Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A1 Receptor

Miao, Yinglong; Bhattarai, Apurba; Nguyen, Thi Ngoc Anh; Christopoulos, Arthur; May, Lauren T.

doi:10.1038/s41598-018-35266-x

“…In contrast, this lysine pointed towards ECL2 in the active A1AR. This was consistent with our previous study (66) , in which the positive allosteric modulator (PAM) enhanced the agonist binding at the orthosteric site by forming a salt-bridge between E172 ECL2 -K265 ECL3 . Moreover, the active A1AR attracted more lipids in the lower leaflet compared with the inactive A1AR.…”

Section: Discussionsupporting

confidence: 93%

G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation state

Bhattarai

¹

,

Wang

²

,

Miao

³

2019

Preprint

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G‐protein‐coupled receptors (GPCRs) are the largest family of human membrane proteins and serve as primary targets of approximately one‐third of currently marketed drugs. In particular, adenosine A1 receptor (A1AR) is an important therapeutic target for treating cardiac ischemia–reperfusion injuries, neuropathic pain, and renal diseases. As a prototypical GPCR, the A1AR is located within a phospholipid membrane bilayer and transmits cellular signals by changing between different conformational states. It is important to elucidate the lipid–protein interactions in order to understand the functional mechanism of GPCRs. Here, all‐atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method were performed on both the inactive (antagonist bound) and active (agonist and G‐protein bound) A1AR, which was embedded in a 1‐palmitoyl‐2‐oleoyl‐glycero‐3‐phosphocholine (POPC) lipid bilayer. In the GaMD simulations, the membrane lipids played a key role in stabilizing different conformational states of the A1AR. Our simulations further identified important regions of the receptor that interacted distinctly with the lipids in highly correlated manner. Activation of the A1AR led to differential dynamics in the upper and lower leaflets of the lipid bilayer. In summary, GaMD enhanced simulations have revealed strongly coupled dynamics of the GPCR and lipids that depend on the receptor activation state. © 2019 Wiley Periodicals, Inc.

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“…In contrast, this lysine pointed toward ECL2 in the active A 1 AR. This was consistent with our previous study, in which the positive allosteric modulator (PAM) enhanced the agonist binding at the orthosteric site by forming a salt‐bridge between E172 ECL2 ‐K265 ECL3 . Moreover, the active A 1 AR attracted more lipids in the lower leaflet compared with the inactive A 1 AR.…”

Section: Discussionsupporting

confidence: 93%

G‐Protein‐Coupled Receptor–Membrane Interactions Depend on the Receptor Activation State

Bhattarai

¹

,

Wang

²

,

Miao

³

2019

Self Cite

View full text Add to dashboard Cite

G‐protein‐coupled receptors (GPCRs) are the largest family of human membrane proteins and serve as primary targets of approximately one‐third of currently marketed drugs. In particular, adenosine A1 receptor (A1AR) is an important therapeutic target for treating cardiac ischemia–reperfusion injuries, neuropathic pain, and renal diseases. As a prototypical GPCR, the A1AR is located within a phospholipid membrane bilayer and transmits cellular signals by changing between different conformational states. It is important to elucidate the lipid–protein interactions in order to understand the functional mechanism of GPCRs. Here, all‐atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method were performed on both the inactive (antagonist bound) and active (agonist and G‐protein bound) A1AR, which was embedded in a 1‐palmitoyl‐2‐oleoyl‐glycero‐3‐phosphocholine (POPC) lipid bilayer. In the GaMD simulations, the membrane lipids played a key role in stabilizing different conformational states of the A1AR. Our simulations further identified important regions of the receptor that interacted distinctly with the lipids in highly correlated manner. Activation of the A1AR led to differential dynamics in the upper and lower leaflets of the lipid bilayer. In summary, GaMD enhanced simulations have revealed strongly coupled dynamics of the GPCR and lipids that depend on the receptor activation state. © 2019 Wiley Periodicals, Inc.

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“…Both experimental and computational studies suggested that flexibility of the ECL2 was important for activation and allosteric modulation of the A1AR. 39,44,45 Therefore, highly flexibility of the ECL2 contributed to activation of the A1AR and receptor coupling to the G protein.…”

Section: Mechanism Of Specific Adenosine Receptor-g Protein Interactimentioning

confidence: 99%

Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors Revealed by Accelerated Molecular Simulations

Wang

¹

,

Miao

²

2019

Preprint

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1

0

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Coupling between G-protein-coupled receptors (GPCRs) and the G proteins is a key step in cellular signaling. Despite extensive experimental and computational studies, the mechanism of specific GPCR-G protein coupling remains poorly understood. This has greatly hindered effective drug design of GPCRs that are primary targets of ~1/3 of currently marketed drugs. Here, we have employed all-atom molecular simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method to decipher the mechanism of the GPCR-G protein interactions. Adenosine receptors (ARs) were used as model systems based on very recently determined cryo-EM structures of the A1AR and A2AAR coupled with the Gi and Gs proteins, respectively. Changing the Gi protein to the Gs led to increased fluctuations in the A1AR and agonist adenosine (ADO), while agonist 5'-N-ethylcarboxamidoadenosine (NECA) binding in the A2AAR could be still stabilized upon changing the Gs protein to the Gi. Free energy calculations identified one stable low-energy conformation for each of the ADO-A1AR-Gi and NECA-A2AAR-Gs complexes as in the cryo-EM structures, similarly for the NECA-A2AAR-Gi complex. In contrast, the ADO agonist and Gs protein sampled multiple conformations in the ADO-A1AR-Gs system. GaMD simulations thus indicated that the ADO-bound A1AR preferred to couple with the Gi protein to the Gs, while the A2AAR could couple with both the Gs and Gi proteins, being highly consistent with experimental findings of the ARs. More importantly, detailed analysis of the atomic simulations showed that the specific AR-G protein coupling resulted from remarkably complementary residue interactions at the protein interface, involving mainly the receptor transmembrane 6 helix and the Gα α5 helix and α4-β6 loop. In summary, the GaMD simulations have provided unprecedented insights into the dynamic mechanism of specific GPCR-G protein interactions at an atomistic level, which is expected to facilitate future drug design efforts of the GPCRs.

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Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A1 Receptor

Cited by 68 publications

References 72 publications

G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation state

G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation state

G‐Protein‐Coupled Receptor–Membrane Interactions Depend on the Receptor Activation State

Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors Revealed by Accelerated Molecular Simulations

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