Ashley C.W. Pike, Andrzej M. Brzozowski, Roderick E. Hubbard,

2000, A structural biologist’s view of the oestrogen receptor, Journal ofSteroid Biochemistry & Molecular Biology.

3. Filippo Minutolo, Marco Macchia, Benita S. Katzenellenbogen, JohnA. Katzenellenbogen, 2009, Estrogen Receptor β Ligands: Recent Ad-vances and Biomedical Applications, Medicinal Research Reviews.

4. Francesca Spyrakis, Pietro Cozzini, 2009, How Computational Meth-ods Try to Disclose the Estrogen Receptor Secrecy - Modeling theFlexibility, Current Medicinal Chemistry.

5. Woody Sherman, Tyler Day, Matthew P. Jacobson, Richard A. Fries-ner, Ramy Farid, 2006, Novel Procedure for Modeling Ligand/Recep-tor Induced Fit Effects, Journal of Medicinal Chemistry.