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.     

Internal Dynamics in Halogen‐Bonded Adducts: A Rotational Study of Chlorotrifluoromethane–Formaldehyde

The rotational spectra of two isotopologues of the 1:1 complex between chlorotrifluoromethane and formaldehyde have been recorded and analyzed by using Fourier‐transform microwave spectroscopy. Only one rotamer was detected, with the two constituent molecules held together through a Cl???O halogen bond (R_Cl???O=3.048 Å). The dimer displays two simultaneous large‐amplitude intramolecular motions. The internal rotation of formaldehyde around its symmetry axis (V₂=28(5) cm^?1) splits all the rotational transitions into two component lines with a relative intensity ratio of 1:3. On the other hand, the almost free internal rotation (V₃≈2.5 cm^?1) of the CF₃ symmetric top increases the “rigid” value of the rotational constant A by almost one order of magnitude. In addition, all the transitions display a hyperfine structure due to the ³⁵Cl (or ³⁷Cl) nucleus quadrupole effects.     

A generic rotamer model to explain the temperature dependence of BSA protein fluorescence

Protein fluorescence signals essential information about the conformational dynamics of proteins. Different types of intrinsic fluorophores reflect different protein local or global structural changes. Bovine Serum Albumin (BSA) is a transport protein that contains two intrinsic fluorophores: Tryptophan134 (Trp134) and Tryptophan213 (Trp213). This protein displays an interesting temperature dependence of the tryptophan fluorescence. However, the molecular mechanism of the temperature dependence is still unclear. In this work, we propose a generic rotamer model to explain this phenomenon. The model assumes the presence of rotamer-specific fluorescence lifetimes. The fluorescence temperature dependence is caused by the population shifts between different rotamers due to thermal effects. As a proof of concept, we show that the tryptophan's two fluorescence lifetimes (𝜏₁ = 0.4–0.5 ns and 𝜏₂ = 2-4 ns) are sufficient to qualitatively explain the fluorescence intensity change at different temperatures, both in buffer solution (water) and in the protein. To computationally verify our rotamer hypothesis, we use an all-atom molecular dynamics simulation to study the effects of temperature on the two tryptophans' rotamer dynamics. The simulations show that Trp134 is more sensitive to temperature, consistent with experimental observations. Overall, the results support that the temperature dependence of fluorescence in the protein BSA is due to local conformational changes at the residue level. This work sheds light on the relationship between tryptophan's rotamer dynamics and its ability to fluorescence.     

Could the presence of sodium ion influence the accuracy and precision of the ligand-posing in the human A<Subscript>2A</Subscript> adenosine receptor orthosteric binding site using a molecular docking approach? Insights from <Emphasis Type="Italic">Dockbench</Emphasis>

The allosteric modulation of G protein-coupled receptors (GPCRs) by sodium ions has received considerable attention as crystal structures of several receptors, in their inactive conformation, show a Na⁺ ion bound to specific residues which, in the human A_2A adenosine receptor (hA_2A AR), are Ser91^3.39, Trp246^6.48, Asn280^7.45, and Asn284^7.49. A cluster of water molecules completes the coordination of the sodium ion in the putative allosteric site. It is absolutely consolidated that the progress made in the field of GPCRs structural determination has increased the adoption of docking-driven approaches for the identification or the optimization of novel potent and selective ligands. Despite the extensive use of docking protocols in virtual screening approaches, to date, almost any of these studies have been carried out without taking into account the presence of the sodium cation and its first solvation shell in the putative allosteric binding site. In this study, we have focused our attention on determining how the presence of sodium ion binding and additionally its first hydration sphere, in hA_2AAR could influence the ligand positioning accuracy during molecular docking simulations for most of the available resting and activated hA_2A AR crystal structures, using DockBench as a comparative benchmarking tool and implementing a new correlation coefficient (EM). This work provides indications on the evidence that the posing performance (accuracy and/or precision) of the docking protocols in reproducing the crystallographic poses of different hA_2A AR antagonists is generally increased in the presence of the sodium cation and its first solvation shell, in agreement with experimental observations. Consequently, the inclusion of sodium ion and its first solvation shell should be considered in order to facilitate the selection of new potential ligands in all molecular docking-based virtual screening protocols that aim to find novel GPCRs antagonists and inverse agonists.     

