Nanobody‐Enabled Reverse Pharmacology on G‐Protein‐Coupled Receptors

The conformational complexity of transmembrane signaling of G‐protein‐coupled receptors (GPCRs) is a central hurdle for the design of screens for receptor agonists. In their basal states, GPCRs have lower affinities for agonists compared to their G‐protein‐bound active state conformations. Moreover, different agonists can stabilize distinct active receptor conformations and do not uniformly activate all cellular signaling pathways linked to a given receptor (agonist bias). Comparative fragment screens were performed on a β₂‐adrenoreceptor–nanobody fusion locked in its active‐state conformation by a G‐protein‐mimicking nanobody, and the same receptor in its basal‐state conformation. This simple biophysical assay allowed the identification and ranking of multiple novel agonists and permitted classification of the efficacy of each hit in agonist, antagonist, or inverse agonist categories, thereby opening doors to nanobody‐enabled reverse pharmacology.     

Designing Point Mutants to Detect Structural Coupling in a Heterotrimeric G Protein α‐subunit by NMR Spectroscopy†

To better understand the mechanism by which the activating signal is transmitted from the receptor‐interacting regions on the G protein α‐subunit (G_α) to the guanine nucleotide‐binding pocket, we generated and characterized mutant forms of G_α with alterations in switch II (Trp‐207→Phe) and the carboxyl‐terminus (Phe‐350→Ala). Previously reported bacterial expression methods for the high‐level production of a uniformly isotope‐labeled G_tα/G_i1α chimera, ChiT, were successfully used to isolate milligram quantities of ¹⁵N‐labeled mutant protein. NMR analysis showed that while the GDP/Mg²⁺‐bound state of both mutants shared an overall conformation similar to that of the GDP/Mg²⁺‐bound state of ChiT, formation of the “transition/activated” state in the presence of aluminum fluoride (AlF₄^?) revealed distinct differences between the wild‐type and mutant G_α subunits, particularly in the response of the ¹HN, ¹⁵N cross‐peak for the Trp‐254 indole in the Trp‐207→Phe mutant and the ¹HN, ¹⁵N cross‐peak for Ala‐350 in the Phe‐350→Ala mutant. Consistent with the NMR data, the F350→Ala mutant showed an increase in intrinsic fluorescence that was similar to G_tα and ChiT upon formation of the “transition/activated” state in the presence of AlF₄^?, whereas the intrinsic fluorescence of the Trp‐207→Phe mutant decreased. These results show that the substitution of key amino acid positions in G_α can effect structural changes that may compromise receptor interactions and GDP/GTP exchange.     

A general equation correlating intramolecular rates with ‘attack’ parameters: distance and angle

Using density functional theory (DFT) at the B3LYP level with the 6-31G(d,p) basis set, a general equation is derived relating activation energy with the distance between the two reactive centers (r_GM), and the hydrogen-bonding angle (α_GM) in an intramolecular proton transfer process. The strong correlation between the values of r_GM and α_GM with the activation energy, ΔG^‡, which reflects the experimental reaction rate, provides an excellent tool to predict reaction rate based on calculated geometrical parameters for a certain system (ΔH^‡, ΔG^‡ vs r_GM and α_GM). The slope of the equation can be used as an indicator of the mode by which the two reacting centers orchestrate in an intramolecular process.     

Functional Dynamics of Deuterated β2‐Adrenergic Receptor in Lipid Bilayers Revealed by NMR Spectroscopy

G‐protein‐coupled receptors (GPCRs) exist in conformational equilibrium between active and inactive states, and the former population determines the efficacy of signaling. However, the conformational equilibrium of GPCRs in lipid bilayers is unknown owing to the low sensitivities of their NMR signals. To increase the signal intensities, a deuteration method was developed for GPCRs expressed in an insect cell/baculovirus expression system. The NMR sensitivities of the methionine methyl resonances from the β₂‐adrenergic receptor (β₂AR) in lipid bilayers of reconstituted high‐density lipoprotein (rHDL) increased by approximately 5‐fold upon deuteration. NMR analyses revealed that the exchange rates for the conformational equilibrium of β₂AR in rHDLs were remarkably different from those measured in detergents. The timescales of GPCR signaling, calculated from the exchange rates, are faster than those of receptor tyrosine kinases and thus enable rapid neurotransmission and sensory perception.     

