Predicted structures and dynamics for agonists and antagonists bound to serotonin 5-HT2B and 5-HT2C receptors

Abstract

Subtype 2 serotonin (5-hydroxytryptamine, 5-HT) receptors are major drug targets for schizophrenia, feeding disorders, perception, depression, migraines, hypertension, anxiety, hallucinogens, and gastrointestinal dysfunctions. (1) We report here the predicted structure of 5-HT2B and 5-HT2C receptors bound to highly potent and selective 5-HT2B antagonist PRX-08066 3, (pKi: 30 nM), including the key binding residues [V103 (2.53), L132 (3.29), V190 (4.60), and L347 (6.58)] determining the selectivity of binding to 5-HT2B over 5-HT2A. We also report structures of the endogenous agonist (5-HT) and a HT2B selective antagonist 2 (1-methyl-1-1,6,7,8-tetrahydro-pyrrolo[2,3-g]quinoline-5-carboxylic acid pyridine-3-ylamide). We examine the dynamics for the agonist- and antagonist-bound HT2B receptors in explicit membrane and water finding dramatically different patterns of water migration into the NPxxY motif and the binding site that correlates with the stability of ionic locks in the D(E)RY region.

Fig. 1

The chemical structures of 5-HT2B receptor antagonists, 1, 2, 3, and agonist 4.

Fig. 2

The chemical structures of several SB-206533 1 derivatives. R5 lipophilic substituent is surrounded by the aliphatic environments (V3.33, L3.29, I4.56, V4.60, M5.39, A5.46), while R6 electron-withdrawing group is in the proximity of L3.29, S5.43, and N6.55.

Fig. 3

The binding site of the 5-HT2B receptor agonist, SNF 4, RNF, DesMeNF, and EthylNF.

Fig. 4

Superimposition of the nonselective 5-HT2B/2C receptor antagonist (SB-206533 1) and the selective 5-HT2B receptor antagonist (2) at the human 5-HT2B receptor. The N-methyl of the cyclohexa indole ring of 2 is closer to the upper part of TM3 leading to unfavorable interactions with bulkier Ile side chains in the 5-HT2C receptors (I132), while the methyl of the cyclopenta-indole ring in SB-206533 1 is pointing toward the upper TM 4.

Fig. 5

The predicted structure of the highly potent and selective 5-HT2B receptor antagonist PRX-08066 3.

Fig. 6

Water path (yellow arrow) of apo-protein, antagonist (2) and agonist (HT) bound 5HT2B receptor complexes during 10 ns dynamics in explicit water and membrane. Ligands and water in the 5 Å proximity of N172, D100, and N310 (NPxxY region) are displayed using a space-filling model. The structure was taken from last trajectory of 10 ns dynamics.

Fig. 7

Trajectory analysis of salt-bridge interactions in the D(E)RY region (Left), the final hetero-atom distance of human 5-HT2B receptor (hHT2BR) structures at 10 ns (Middle), and the root mean square deviation (RMSD) of backbone in each TM (Right). Top) antagonist (2)-hHT2BR, Middle) Apo-hHT2BR, Bottom) agonist (HT)-hHT2BR.