A combined spectroscopic and theoretical study of a series of conformationally restricted hexapeptides carrying a rigid binaphthyl-nitroxide donor-acceptor pair

The structural features of a series of linear hexapeptides of general formula Boc‐B‐A_r‐T‐A_m‐OtBu, where A is L ‐Ala or Aib (α‐aminoisobutyric acid), B is (R)‐Bin, a binaphthyl‐based C^α,α‐disubstituted Gly residue, T is Toac, a nitroxide spin‐labeled C^α,α‐disubstituted Gly, and r+m=4, were investigated in methanol solution by fluorescence, transient absorption, IR and CD spectroscopic studies, and by molecular mechanics calculations. These peptides are denoted as B‐T/r‐m, to emphasize the different position of Toac with respect to that of the Bin fluorophore in the amino acid sequence. The rigidity of the B‐T donor–acceptor pair and of the Aib‐rich backbone allowed us to investigate the influence of the interchromophoric distance and orientation on the photophysics of the peptides examined. The excited state relaxation processes of binaphthyl were investigated by time‐resolved fluorescence and transient absorption experiments. Dynamic quenching of the excited singlet state of binaphthyl by Toac was successfully interpreted by the Förster energy transfer model, provided that the mutual orientation of the chromophores is taken into account. This implies that interconversion among conformational substates, which involves puckering of the Toac piperidine ring, is slow on the time scale of the transfer process, that is slower than 5 ns. By comparison of the experimental and theoretical data, the type of secondary structure (right‐handed 3₁₀ helix) from the B‐T/r‐m peptides in solution was determined; this would not have been achievable by using the CD and NMR data only, as the data are not diagnostic in this case. Static quenching was observed in all peptides examined but B‐T/1‐3, where the effect can be ascribed to a non‐fluorescent complex. Among the computed low‐energy conformers of these peptides, there is one structure exhibiting a NO ^. –naphthalene center‐to‐center distance <6 Å, which might be assigned to this complex. The overall results emphasize the versatility of fluorescence experiments in 3D‐structural studies in solution.     

The Molecular Mechanism of P2Y1 Receptor Activation

Human purinergic G protein‐coupled receptor P2Y₁ (P2Y₁R) is activated by adenosine 5′‐diphosphate (ADP) to induce platelet activation and thereby serves as an important antithrombotic drug target. Crystal structures of P2Y₁R revealed that one ligand (MRS2500) binds to the extracellular vestibule of this GPCR, whereas another (BPTU) occupies the surface between transmembrane (TM) helices TM2 and TM3. We introduced a total of 20 μs all‐atom long‐timescale molecular dynamic (MD) simulations to inquire why two molecules in completely different locations both serve as antagonists while ADP activates the receptor. Our results indicate that BPTU acts as an antagonist by stabilizing extracellular helix bundles leading to an increase of the lipid order, whereas MRS2500 blocks signaling by occupying the ligand binding site. Both antagonists stabilize an ionic lock within the receptor. However, binding of ADP breaks this ionic lock, forming a continuous water channel that leads to P2Y₁R activation.     

Assessment of structurally and functionally high-risk nsSNPs impacts on human bone morphogenetic protein receptor type IA (BMPR1A) by computational approach

