Theoretical approach to the pharmacophoric pattern of GABAB analogs

In order to determine the structural requirements that are important for GABA_B binding affinity, a quantum-chemical-based conformational study has been performed, followed by a similarity analysis which includes 12 GABA_B analogs. Due to the flexibility of the structures, a semigrid GABA_B analog [2RS-(5,5-dimethyl) morpholinyl-acetic acid] has been used as a template for the amonium moiety in order to help to identify the active conformation. Both in vacuo, and solvent-simulated calculations, for the physiological media modeled as water molecules, have been compared, for this analog, at ab initio (G94, 6-31+G(d,p)) and semiempirical (PM3) levels, respectively. On the basis of this comparison, the results of in vacuo PM3 calculations have been chosen for the similarity analysis. We have included, in the calculations, a group of molecules heterogeneous enough to become representative of the different families that can bind to the GABA_B receptor site. Following their comparison we report the leading characteristics that can be related to their binding capability and define a pharmacophoric pattern for GABA_B analogs. The latter is compared with the one previously found for the binding affinity at the GABA_A receptor site. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1195–1208, 1998     

Molecular mechanism of secreted amyloid-β precursor protein in binding and modulating GABABR1a

A recent phenomenal study discovered that the extension domain of secreted amyloid-β precursor protein (sAPP) can bind to the intrinsically disordered sushi 1 domain of the γ-aminobutyric acid type B receptor subunit 1a (GABA_BR1a) and modulate its synaptic transmission. The work provided an important structural foundation for the modulation of GABA_BR1a; however, the detailed molecular interaction mechanism, crucial for future drug design, remains elusive. Here, we further investigated the dynamical interactions between sAPP peptides and the natively unstructured sushi 1 domain using all-atom molecular dynamics simulations, for both the 17-residue sAPP peptide (APP 17-mer) and its minimally active 9 residue segment (APP 9-mer). We then explored mutations of the APP 9-mer with rigorous free energy perturbation (FEP) calculations. Our in silico mutagenesis studies revealed key residues (D4, W6, and W7) responsible for the binding with the sushi 1 domain. More importantly, one double mutation based on different vertebrate APP sequences from evolution exhibited a stronger binding (ΔΔG = −1.91 ± 0.66 kcal mol⁻¹), indicating a potentially enhanced GABA_BR1a modulator. These large-scale simulations may provide new insights into the binding mechanism between sAPP and the sushi 1 domain, which could open new avenues in the development of future GABA_BR1a-specific therapeutics.

A recent phenomenal study discovered that the extension domain of secreted amyloid-β precursor protein (sAPP) can bind to the intrinsically disordered sushi 1 domain of the γ-aminobutyric acid type B receptor subunit 1a (GABA_BR1a) and modulate its synaptic transmission.     

DIRECT‐ID: An automated method to identify and quantify conformational variations—application to β2‐adrenergic GPCR

The conformational dynamics of a macromolecule can be modulated by a number of factors, including changes in environment, ligand binding, and interactions with other macromolecules, among others. We present a method that quantifies the differences in macromolecular conformational dynamics and automatically extracts the structural features responsible for these changes. Given a set of molecular dynamics (MD) simulations of a macromolecule, the norms of the differences in covariance matrices are calculated for each pair of trajectories. A matrix of these norms thus quantifies the differences in conformational dynamics across the set of simulations. For each pair of trajectories, covariance difference matrices are parsed to extract structural elements that undergo changes in conformational properties. As a demonstration of its applicability to biomacromolecular systems, the method, referred to as DIRECT‐ID, was used to identify relevant ligand‐modulated structural variations in the β₂‐adrenergic (β₂AR) G‐protein coupled receptor. Micro‐second MD simulations of the β₂AR in an explicit lipid bilayer were run in the apo state and complexed with the ligands: BI‐167107 (agonist), epinephrine (agonist), salbutamol (long‐acting partial agonist), or carazolol (inverse agonist). Each ligand modulated the conformational dynamics of β₂AR differently and DIRECT‐ID analysis of the inverse‐agonist vs. agonist‐modulated β₂AR identified residues known through previous studies to selectively propagate deactivation/activation information, along with some previously unidentified ligand‐specific microswitches across the GPCR. This study demonstrates the utility of DIRECT‐ID to rapidly extract functionally relevant conformational dynamics information from extended MD simulations of large and complex macromolecular systems. © 2015 Wiley Periodicals, Inc.     

