INPHARMA-Based Determination of Ligand Binding Modes at α1-Adrenergic Receptors Explains the Molecular Basis of Subtype Selectivity

The structural poses of ligands that bind weakly to protein receptors are challenging to define. In this work we have studied ligand interactions with the adrenoreceptor (AR) subtypes, α_1A-AR and α_1B-AR, which belong to the G protein-coupled receptor (GPCR) superfamily, by employing the solution-based ligand-observed NMR method interligand NOEs for pharmacophore mapping (INPHARMA). A lack of receptor crystal structures and of subtype-selective drugs has hindered the definition of the physiological roles of each subtype and limited drug development. We determined the binding pose of the weakly binding α_1A-AR-selective agonist A-61603 relative to an endogenous agonist, epinephrine, at both α_1A-AR and α_1B-AR. The NMR experimental data were quantitatively compared, by using SpINPHARMA, to the back-calculated spectra based on ligand poses obtained from all-atom molecular dynamics simulations. The results helped mechanistically explain the selectivity of (R)-A-61603 towards α_1A-AR, thus demonstrating an approach for targeting subtype selectivity in ARs.     

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.     

Molecular Simulations and Drug Discovery of Adenosine Receptors

G protein-coupled receptors (GPCRs) represent the largest family of human membrane proteins. Four subtypes of adenosine receptors (ARs), the A₁AR, A_2AAR, A_2BAR and A₃AR, each with a unique pharmacological profile and distribution within the tissues in the human body, mediate many physiological functions and serve as critical drug targets for treating numerous human diseases including cancer, neuropathic pain, cardiac ischemia, stroke and diabetes. The A₁AR and A₃AR preferentially couple to the G_i/o proteins, while the A_2AAR and A_2BAR prefer coupling to the G_s proteins. Adenosine receptors were the first subclass of GPCRs that had experimental structures determined in complex with distinct G proteins. Here, we will review recent studies in molecular simulations and computer-aided drug discovery of the adenosine receptors and also highlight their future research opportunities.     

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.     

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.     

A Combination of Spin Diffusion Methods for the Determination of Protein–Ligand Complex Structural Ensembles

Structure‐based drug design (SBDD) is a powerful and widely used approach to optimize affinity of drug candidates. With the recently introduced INPHARMA method, the binding mode of small molecules to their protein target can be characterized even if no spectroscopic information about the protein is known. Here, we show that the combination of the spin‐diffusion‐based NMR methods INPHARMA, trNOE, and STD results in an accurate scoring function for docking modes and therefore determination of protein–ligand complex structures. Applications are shown on the model system protein kinase A and the drug targets glycogen phosphorylase and soluble epoxide hydrolase (sEH). Multiplexing of several ligands improves the reliability of the scoring function further. The new score allows in the case of sEH detecting two binding modes of the ligand in its binding site, which was corroborated by X‐ray analysis.     

Molecular dynamics of 5-HT1A and 5-HT2A serotonin receptors with methylated buspirone analogues

In the present study experimentally determined ligand selectivity of three methylated buspirone analogues (denoted as MM2, MM5 and P55) towards 5-HT_1A and 5-HT_2A serotonin receptors was theoretically investigated on a molecular level. The relationships between the ligand structure and 5-HT_1A and 5-HT_2A receptor affinities were studied and the results were found to be in agreement with the available site-directed mutagenesis and binding affinity data. Molecular dynamics (MD) simulations of ligand-receptor complexes were performed for each investigated analogue, docked twice into the central cavity of 5-HT_1A/5-HT_2A, each time in a different orientation. Present results were compared with our previous theoretical results, obtained for buspirone and its non-methylated analogues. It was found that due to the presence of the methyl group in the piperazine ring the ligand position alters and the structure of the ligand-receptor complex is modified. Further, the positions of derivatives with pyrimidinyl aromatic moiety and quinolinyl moiety are significantly different at the 5-HT_2A receptor. Thus, methylation of such derivatives alters the 3D structures of ligand-receptor complexes in different ways. The ligand-induced changes of the receptor structures were also analysed. The obtained results suggest, that helical domains of both receptors have different dynamical behaviour. Moreover, both location and topography of putative binding sites for buspirone analogues are different at 5-HT_1A and 5-HT_2A receptors.     