BMPR1A (BMP type 1 receptor) is a transmembrane cell-surface receptor also known as ALK3 (activin-like kinases-3) encodes for a type I serine/threonine kinase receptor and a member of the transforming growth-factor β–receptor (TGF-β) super family. The BMPR1A has a significant interaction with BMP-2 for protein activity and also has a low affinity with growth and differentiation factor 5 (GDF5); positively regulates chondrocyte differentiation. The genetic variations can alter the structure and function of the BMPR1A gene that causes several diseases such as juvenile polyposis syndrome or hereditary cancer-predisposing syndrome. The current study was carried out to identify potential deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in BMPR1A by implementing different computational algorithms such as SIFT, PolyPhen2, SNAP2, PROVEAN, PhD-SNP, SNPs&GO, nsSNPAnalyzer, and P-Mut. From 205 nsSNPs in BMPR1A, 7 nsSNPs (C76Y, C124R, C124Y, C376Y, R443C, R480W, and W487R) were predicted as deleterious in 8 prediction algorithms. The Consurf analysis showed that selected 7 nsSNPs were present in the highly conserved regions. Molecular dynamics simulation analysis also performed to explore conformational changes in the variant structure with respect to its native structure. According to the MDS result, all variants flexibility and rigidity were unbalanced, which may alter the structural and functional behavior of the native protein. Although, three nsSNPs i.e., C124R, C376Y, and R443C have already been reported in patients associated with JPS, but their structural and functional molecular studies remain uncharacterized. Therefore, the findings of this study can provide a better understanding of uncharacterized nsSNPS and to find their association with disease susceptibility and also facilitate to the researchers for designing or developing the target dependent drugs.     

Conformational dynamics of the nicotinic acetylcholine receptor channel: a 35-ns molecular dynamics simulation study

The nicotinic acetylcholine receptor (AChR) is the paradigm of ligand-gated ion channels, integral membrane proteins that mediate fast intercellular communication in response to neurotransmitters. A 35-ns molecular dynamics simulation has been performed to explore the conformational dynamics of the entire membrane-spanning region, including the ion channel pore of the AChR. In the simulation, the 20 transmembrane (TM) segments that comprise the whole TM domain of the receptor were inserted into a large dipalmitoylphosphatidylcholine (DPPC) bilayer. The dynamic behavior of individual TM segments and their corresponding AChR subunit helix bundles was examined in order to assess the contribution of each to the conformational transitions of the whole channel. Asymmetrical and asynchronous motions of the M1-M3 TM segments of each subunit were revealed. In addition, the outermost ring of five M4 TM helices was found to convey the effects exerted by the lipid molecules to the central channel domain. Remarkably, a closed-to-open conformational shift was found to occur in one of the channel ring positions in the time scale of the present simulations, the possible physiological significance of which is discussed.     

Modelling and mutation studies on the histamine H1-receptor agonist binding site reveal different binding modes for H1-agonists: Asp116 (TM3) has a constitutive role in receptor stimulation

Summary A modelling study has been carried out, investigating the binding of histamine (Hist), 2-methylhistamine (2-MeHist) and 2-phenylhistamine (2-PhHist) at two postulated agonistic binding sites on transmembrane domain 5 (TM5) of the histamine H₁-receptor. For this purpose a conformational analysis study was performed on three particular residues of TM5, i.e., Lys²⁰⁰, Thr²⁰³ and Asn²⁰⁷, for which a functional role in binding has been proposed. The most favourable results were obtained for the interaction between Hist and the Lys²⁰⁰/Asn²⁰⁷ pair. Therefore, Lys²⁰⁰ was subsequently mutated and converted to an alanine, resulting in a 50-fold decrease of H₁-receptor stimulation by histamine. Altogether, the data suggest that the Lys²⁰⁰/Asn²⁰⁷ pair is important for activation of the H₁-receptor by histamine. In contrast, analogues of 2-PhHist seem to belong to a distinct subclass of histamine agonists and an alternative mode of binding is proposed in which the 2-phenyl ring binds to the same receptor location as one of the aromatic rings of classical histamine H₁-antagonists. Subsequently, the binding modes of the agonists Hist, 2-MeHist and 2-PhHist and the H₁-antagonist cyproheptadine were evaluated in three different seven--helical models of the H₁-receptor built in homology with bacteriorhodopsin, but using three different alignments. Our findings suggest that the position of the carboxylate group of Asp¹¹⁶ (TM3) within the receptor pocket depends on whether an agonist or an antagonist binds to the protein; a conformational change of this aspartate residue upon agonist binding is expected to play an essential role in receptor stimulation.Abbreviations 2-MeHist 2-methylhistamine - 2-PEA 2-pyridyl-ethylamine - 2-PhHist 2-phenylhistamine - CHO Chinese hamster ovary - E_int interaction energy - E_str strain energy - GES global energy structure - gpH₁R guinea pig H₁-receptor - GPCR G-protein coupled receptor - Hist histamine - N proximal nitrogen - N tele nitrogen - TM transmembrane domain - WT wild type     