Structure–Activity Studies of Cysteine‐Rich α‐Conotoxins that Inhibit High‐Voltage‐Activated Calcium Channels via GABAB Receptor Activation Reveal a Minimal Functional Motif

α‐Conotoxins are disulfide‐rich peptides that target nicotinic acetylcholine receptors. Recently we identified several α‐conotoxins that also modulate voltage‐gated calcium channels by acting as G protein‐coupled GABA_B receptor (GABA_BR) agonists. These α‐conotoxins are promising drug leads for the treatment of chronic pain. To elucidate the diversity of α‐conotoxins that act through this mechanism, we synthesized and characterized a set of peptides with homology to α‐conotoxins known to inhibit high voltage‐activated calcium channels via GABA_BR activation. Remarkably, all disulfide isomers of the active α‐conotoxins Pu1.2 and Pn1.2, and the previously studied Vc1.1 showed similar levels of biological activity. Structure determination by NMR spectroscopy helped us identify a simplified biologically active eight residue peptide motif containing a single disulfide bond that is an excellent lead molecule for developing a new generation of analgesic peptide drugs.     

Nuclear quantum and H/D isotope effects on three-centered bonding diborane: Path integral molecular dynamics simulations

Nuclear quantum and H/D isotope effects of bridging and terminal hydrogen atoms of diborane (B₂H₆) molecules were systematically studied by classical ab initio molecular dynamics (CLMD) and ab initio path integral molecular dynamics (PIMD) simulations with BHandHLYP/6-31++G** level of theory at room temperature (298.15 K). Calculated results clearly show that H/D isotope effect appears in the distribution of hydrogen (deuterium) of B₂H₆ (B₂D₆). Geometry of B₂H₆ also plays a significant role in the nuclear quantum effect proved by PIMD simulations, but slightly deviated from its equilibrium structure when simulated via CLMD simulation. The bond lengths between boron atoms R (B1 … B2) and the bridging hydrogen atoms R_HH (H_B1 … H_B2) of the B₂H₆ molecule obtained from PIMD simulations are slightly longer than those of the deuterated form of the diborane (B₂D₆) molecule. The principal component analysis (PCA) was also employed to distinguish the important modes of bridging hydrogen as related to the nuclear quantum and H/D isotope effects. The highest level of contribution obtained from PCA of PIMD simulations is bending, while various mixed vibrations with less contribution were also found. Therefore, the nuclear quantum and H/D isotope effects need to be taken into account for a better understanding of diborane geometry.     

Dynamic Mg2B8 Cluster: A Nanoscale Compass

Boron‐based binary cluster Mg₂B₈ is shown to adopt a compass‐like structure via computational global searches, featuring an Mg₂ dimer as the needle and a disk‐shaped B₈ molecular wheel as baseplate. The nanocompass has a diameter of 0.35 nm. Born–Oppenheimer molecular dynamics simulations indicate that Mg₂B₈ is structurally fluxional with the needle rotating freely on the baseplate, analogous to a functioning compass. The dynamics is readily initiated via a ultrasoft vibrational mode. The rotational barrier is only 0.1 kcal mol⁻¹ at the single‐point CCSD(T) level. Chemical bonding analysis suggests that the cluster compass can be formulated as [Mg₂]²⁺[B₈]²⁻; that is, the baseplate and the needle are held together primarily through ionic interactions. The baseplate is doubly aromatic with π and σ sextets. The bonding pattern provides a dilute, continuous, and delocalized electron cloud, which underlies the dynamics of the nanocompass.     