DNA Microenvironment Monitored by Controlling Redox Blinking

The rate of a bimolecular reaction between a fluorophore and a freely diffusing molecule in the solvent depends on the accessibility of the fluorophore for collision with the molecule. We previously reported that the observation of blinking, caused by the formation of R6G in the excited triplet state (³R6G*) and its quenching reaction with O₂, allowed us to monitor the DNA conformational changes between a duplex and a hairpin. However, the small molecular size of O₂ hampered sensitive monitoring of the microenvironment changes around R6G. In this study, we control redox blinking by adding a reductant ascorbic acid 2‐phosphate (VcP), which converts ³R6G* into the radical anion form R6G^.?, and by adding a bulky oxidant FeDTPA. The bimolecular electron‐transfer rate between R6G^.? and bulky FeDTPA was more strongly affected by microenvironment changes around R6G, compared with that between ³R6G* and the smaller O₂. This allowed us to monitor subtle DNA conformational changes caused by a single different nucleotide.     

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

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.     

Interpretation of the microwave spectrum of 2-methoxy ethylamine using its ab initio structures

The 7₃ ← 6₃ μ_aK₋₁ doublet line series of 2-methoxy ethylamine, previously recorded with the radiofrequency microwave double resonance technique, was interpreted for the T and G conformations of this compound with a number of structural models including the 4-21G optimized geometries. A single model of G can reproduce the doublet series as the vibrational progression of the CO skeletal mode, starting with the υ_CO = 0 groundstate at 35 457 MHz, and stepping in approximately 95 MHz intervals up to the vibrational satellite of υ_CO = 9, with the υ_CO = 5 doublet missing. When model calculations are performed for T with the structural parameters of G which reproduce the 7₃ ← 6₃K₋₁ doublet series, except for rotating the NH₂ group by 120° to obtain T, the frequency of its groundstate doublet is found at lower frequencies than that of G. In contrast to this, when the empirically corrected 4-21G parameters of T are used in the analysis, the calculated groundstate of T coincides with the expected υ_CO = 6 doublet of G. The 4-21G geometries of G and T are in good agreement with the rotational constants and the conformational energy difference derived from the microwave spectra. Thus, this analysis clearly confirms the assignment of the observed 7₃ ← 6₃K₋₁ series as the progressions of the υ_CO = 0 to υ_CO = 4 states of G, and the υ_CO = 0 to υ_CO = 3 states of T.     

Conformational analysis of 2,2-dimethyl-5-alkyl-1,3-dioxa-2-silacyclohexanes

Study of conformational isomerization of 2,2-dimethyl-5-alkyl-1,3-dioxa-2-silacyclohexanes using quantum-chemical HF/6-31G(d) and PBE/3z approximations showed that its route involves an equilibrium between the chair conformers with different orientation of substituent at C⁵ ring atom and proceeds through a transition state corresponding to the 2,5-twist conformation. Molecular dynamics method showed that at room temperature this conformation transforms into the equatorial or axial chair conformers through 1,4-twist or sofa forms. Based on the experimental and theoretical values of vicinal ¹H NMR coupling constants we determined quantitative conformational composition of the molecules of these compounds and the values of ??G ⁰ of the conformational equilibrium.     

Conformational analysis of 2-methyl-5-nitro-1,3,2-dioxaborinane

Quantum-chemical methods HF/6-31G(d), HF/6-31+G(d), MP2/6-31G(d)//HF/6-31G(d), and MP2/6-31+G(d)//HF/6-31+G(d) were used to investigate the conformational isomerization of 2-methyl-5-nitro-1,3,2-dioxaborinane. It has been shown that a potential energy surface of this compound includes two minima: an axial form of semi-chair and equatorial sofa together with a transition state belonging to the conformation of 2,5-twist-form. A comparison between experimental NMR ¹H and theoretical vicinal coupling constants was used to determine the quantitative conformational composition of cyclic boric acid ester and a value of ΔG ⁰ for nitro group at the ring carbon atom C⁵ in CCl₄ and C₆D₅NO₂ solutions.     

