Theoretical Conformational Analysis for Neurotransmitters in the Gas Phase and in Aqueous Solution. Norepinephrine

• Published in: Journal of the American Chemical Society 2003-03, Vol.125 (9), p.2770-2785
• Main Authors: Nagy, Peter I, Alagona, Giuliano, Ghio, Caterina, Takács-Novák, Krisztina
• Format: Article
• Language: English
• Subjects: Amines - chemistry; Biological and medical sciences; Computer Simulation; Conformational dynamics in molecular biology; Fundamental and applied biological sciences. Psychology; Gases; Hydrogen Bonding; Hydrogen-Ion Concentration; Molecular biophysics; Monte Carlo Method; Norepinephrine - chemistry; Potentiometry; Protein Conformation; Receptors, Adrenergic, beta - chemistry; Solutions; Thermodynamics; Water - chemistry
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja028952n

The natural neurotransmitter (R)-norepinephrine takes the monocationic form in 93% abundance at the physiological tissue pH of 7.4. Ab initio and DFT/B3LYP calculations were performed for 12 protonated conformers of (R)-norepinephrine in the gas phase with geometry optimizations up to the MP2/6-311++G** level, and with single-point calculations up to the QCISD(T) level at the HF/6-31G*-optimized geometries. Four monohydrates were studied at the MP2/6-31G*//HF/6-31G* level. In the gas phase, the G1 conformer is the most stable with phenyl···NH3 + gauche and HO(alc)···NH3 + gauche arrangements. A strained intramolecular hydrogen bond was found for conformers (G1 and T) with close NH3 + and OH groups. Upon rotation of the NH3 + group as a whole unit about the Cβ−Cα axis, a 3-fold potential was calculated with free energies for barriers of 3−12 kcal/mol at the HF/6-31G* level. Only small deviations were found in MP2/6-311++G** single-point calculations. A 2-fold potential was calculated for the phenyl rotation with free energies of 11−13 kcal/mol for the barriers at T = 310 K and p = 1 atm. A molecular mechanics docking study of (R)-norepinephrine in a model binding pocket of the β-adrenergic receptor shows that the ligand takes a conformation close to the T(3) arrangement. The effect of aqueous solvation was considered by the free energy perturbation method implemented in Monte Carlo simulations. There are 4−5 strongly bound water molecules in hydrogen bonds to the conformers. Although hydration stabilizes mostly the G2 form with gauche phenyl···NH3 + arrangement and a water-exposed NH3 + group, the conformer population becomes T > G1 > G2, in agreement with the PMR spectroscopy measurements by Solmajer et al. (Z. Naturforsch. 1983, 38c, 758). Solvent effects reduce the free energies for barriers to 3−6 and 9−12 kcal/mol for rotations about the Cβ−Cα and the C1(ring)−Cβ axes, respectively.