An unconventional ligand-binding mechanism of substrate-binding proteins: MD simulation and Markov state model analysis of BtuF

In conventional “Venus Flytrap” mechanism, substrate-binding proteins (SBPs) interconvert between the open and closed conformations. Upon ligand binding, SBPs form a tightly closed conformation with the ligand bound at the interface of two domains. This mechanism was later challenged by many type III SBPs, such as the vitamin B₁₂-binding protein BtuF, in which the apo- and holo-state proteins adopt very similar conformations. Here, we combined molecular dynamics simulation and Markov state model analysis to study the conformational dynamics of apo- and B₁₂-bound BtuF. The results indicate that the crystal structures represent the only stable conformation of BtuF. Meanwhile, both apo- and holo-BtuF undergo large-scale interdomain motions with little energy cost. B₁₂ binding casts little restraints on the interdomain motions, suggesting that ligand binding affinity is enhanced by the remaining conformational entropy of holo-BtuF. These results reveal a new paradigm of ligand recognition mechanism of SBPs. © 2019 Wiley Periodicals, Inc.     

The COMPASS force field: parameterization and validation for phosphazenes

A new, condensed-phase optimised ab-initio force field, COMPASS, has been developed recently. In this paper, the validation of COMPASS for phosphazenes is presented. The functional forms of this force field are of the consistent force field (CFF) type. Charges and bonded terms were derived from HF/6–31G1 calculations, while the nonbonded parameters (L-J 9-6 vdW potential) were initially transferred from the polymer consistent force field, pcff, and optimised using MD simulations of condensed-phase properties. As a validation of COMPASS, molecular mechanics calculations and molecular dynamics simulations have been made on a number of isolated molecules, liquids, and crystals. The calculated molecular structure, vibration frequencies, conformational properties for isolated molecules, crystal cell parameters and density, liquid density, and heat of evaporation agreed favourably with most experimental data. The special conformational properties of the tetracyclophosphazenes, (NPCI₂)₄ and (NPF₂)₄, in the solid state are discussed based on molecular mechanics and CASTEP ab-initio calculations. The effect of nonbonded cutoff distance and different algorithms for pressure control in NPT simulation was also investigated. Finally, molecular dynamics using the COMPASS force field was used to predict properties of three isomers of high-molecular-weight amorphous poly(dibutoxyphosphazenes). In this case, excellent agreement was achieved between densities and glass transition temperatures obtained from dynamics and experimental data.     

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.     

Molecular dynamics simulation of the A-DNA to B-DNA transition in aqueous RbCl solution

Unrestrained molecular dynamics (MD) simulations have been carried out to characterize the stability of DNA conformations and the dynamics of A-DNA→B-DNA conformational transitions in aqueous RbCl solutions. The PARM99 force field in the AMBER8 package was used to investigate the effect of RbCl concentration on the dynamics of the A→B conformational transition in the DNA duplex d(CGCGAATTCGCG)2 . Canonical Aand B-form DNA were assumed for the initial conformation and the final conformation had a length per complete turn that matched the canonical B-DNA. The DNA structure was monitored for 3.0 ns and the distances between the C5′ atoms were obtained from the simulations. It was found that all of the double stranded DNA strands of A-DNA converged to the structure of B-form DNA within 1.0 ns during the unrestrained MD simulations. In addition, increasing the RbCl concentration in aqueous solution hindered the A→B conformational transition and the transition in aqueous RbCl solution was faster than that in aqueous NaCl solution for the same electrolyte strength. The effects of the types and concentrations of counterions on the dynamics of the A→B conformational transition can be understood in terms of the variation in water activity and the number of accumulated counterions in the major grooves of A-DNA. The rubidium ion distributions around both fixed A-DNA and B-DNA were obtained using the restrained MD simulations to help explain the effect of RbCl concentration on the dynamics of the A→B conformational transition.     

