Understanding the molecular basis of agonist/antagonist mechanism of human mu opioid receptor through gaussian accelerated molecular dynamics method

Abstract

The most powerful analgesic and addictive properties of opiate alkaloids are mediated by the μ opioid receptor (MOR). The MOR has been extensively investigated as a drug target in the twentieth century, with numerous compounds of varying efficacy being identified. We employed molecular dynamics and Gaussian accelerated molecular dynamics techniques to identify the binding mechanisms of MORs to BU72 (agonist) and β-funaltrexamine (antagonist). Our approach theoretically suggests that the 34 residues (Lys209-Phe221 and Ile301-Cys321) of the MORs were the key regions enabling the two compounds to bind to the active site of the MORs. When the MORs were in the holo form, the key region was in the open conformation. When the MORs were in the apo form, the key region was in the closed conformation. The key region might be responsible for the selectivity of new MOR agonists and antagonists.

Figure 1

Free energy profiles (PMF) of reaction coordinates. The PMF profiles were calculated with five individual 1000-ns GaMD simulations. (A) Agonist (BU72) (B) Antagonist (Beta-funaltrexamine).

Figure 2

Binding modes (X-ray structures) of active/inactive MORs with BU72 and β-funaltrexamine. (A) Active MOR with BU72. (B) Inactive MOR with β-funaltrexamine.

Figure 3

RMSF profiles of an MOR with BU72. (A) RC: 18–23 Å; the order of the residues is as follows: Val126, Asn127, Tyr128, Leu129, Met130, Gly131, Thr132, Trp133, Pro134, Cys140, Val143, Ile144, Asp147, Lys209, Tyr210, Arg211, Gln212, Gly213, Ser214, Ile215, Asp216, Cys217, Thr218, Leu219, Thr225, Trp226, Glu229, Lys303, Ala304, Leu305, Thr307, and Glu310. (B) RC: 3–10 Å.

Figure 4

RMSF profiles of MOR with β-funaltrexamine. (A) RC: 18–23 Å; the order of the residues is as follows: Met65, Val66, Thr67, Ala68, Ile69, Thr70, Ile71, Met72, Ala73, Leu74, Tyr75, Phe123, Gln124, Ser125, Val126, Asn127, Tyr128, Leu129, Met130, Gly131, Thr132, Trp133, Pro134, Phe135, Lys209, Arg211, Gln212, Gly213, Ser214, Ile215, Asp216, Cys217, Thr218, Tyr299, Lys303, Ile308, Glu310, Thr312, Gln314, Thr315, Val316, Trp318, His319, Phe320, Ile322, and Ala323. (B) RC: 3–10 Å.

Figure 5

(A) Initial structure of an active MOR with BU72. (B) Snapshots of an active MOR with BU72 (cyan: initial structure; magenta: structure derived after 1000-ns GaMD).