ONIOM and FMO‐EDA study of metabotropic glutamate receptor 1: Quantum insights into the allosteric binding site

The crystal structure of metabotropic glutamate receptor 1 (mGluR1) complexed with 4‐fluoro‐N‐(4‐(6‐(isopropylamino)pyrimidin‐4‐yl)thiazol‐2‐yl)‐N‐methylbenzamide (FITM, a negative allosteric modulator) and its twelve close structural analogs with a broad spectrum of affinities (2.4 nM < IC₅₀ > 10 000 nM) were investigated using quantum mechanical methods. The our own N‐layered integrated molecular orbital and molecular mechanics (ONIOM) was used to optimize the molecular geometries of the receptor with complexed ligands, which were then used to perform the ab initio calculations using the fragment molecular orbitals method with energy decomposition analysis (FMO‐EDA). The results clearly showed that residues Q660^3.28 and/or Y805^6.55 were the anchoring points for all the studied analogs of FITM, while the H‐bond with T815^7.38 determined only the orientation of very active molecules containing an amino substituent in the pyrimidine moiety (e.g., FITM). The orientation of the other parts of ligands resulted from hydrophobic interactions mainly with L757^5.44, F801^6.51, or W798^6.48. The applied ONIOM/FMO–EDA approach facilitated the study of effects related to very small changes in the ligand structure and led to conclusions regarding the significance of individual interactions in the allosteric binding pocket of mGluR1.     

In search of novel ligands using a structure-based approach: a case study on the adenosine A<Subscript>2A</Subscript> receptor

In this work, we present a case study to explore the challenges associated with finding novel molecules for a receptor that has been studied in depth and has a wealth of chemical information available. Specifically, we apply a previously described protocol that incorporates explicit water molecules in the ligand binding site to prospectively screen over 2.5 million drug-like and lead-like compounds from the commercially available eMolecules database in search of novel binders to the adenosine A_2A receptor (A_2AAR). A total of seventy-one compounds were selected for purchase and biochemical assaying based on high ligand efficiency and high novelty (Tanimoto coefficient ≤0.25 to any A_2AAR tested compound). These molecules were then tested for their affinity to the adenosine A_2A receptor in a radioligand binding assay. We identified two hits that fulfilled the criterion of ~50 % radioligand displacement at a concentration of 10 μM. Next we selected an additional eight novel molecules that were predicted to make a bidentate interaction with Asn253^6.55, a key interacting residue in the binding pocket of the A_2AAR. None of these eight molecules were found to be active. Based on these results we discuss the advantages of structure-based methods and the challenges associated with finding chemically novel molecules for well-explored targets.     

Computational Methods for Understanding the Selectivity and Signal Transduction Mechanism of Aminomethyl Tetrahydronaphthalene to Opioid Receptors

Opioid receptors are members of the group of G protein-couple receptors, which have been proven to be effective targets for treating severe pain. The interactions between the opioid receptors and corresponding ligands and the receptor’s activation by different agonists have been among the most important fields in opioid research. In this study, with compound M1, an active metabolite of tramadol, as the clue compound, several aminomethyl tetrahydronaphthalenes were designed, synthesized and assayed upon opioid receptors. With the resultant compounds FW-AII-OH-1 (Ki = 141.2 nM for the κ opioid receptor), FW-AII-OH-2 (Ki = 4.64 nM for the δ opioid receptor), FW-DI-OH-2 (Ki = 8.65 nM for the δ opioid receptor) and FW-DIII-OH-2 (Ki = 228.45 nM for the δ opioid receptor) as probe molecules, the structural determinants responsible for the subtype selectivity and activation mechanisms were further investigated by molecular modeling and molecular dynamics simulations. It was shown that Y^7.43 was a key residue in determining the selectivity of the three opioid receptors, and W^6.58 was essential for the selectivity of the δ opioid receptor. A detailed stepwise discovered agonist-induced signal transduction mechanism of three opioid receptors by aminomethyl tetrahydronaphthalene compounds was proposed: the 3–7 lock between TM3 and TM7, the DRG lock between TM3 and TM6 and rearrangement of I^3.40, P^5.50 and F^6.44, which resulted in the cooperative movement in 7 TMs. Then, the structural relaxation left room for the binding of the G protein at the intracellular site, and finally the opioid receptors were activated.     