A proton nuclear magnetic resonance spectroscopic study of conformational equilibration of 3-azabicyclo[3.2.2]nonane

The 251 MHz ₁H NMR spectra of 3-azabicyclo[3.2.2]nonane (1) have been measured from ?40 to ?175°C. Below about ?140°C a conformational process which equilibrates the methylene protons of the CH₂NCH₂ moiety of 1 becomes slow on the NMR time scale. The free-energy of activation (ΔG^#) for this process is 5.9 kcal mol^?1. The results can be interpreted either in terms of ring inversion of the seven-membered ring or limited pseudorotation of the six-membered ring. Possible pathways for effecting conformational equilibration in 1 are discussed.     

The Aminotriazole Antagonist Cmpd‐1 Stabilises a Distinct Inactive State of the Adenosine 2A Receptor

The widely expressed G‐protein coupled receptors (GPCRs) are versatile signal transducer proteins that are attractive drug targets but structurally challenging to study. GPCRs undergo a number of conformational rearrangements when transitioning from the inactive to the active state but have so far been believed to adopt a fairly conserved inactive conformation. Using ¹⁹F NMR spectroscopy and advanced molecular dynamics simulations we describe a novel inactive state of the adenosine 2A receptor which is stabilised by the aminotriazole antagonist Cmpd‐1. We demonstrate that the ligand stabilises a unique conformation of helix V and present data on the putative binding mode of the compound involving contacts to the transmembrane bundle as well as the extracellular loop 2.     

Influences of Co-60 gamma-ray irradiation on electrical characteristics of Al2O3 MOS capacitors

Effects of gamma-ray irradiation on the electrical characteristics of Al₂O₃ MOS capacitors such as barrier height, acceptor concentration, series resistance and interface state parameters have been studied by analyzing capacitance–voltage (C–V) and conductance–voltage (G/ω–V) measurements. The fabricated MOS capacitors were irradiated with gamma-rays at doses up to five grays. C–V and G/ω–V measurements were recorded prior to and after irradiation at high frequency. The results show that the measured capacitance and conductance values decreased with increasing in irradiation dose and C–V and G/ω curves has been shifted toward the negative voltages. Moreover, the series resistance (R _s) and density of interface states increased with increasing in irradiation dose and density of interface states (D _it) were calculated as order of 10¹² eV^?1cm^?2 prior to and after irradiation. Due to presence and variations in the R _s values, the corrected and the measured C–V and G/ω–V exhibited different behaviors. Therefore other electrical characteristics were assessed from corrected C _c characteristics. It was observed that acceptor concentration decreased with increasing in barrier height of device due to changes in interface states and diffusion potential.     

Infrared,Raman and NMR spectra,conformational stability,and ab initio calculations of divinylmethoxyborane

The infrared spectra (4000–50 cm⁻¹) of gaseous and solid divinylmethoxyborane, (CH₂=CH)₂BOCH₃, as well as the Raman spectra (3500–20 cm⁻¹) of the liquid and solid have been recorded. Qualitative depolarization values have been obtained from the Raman spectrum of the liquid. All normal modes, except the torsions, have been assigned based on infrared band contours, depolarization values, group frequencies, and normal coordinate calculations. From a comparison of the spectra in the fluid and solid states, it is concluded that the molecule exists predominantly in a single conformation in all physical states. Frequencies and potential energy distributions for the normal modes have been calculated with the 3–21G basis set. A comparison of these calculated frequencies to the observed spectra is consistent with the predominant form having a “planar” heavy atom skeleton with C_s, symmetry. From the variable low temperature ¹³C NMR data, a barrier to rotation about the B-O bond of 10.1 ± 0.1 kcal mol⁻¹ has been determined, which is in excellent agreement with a barrier of 8.5 kcal mol"1 obtained from ab initio calculations. Structural parameters, conformational stability, and barriers to internal rotation have been obtained from ab initio Hartree-Fock gradient calculations employing both the 3–21G and 6–31G^* basis sets. The results are compared to the corresponding data for some similar organoboranes.     