Mechanistic Studies on the Stereoselectivity of the Serotonin 5‐HT1A Receptor

G‐protein‐coupled receptors (GPCRs) are involved in a wide range of physiological processes, and they have attracted considerable attention as important targets for developing new medicines. A central and largely unresolved question in drug discovery, which is especially relevant to GPCRs, concerns ligand selectivity: Why do certain molecules act as activators (agonists) whereas others, with nearly identical structures, act as blockers (antagonists) of GPCRs? To address this question, we employed all‐atom, long‐timescale molecular dynamics simulations to investigate how two diastereomers (epimers) of dihydrofuroaporphine bind to the serotonin 5‐HT_1A receptor and exert opposite effects. By using molecular interaction fingerprints, we discovered that the agonist could mobilize nearby amino acid residues to act as molecular switches for the formation of a continuous water channel. In contrast, the antagonist epimer remained firmly stabilized in the binding pocket.     

Snooker: a structure-based pharmacophore generation tool applied to class A GPCRs

G-protein coupled receptors (GPCRs) are important drug targets for various diseases and of major interest to pharmaceutical companies. The function of individual members of this protein family can be modulated by the binding of small molecules at the extracellular side of the structurally conserved transmembrane (TM) domain. Here, we present Snooker, a structure-based approach to generate pharmacophore hypotheses for compounds binding to this extracellular side of the TM domain. Snooker does not require knowledge of ligands, is therefore suitable for apo-proteins, and can be applied to all receptors of the GPCR protein family. The method comprises the construction of a homology model of the TM domains and prioritization of residues on the probability of being ligand binding. Subsequently, protein properties are converted to ligand space, and pharmacophore features are generated at positions where protein ligand interactions are likely. Using this semiautomated knowledge-driven bioinformatics approach we have created pharmacophore hypotheses for 15 different GPCRs from several different subfamilies. For the beta-2-adrenergic receptor we show that ligand poses predicted by Snooker pharmacophore hypotheses reproduce literature supported binding modes for ～75% of compounds fulfilling pharmacophore constraints. All 15 pharmacophore hypotheses represent interactions with essential residues for ligand binding as observed in mutagenesis experiments and compound selections based on these hypotheses are shown to be target specific. For 8 out of 15 targets enrichment factors above 10-fold are observed in the top 0.5% ranked compounds in a virtual screen. Additionally, prospectively predicted ligand binding poses in the human dopamine D3 receptor based on Snooker pharmacophores were ranked among the best models in the community wide GPCR dock 2010.     

Peptide Modifications Differentially Alter G Protein‐Coupled Receptor Internalization and Signaling Bias

Although G protein‐coupled receptors (GPCRs) are targeted by more clinically used drugs than any other type of protein, their ligand development is particularly challenging. Humans have four neuropeptide Y receptors: hY₁R and hY₅R are orexigenic, while hY₂R and hY₄R are anorexigenic, and represent important anti‐obesity drug targets. We show for the first time that PEGylation and lipidation, chemical modifications that prolong the plasma half‐lives of peptides, confer additional benefits. Both modifications enhance pancreatic polypeptide preference for hY₂R/hY₄R over hY₁R/hY₅R. Lipidation biases the ligand towards arrestin recruitment and internalization, whereas PEGylation confers the opposite bias. These effects were independent of the cell system and modified residue. We thus provide novel insights into the mode of action of peptide modifications and open innovative venues for generating peptide agonists with extended therapeutic potential.     

EPR-Untersuchungen am Kupfer(II)-Chelat einesα-Cyano-β-amino-dithioacrylsäureesters

EPR Investigations on a Copper Chelate of anα-Cyano-β-amino-dithioacryl Acid Ester EPR studies on copper(II) chelates of anα-cyano-β-amino-dithioacryl acid ester are reported. The EPR spectra were obtained from solutions, diamagnetically diluted powders, and single-crystals which are stable for a short time only. The corresponding nickel(II) chelate was used as host lattice. The ¹⁴N ligand hyperfine structure observed in the spectra is in agreement with a [CuN₂S₂] coordination sphere. In some orientations of the recorded angular dependencies the EPR spectra show a hyperfine splitting due to the interaction of the unpaired electron with the N? H protons. In addition spin flip satellite lines are observed in the single-crystal spectra. The g, A^Cu and A^N tensors obtained from the powder and single-crystal spectra have an axial symmetry within the experimental errors. The unpaired electron occupies a MO which consists mainly of the copper 3d_xy and the corresponding donor atom orbitals. The co-valency of the metal ligand bond is very high.     