Adsorption of molecular hydrogen on inorganometallic complexes B<Subscript>2</Subscript>H<Subscript>4</Subscript>M (M=Li,Be, Sc,Ti, V)

Molecular interaction between hydrogen molecules and B₂H₄M (M=Li, Be, Sc, Ti, V) complexes has been studied using the DFT method (M06 functional) and 6-311++G** basis set. The hydrogen uptake capacity of the complexes considered is higher than the target set by the US Department of Energy (5.5 wt% by 2020). The metal atom bound strongly to the B₂H₄ substrate. Adsorption of molecular hydrogen on Be-, Ti-, and V-decorated complexes is thermodynamically possible for all the pressures and temperatures considered whereas it is unfavorable for Li-decorated complexes for all the pressure and temperatures. For the Sc-doped complexes, adsorption of molecular hydrogen is favorable below 330 K and entire pressure range considered. All the H₂ adsorbed complexes are kinetically stable. For all the complexes, the interaction between the inorganometallic complexes and the H₂ molecules adsorbed is attractive whereas that between adsorbed H₂ molecules is repulsive. We have also performed molecular dynamics simulations to confirm the same number of H₂ molecule adsorption from the simulations and DFT calculations.     

Structure and Fluxionality of B13+ Probed by Infrared Photodissociation Spectroscopy

We use cryogenic ion vibrational spectroscopy to characterize the structure and fluxionality of the magic number boron cluster B₁₃⁺. The infrared photodissociation (IRPD) spectrum of the D₂‐tagged all‐¹¹B isotopologue of B₁₃⁺ is reported in the spectral range from 435 to 1790 cm⁻¹ and unambiguously assigned to a planar boron double wheel structure based on a comparison to simulated IR spectra of low energy isomers from density‐functional‐theory (DFT) computations. Born–Oppenheimer DFT molecular dynamics simulations show that B₁₃⁺ exhibits internal quasi‐rotation already at 100 K. Vibrational spectra derived from these simulations allow extracting the first spectroscopic evidence from the IRPD spectrum for the exceptional fluxionality of B₁₃⁺.     

Insights from first principles molecular dynamics studies toward infrared multiple-photon and single-photon action spectroscopy: case study of the proton-bound dimethyl ether dimer

We have used finite temperature ab initio molecular dynamics simulations in conjunction with computation of critical quantum nuclear effects to probe the differences between single-photon argon tagged action spectral results and infrared multiple-photon dissociation experiments for a proton bound molecular ion system. We find that the principal difference between the results in these experimental techniques is essentially that of cluster temperature. The multiple-photon dissociation experiments conducted using room temperature ions reflect a larger degree of conformational freedom compared to the colder single-photon argon tagged action spectral results. Our ab initio molecular dynamics simulation techniques accurately capture the effects of conformational sampling, adequately reproduce both spectra, and can be utilized to assign the dynamically averaged finite temperature spectra.     

Force-field parametrization and molecular dynamics simulations of p-menthan-3,9-diols: a family of amphiphilic compounds derived from terpenoids

A set of amphiphilic p-menthan-3,9-diols have been investigated by molecular dynamics simulations. These are four stereoisomers than can be specifically obtained from two terpenoids widely used in biorganic chemistry. For this purpose, the p-menthan-3,9-diols have been explicitly parametrized using both semiempirical and ab initio quantum mechanical calculations. The reliability of these parameters has been validated by predicting different molecular and thermodynamic properties. Molecular dynamics simulations in aqueous solution have been performed with the new parameters. The results provide useful insights about the conformational properties of this family of compounds and the formation of intra- and intermolecular hydrogen bonds.     

Methodological approaches for the study of GABA<Subscript>A</Subscript> receptor pharmacology and functional responses