(Thermo)dynamic Role of Receptor Flexibility,Entropy, and Motional Correlation in Protein–Ligand Binding

The binding of 2‐amino‐5‐methylthiazole to the W191G cavity mutant of cytochrome c peroxidase is an ideal test case to investigate the entropic contribution to the binding free energy due to changes in receptor flexibility. The dynamic and thermodynamic role of receptor flexibility are studied by 50 ns‐long explicit‐solvent molecular dynamics simulations of three separate receptor ensembles: W191G binding a K⁺ ion, W191G–2a5mt complex with a closed 190–195 gating loop, and apo with an open loop. We employ a method recently proposed to estimate accurate absolute single‐molecule configurational entropies and their differences for systems undergoing conformational transitions. We find that receptor flexibility plays a generally underestimated role in protein–ligand binding (thermo)dynamics and that changes of receptor motional correlation determine such large entropy contributions.     

Intrakonfigurations‐, Trip‐Multiplett‐ sowie anomal polarisierte A1gund A2g‐Übergänge in elektronischen und vibratorischen Resonanz‐Raman‐Spektren von (spinentarteten) trans‐Di(cyano)phthalocyaninatorhenaten

Intraconfigurational, Trip‐Multiplet, and Anomalously Polarised A_1g and A_2g Transitions in Electronic and Vibrational Resonance Raman Spectra of (Spin‐Degenerate) trans ‐Di(cyano)phthalocyaninatorhenates Brown bis(tetra(n‐butyl)ammonium) trans‐di(cyano)phthalocyaninato(2‐)rhenate(II) ( 1 ) is prepared by melting bis(phthalocyaninato(2‐)rhenium(II)) with tetra(n‐butyl)ammonium cyanide. According to electrochemical data, 1 is oxidised by iodine to yield blue tetra(n‐butyl)ammonium trans‐di(cyano)phthalocyaninato(2‐)rhenate(III) ( 2 ), whose cation exchange in the presence of bis(triphenylphosphine)iminium salts has been confirmed by x‐ray structure determination. 1 and 2 dissolve without dissociation of the cyano ligands in conc. sulfuric acid. Dilution with cold water precipitates blue trans‐di(cyano)phthalocyaninato(2‐)rhenium(III) acid. 1 and 2 are oxidised by bromine yielding violet trans‐di(cyano)phthalocyaninato(1‐)rhenium(III). Oxidation of 2 with dibenzoylperoxide and N‐chlorsuccinimide is described. 1 and 2 are characterised by polarised resonance Raman(RR) spectra, FIR/MIR spectra, and UV‐Vis‐NIR spectra. Due to a Kramers degenerate ground electronic state of low‐spin Re^II, a polarisation anomaly of the totally symmetric vibrations a_1g at 598 and 672 cm^–1 with depolarisation ratios ρ_l > 3 is observed in the RR spectra of 1 . Weak bands in the unusual UV‐Vis‐NIR spectrum of 1 , starting at 10200 cm^–1, are attributed to trip‐multiplet (TM) transitions. An electronic RR effect is detected for 2 . The selectively enhanced anomalously polarised line at 1009 cm^–1 with ρ_l ≈ 15 and the (de)polarised lines between 1688 and 2229 cm^–1 are attributed to intraconfigurational transitions A_1g → A_2g > A_1g, B_1g, B_2g, E_g arising from the ³T_1g ground electronic state of low‐spin Re^III split by spin‐orbit coupling and low symmetry (D ). Some of their vibronic bands are detected in the IR spectrum between 1900 and 4000 cm^–1. B and Q transitions of 2 at 16700 and 31900 cm^–1, respectively, as well as eight weak TM transitions are observed between 5050 and 26100 cm^–1.     