Syntheses and conformational analyses of mono- and trans-1,4-dialkoxy substituted cyclohexanes—the steric substituent/skeleton interactions

Mono- and trans-1,4-dialkoxy substituted cyclohexanes (alkyl=Me, Et, i-Pr, t-Bu) were prepared using the solvomercuration-demercuration (SM-DM) procedure. The axial?axial and axial,axial?equatorial, equatorial conformational equilibria of the products were studied by low temperature ¹H and ¹³C NMR spectroscopy in CD₂Cl₂. The structures and relative energies of the participating conformers were calculated at both the B3LYP (6-311G^∗//6-311+G^∗) and MP2 (6-311+G^∗//6-311G^∗) levels of theory. In the case of DFT, good correlations of ΔG^o_calcd versus ΔG^o_exptl were obtained. Both the structures and the energy differences of the conformers have been discussed with respect to established models of conformational analysis, viz. steric and hyperconjugative interactions. In addition, ¹J_H,C coupling constants were considered with respect to the hyperconjugation present.     

Unwinding of the C‐Terminal Residues of Neuropeptide Y is critical for Y2 Receptor Binding and Activation

Despite recent breakthroughs in the structural characterization of G‐protein‐coupled receptors (GPCRs), there is only sparse data on how GPCRs recognize larger peptide ligands. NMR spectroscopy, molecular modeling, and double‐cycle mutagenesis studies were integrated to obtain a structural model of the peptide hormone neuropeptide Y (NPY) bound to its human G‐protein‐coupled Y₂ receptor (Y₂R). Solid‐state NMR measurements of specific isotope‐labeled NPY in complex with in vitro folded Y₂R reconstituted into phospholipid bicelles provided the bioactive structure of the peptide. Guided by solution NMR experiments, it could be shown that the ligand is tethered to the second extracellular loop by hydrophobic contacts. The C‐terminal α‐helix of NPY, which is formed in a membrane environment in the absence of the receptor, is unwound starting at T³² to provide optimal contacts in a deep binding pocket within the transmembrane bundle of the Y₂R.     

Conformational analysis of methyl 2-methyl-2-(1-naphthyl)propionate

(S)-2-Methoxy-2-(1-naphthyl)propionic acid (MαNP acid 1) is used for enantioseparation of many secondary alcohols and for determining the stereogenic centers. In the liquid state, based on the ¹H NMR anisotropy effect and reported results, it was shown that the MαNP ester preferred a coplanar relation between the methyl and naphthyl groups and a synperiplanar relation between the Cα-OMe and CO groups. In the case of 1,2,3,4-tetrahydro-4-phenanthrenol, which is a secondary alcohol, the stereogenic center was determined by X-ray analysis. It was shown that MαNP ester adopted similar arrangements in the solid state. However, it was presumed that the strong repulsion between oxygen atoms may be disadvantageous in the solid state. Therefore, we carried out conformational analysis using the simplest MαNP methyl ester to clarify this unique relationship. From detailed results based on the energy surface determined using the RHF/STO-3G basis set, the synperiplanar positional relation was the most stable, and the calculated results agreed with many reported experimental results. At the same time, all conformational isomers of the MαNP methyl ester were used to clarify the internal conversion pathways.     