Inhibitory GABA_A receptor ion channels are the target for a wide range of clinically-used therapeutic agents. The complex structural diversity of these ligand-gated channels, revealed by molecular cloning studies, together with increasing requirements for higher-throughput functional assays in drug discovery, has led to the development of a wide range of techniques to examine GABA_A receptor pharmacology and function. In the current article we review some of the methodologies which have contributed to the expansion of knowledge in this field. The techniques include: molecular approaches, immunoprecipitation, and immunopurification to study receptor assembly, structure, and functional expression; in situ hybridization, immunocytochemistry, and autoradiography to examine receptor distribution in native tissues; radioligand binding, site-directed mutagenesis, and electrophysiology to examine pharmacology and allosteric modulation; and patch clamp, ion flux, microphysiometry, and a variety of novel fluorescence-based technologies to examine ion-channel function. The use of gene targetting approaches in transgenic mice has also provided important insights into the role of specific GABA_A receptor subtypes in vivo. The continuing evolution of novel technologies and assay approaches with appropriate sensitivity and resolution to measure subtle modulation of GABA_A ion channels will facilitate ongoing investigation of the physiological functions of these important inhibitory receptors.     

Impact of the solvent on the conformational isomerism of calix[4]arenes: a study based on continuum solvation models

The influence of solvation on the conformational isomerism of calix[4]arene and p-tert-butylcalix[4]arene has been investigated by using the continuum model reported by Miertus, Scrocco, and Tomasi (MST). The quantum mechanical (QM) and semiclassical (SC) formalisms of the MST model have been considered for two different solvents (chloroform and water). The suitability of the QM-MST and SC-MST methods has been examined by comparison with previous results derived from classical molecular dynamics (MD) simulations with explicit solvent molecules. The application of the continuum model to the solute configurations generated by using in vacuo classical MD simulations provides a fast strategy to evaluate the effects of the solvent on the conformational preferences of calixarenes. These encouraging results allow us to propose the use of continuum models to solutes with complex molecular structures, which are traditionally studied by MD simulations.     

A Novel GABABR1a Receptor Electrochemical Biosensor Based on Gold Nanoparticles Chitosan-horseradish Peroxidase

A novel gamma aminobutyric acid type B receptor subunit 1a (GABA_BR1a) biosensor modified with double-layer gold has been developed for the first time. In this work, the synthesized plasmid was transfected into HEK-293T cells by liposome transfection, and the target protein GABA_BR1a was obtained. The horseradish peroxidase was used as a signal amplification system to produce a double-layer gold modified GABA_BR1a receptor biosensor. The ligand gamma aminobutyric acid (GABA), jujuboside A and baclofen were detected by the time-current method with the biosensor. The results showed that the action regularity of GABA, jujuboside A, and baclofen on GABA_BR1a receptor was fitted with hyperbolic fitting (R² was 0.9740, 0.9770 and 0.9770, respectively). The double reciprocal method was used to figure out the affinity constant (K_a) of GABA, jujuboside A, and baclofen with the receptor, i. e. 2.1016×10⁻¹⁵ mol/L, 1.7601×10⁻¹⁴ mol/L, and 1.633×10⁻¹⁴ mol/L, respectively, indicating that these measured compounds exhibited different action strength on the receptor. Based on the above, this study will provide a basis for drug screening and will also provide a new idea and method for investigating quantitatively the interaction between receptors and ligands in the future.     

Impact of Deuteration and Temperature on Furan Ring Dynamics

Despite significant progress in conformational analysis of cyclic molecules, the number of computational studies is still limited while most of that available in the literature data have been obtained long time ago with outdated methods. In present research, we have studied temperature driven conformational changes of the furan ring at three different temperatures. Additionally, the effect of deuteration on the ring dynamics is discussed; in addition, the aromaticity indices following the Bird and HOMA schemes are computed along all trajectories. Our ab initio molecular dynamic simulations revealed that deuteration has changed the furan ring dynamics and the obvious consequences; in addition, the shape and size of molecule are expected to be different.     

Transport in molten LiF-NaF-ZrF4 mixtures: A combined computational and experimental approach

The transport properties of several LiF-NaF-ZrF₄ mixtures have been determined. Our work primarily consisted in the determination of the electrical conductivity from experimental measurements and from computer simulations. A good agreement was observed between both approaches. The simulations are based on the molecular dynamics technique and they employ a polarizable interaction potential, which was parameterized from first-principles calculations only. The diffusion coefficients were also determined from the simulations, which allowed us to understand the mechanisms responsible for the variations of electrical conductivity with temperature and composition of the melt.