GPCR A2A AR腺苷受体蛋白的激动剂结合及其诱导的蛋白活性开关构象变化

运用分子动力学模拟,研究了腺苷酸（激动剂）与A2AAR腺苷受体蛋白的相互作用和配体结合诱导的蛋白动力学变化．识别了与腺苷酸结合力强于0．5kcal／mol的关键基团：A63^2．61,I66^2．64,V84^3.32,L85^3.33,T88^3.36,F168^5.29,M177^5.38,L249^6.51,H250^6.52和N253^6.55,观察到腺苷酸没有与L167^5.28相互作用,这一结果支持了L167^5.28是抑制剂特异性结合位点,不与激动剂结合．未结合配体（激动剂或抑制剂）的单体A2AAR和腺苷酸结合后的A2AAR在构象上有三个不同功能性开关．腺苷酸结合可以诱导A2AAR腺苷受体蛋白的构象调整,使得三个功能性开关器件的构象与单体A2AAR不同．     

Comparison of three GPCR structural templates for modeling of the P2Y<Subscript>12</Subscript> nucleotide receptor

The P2Y₁₂ receptor (P2Y₁₂R) is an ADP-activated G protein-coupled receptor (GPCR) that is an important target for antithrombotic drugs. Three homology models of P2Y₁₂R were compared, based on different GPCR structural templates: bovine rhodopsin (bRHO), human A_2A adenosine receptor (A_2AAR), and human C-X-C chemokine receptor type 4 (CXCR4). By criteria of sequence analysis (25.6% identity in transmembrane region), deviation from helicity in the second transmembrane helix (TM2), docked poses of ligands highlighting the role of key residues, accessibility of a conserved disulfide bridge that is reactive toward irreversibly-binding antagonists, and the presence of a shared disulfide bridge between the third extracellular loop (EL3) and the N-terminus, the CXCR4-based model appeared to be the most consistent with known characteristics of P2Y₁₂R. The docked poses of agonist 2MeSADP and charged anthraquinone antagonist PSB-0739 in the binding pocket of P2Y₁₂R-CXC agree with previously published site-directed mutagenesis studies of Arg256 and Lys280. A sulfonate at position 2 of the anthraquinone core created a strong interaction with the Lys174(EL2) side chain. The docking poses of the irreversibly-binding, active metabolite (existing as two diastereoisomers in vivo) of the clinically utilized antagonist Clopidogrel were compared. The free thiol group of the 4S diastereoisomer, but not the 4R isomer, was found in close proximity (~4.7 Å) to the sulfur atom of a disulfide bridge involving Cys175, suggesting greater activity in covalent binding. Therefore, ligand docking to the CXCR4-based model of the P2Y₁₂R predicted poses of both reversibly and irreversibly-binding small molecules, consistent with observed pharmacology and mutagenesis studies.     

Cancer-Related Somatic Mutations in Transmembrane Helices Alter Adenosine A1 Receptor Pharmacology

Overexpression of the adenosine A₁ receptor (A₁AR) has been detected in various cancer cell lines. However, the role of A₁AR in tumor development is still unclear. Thirteen A₁AR mutations were identified in the Cancer Genome Atlas from cancer patient samples. We have investigated the pharmacology of the mutations located at the 7-transmembrane domain using a yeast system. Concentration–growth curves were obtained with the full agonist CPA and compared to the wild type hA₁AR. H78L^3.23 and S246T^6.47 showed increased constitutive activity, while only the constitutive activity of S246T^6.47 could be reduced to wild type levels by the inverse agonist DPCPX. Decreased constitutive activity was observed on five mutant receptors, among which A52V^2.47 and W188C^5.46 showed a diminished potency for CPA. Lastly, a complete loss of activation was observed in five mutant receptors. A selection of mutations was also investigated in a mammalian system, showing comparable effects on receptor activation as in the yeast system, except for residues pointing toward the membrane. Taken together, this study will enrich the view of the receptor structure and function of A₁AR, enlightening the consequences of these mutations in cancer. Ultimately, this may provide an opportunity for precision medicine for cancer patients with pathological phenotypes involving these mutations.     