In silico analysis of the histaprodifen induced activation pathway of the guinea-pig histamine H<Subscript>1</Subscript>-receptor

The binding of (partial) agonists in the binding pocket of biogenic amine receptors induces a conformational change from the inactive to the active state of the receptors. There is only little knowledge about the binding pathways of ligands into binding pocket on molecular level. So far, it was not possible with molecular dynamic simulations to observe the ligand binding and receptor activation. Furthermore, there is nearly nothing known, in which state of ligand binding, the receptor gets activated. The aim of this study was to get more detailed insight into the process of ligand binding and receptor activation. With the recently developed LigPath algorithm, we scanned the potential energy surface of the binding process of dimeric histaprodifen, a partial agonist at the histamine H₁-receptor, into the guinea pig histamine H₁-receptor, taking also into account the receptor activation. The calculations exhibited large conformational changes of Trp^6.48 and Phe^6.55 during ligand binding and receptor activation. Additionally, conformational changes were also observed for Phe^6.52, Tyr^6.51 and Phe^6.44. Conformational changes of Trp^6.48 and Phe^6.52 are discussed in literature as rotamer toggle switch in context with receptor activation. Additionally, the calculations indicate that the binding of dimeric histaprodifen, accompanied by receptor activation is energetically preferred. In general, this study gives new, theoretical insights onto ligand binding and receptor activation on molecular level.     

New insight into the substituent effects on the hydrolytic deamination of saturated and unsaturated cytosine

Ab initio calculations were carried out to understand the effect of electron donating groups (EDG) and electron withdrawing groups (EWG) at the C5 position of cytosine (Cyt) and saturated cytosine (H₂Cyt) of the deamination reaction. Geometries of the reactants, transition states, intermediates, and products were fully optimized at the B3LYP/6-31G(d,p) level in the gas phase as this level of theory has been found to agree very well with G3 theories. Activation energies, enthalpies, and Gibbs energies of activation along with the thermodynamic properties (ΔE, ΔH, and ΔG) of each reaction were calculated. A plot of the Gibbs energies of activation (ΔG^‡) for C5 substituted Cyt and H₂Cyt against the Hammett σ-constants reveal a good linear relationship. In general, both EDG and EWG substituents at the C5 position in Cyt results in higher ΔG^‡ and lower σ values compared to those of H₂Cyt deamination reactions. C5 alkyl substituents ( H,  CH₃,  CH₂CH₃,  CH₂CH₂CH₃) increase ΔG^‡ values for Cyt, while the same substituents decrease ΔG^‡ values for H₂Cyt which is likely due to steric effects. However, the Hammett σ-constants were found to decrease at the C5 position of cytosine (Cyt) and saturated cytosine (H2Cyt) on the deamination reaction. Both ΔG^‡ and σ values decrease for the substituents Cl and Br in the Cyt reaction, while ΔG^‡ values increase and σ decrease in the H₂Cyt reaction. This may be due to high polarizability of bromine which results in a greater stabilization of the transition state in the case of bromine compared to chlorine. Regardless of the substituent at C5, the positive charge on C4 is greater in the TS compared to the reactant complex for both the Cyt and H₂Cyt. Moreover, as the charges on C4 in the TS increase compared to reactant, ΔG^‡ also increase for the C5 alkyl substituents ( H,  CH₃,  CH₂CH₃,  CH₂CH₂CH₃) in Cyt, while ΔG^‡ decrease in H₂Cyt. In addition, analysis of the frontier MO energies for the transition state structures shows that there is a correlation between the energy of the HOMO–LUMO gap and activation energies.     

Stark and Zeeman spectroscopies of 4f 66s6p 7G1-6 levels in Sm I under external electric and magnetic fields

Systematic study of hyperfine structures, Zeeman and Stark effects in Sm I is performed for the lowest ⁷G_1-6 levels belonging to the configuration 4f ⁶6s6p by atomic-beam laser spectroscopy with fluorescence detection. The hyperfine coupling constants of ⁷G_2-6 levels are determined. From the Zeeman splittings for the 4f ⁶6s ^{2 7}F_2-6 ? 4f ⁶6s6p ⁷G_2-6 transitions, g-values are determined for the ⁷G_2.6 levels and the precision is improved by several orders of magnitude. From the Stark splittings for the ⁷F_0-3 ? ⁷G_1-3 transitions, tensor polarizabilities α ₂(J) are determined for the upper ⁷G_1-3 levels. Particularly for the ⁷G₁ level (15 650.55 cm^?1) which has close-lying opposite-parity level, the isotope dependence of α ₂(J) is clearly observed for the first time.