Density functional theory study of a molecular allosteric switch for 2,2′‐bipyridyl‐3,3′‐15‐crown‐5

A classical model of “molecular machine,” which acts as an ON–OFF switch for 2,2′‐bipyridyl‐3,3′‐15‐crown‐5 ( L ), has been theoretically studied. It is highly important to understand the mechanism of this switch. The alkali‐metal cations (Na⁺ and K⁺) and W(CO)₄ fragment are introduced to coordinate with the different active sites of L , respectively. The density functional theory (DFT) method is used for understanding the stereochemical structural natures and thermodynamic properties of all the target molecules at B3LYP/6‐31G(d) and SDD (Stuttgart–Dresden) level, together with the corresponding effective core potential (ECP) for tungsten (W). The fully optimized geometries have been performed with real frequencies, which indicate the minima states. The nucleophilicity of L has been investigated by the Fukui functions. The natural bond orbital analysis is used to study the intermolecular charge‐transfer interactions and explore the origin of the internal forces of the molecular switch. In addition, the binding energies, enthalpies, Gibbs free energies, and the cation exchange energies have been studied for L , W(CO)₄ L , and their corresponding complexes. The properties of the complexes displayed by in presence or absence of the W(CO)₄ fragment are also analyzed. The calculated results of allosterism displayed by L are in a good agreement with the experimental results. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Infrared and Raman spectra, conformational stability, ab initio calculations and vibrational assignment for 1,2-pentadiene (ethyl allene)

The infrared (3500-50 cm⁻¹) and Raman (3500-20 cm⁻¹) spectra of 1,2-pentadiene, H₂C=C=C(H)CH₂CH₃ (ethyl allene), have been recorded for both the gaseous and solid states. Additionally, the Raman spectrum of the liquid has been obtained with qualitative depolarization values. In the fluid phases both the cis and gauche conformers have been identified, with the gauche rotamer being the predominant form although it may not be the conformer of lowest energy. In the solid state only the cis conformer remains after repeated annealing of the crystal. The asymmetric torsion of the cis conformer is observed as a series of Q-branch transitions beginning at 103.4 cm⁻¹ and falling to lower frequency. An estimate of the potential function governing conformer interconversion is provided. A complete assignment of the normal modes for the cis conformer is given and several of the fundamentals are assigned for the gauche rotamer. Ab initio electronic structure calculations of energies, conformational geometries, vibrational frequencies, and potential energy functions have been made to complement and assist the interpretation of the infrared and Raman spectra. In particular, the transitions among torsional energy levels for both the symmetric (methyl) and asymmetric (ethyl) motions have been calculated. The results are compared to the corresponding quantities for some similar molecules.     

A novel urea derivative anticonvulsant: In vivo biological evaluation,radioreceptor analysis of GABAA receptors and molecular docking studies of enantiomers

It has been experimentally established that the original new generation anticonvulsant Galodif, N-[(3-chlorophenyl)-(phenyl)methyl]urea, allosterically modulates GABA_A receptor (GABA_AR). Binding of [³H]flunitrazepam and [³H]Ro5-4864 to the benzodiazepine (BZD) site of GABA_AR in the brain of Galodif-treated rats showes an increase in receptor affinity in Scatchard Plot for Ligand Receptor binding analysis. The results of molecular docking (Schrödinger program Glide) reveal that the enantiomers of Galodif are complementary to the BZD binding site of GABA_AR; binding energy of R-Galodif is lower than that of S-Galodif (scoring GScore being –11.14 and –10.7 kcal mol^–1, respectively); R-Galodif interacts with key amino acids at the α1γ2 interface: Tyr159, Tyr209, H101 Phe77 with high model fit – dG of insert: 7.41.