Improvement of anti-inflammatory and anticancer activities of poly(lactic-co-glycolic acid)-sulfasalazine microparticle via density functional theory,molecular docking and ADMET analysis

In the present study, we assessed improvement of anti-inflammatory activity and drug delivery of sulfasalazine (SSZ) by the poly(lactic-co-glycolic acid), (PLGA), in H₂O and dichloromethane (DCM) environments via density functional theory (DFT), ADMET, and molecular docking. Our calculated results based on binding energy and thermodynamic parameter represents that the interaction between SSZ and PLGA in Complex A via double hydrogen bonds is stronger in comparison with Complex B. The analysis of Ultraviolet–visible (UV–VIS) spectra proved the interaction of SSZ with PLGA by time-dependent density functional theory (TDDFT). Infrared (IR) spectra demonstrated that the structure of PLGA was shifted in the presence of the SSZ. The interaction of SSZ with PLGA leads to an increase in dipole moment and higher solubility with more negative Gibbs free solvation energy (ΔG_solv) values and lowering of the energy gap (E_g). The obtained results by Molecular docking demonstrates that the interaction of SSZ via its carboxylate group with PLGA (complex A) had a strong interaction towards the binding pocket of the target and as a potential inhibitor of the COX-2, TNF-α, and IL-1 receptors at the binding site as compared with the complex B.     

Peripheral Templation‐Modulated Interconversion between an A4L6 Tetrahedral Anion Cage and A2L3 Triple Helicate with Guest Capture/Release

An anion‐coordination‐based A₄L₆ (“A” denotes anion and “L” is ligand) tetrahedral cage was constructed by a C₂‐symmetric bis‐bis(urea) ligand and phosphate anion, which showed reversible interconversion with the A₂L₃ triple helicate as a response to the template, concentration, or solvent. Notably, an unusual “peripheral” templation was found to be critical to stabilize the tetrahedral structure. This peripheral effect was utilized to assemble an “empty” A₄L₆ cage that allows the multi‐stimuli‐controlled capture/release of biologically important species such as choline and acetylcholine.     

Effect of S–Se Bioisosteric Exchange on Affinity and Intrinsic Efficacy of Novel N-acylhydrazone Derivatives at the Adenosine A2A Receptor

In this work, we evaluated the conformational effect promoted by the isosteric exchange of sulfur by selenium in the heteroaromatic ring of new N-acylhydrazone (NAH) derivatives (3–8, 13, 14), analogues of the cardioactive compounds LASSBio-294 (1) and LASSBio-785 (2). NMR spectra analysis demonstrated a chemical shift variation of the iminic Csp² of NAH S/Se-isosters, suggesting a stronger intramolecular chalcogen interaction for Se-derivatives. To investigate the pharmacological profile of these compounds at the adenosine A_2A receptor (A_2AR), we performed a previously validated functional binding assay. As expected for bioisosteres, the isosteric-S/Se replacement affected neither the affinity nor the intrinsic efficacy of our NAH derivatives (1–8). However, the N-methylated compounds (2, 6–8) presented a weak partial agonist profile at A_2AR, contrary to the non-methylated counterparts (1, 3–5), which appeared as weak inverse agonists. Additionally, retroisosterism between aromatic rings of NAH on S/Se-isosters mimicked the effect of the N-methylation on intrinsic efficacy at A_2AR, while meta-substitution in the phenyl ring of the acyl moiety did not. This study showed that the conformational effect of NAH-N-methylation and aromatic rings retroisosterism changed the intrinsic efficacy on A_2AR, indicating the S/Se-chalcogen effect to drive the conformational behavior of this series of NAH.     

From Planar Toward Tetrahedral Copper(Il) Complexes: Structural and Electron Paramagnetic Resonance Studies of Substituent Steric Effects in an Extended Class of Pyrrolate-Imine Ligands

A series (1a-1h) of crystalline bis-pyrrolate-imine copper(II) complexes was isolated in good yield (typically 60-90%) by reaction of the Schiff base 2-N-(R)-pyrrolecarbaldimine (where R is an alkyl group of variable steric capacity) with a copper(II) salt and base in methanol or water. For new complexes 1f-1h, pyrrolate-imine coordination is inferred by loss of ν(N-H) and a shift (ca. 40 cm^?1) to lower energy for ν(C=N) in the infrared spectra relative to free Schiff base. The X-ray crystal structures of 1f, where R = benzyl, and 1g, where R = diphenylmethyl, show trans geometry of the pyrrolate-imine moieties around Cu(II). The distortion from planarity of the CuN₄ coordination sphere, defined as the dihedral angle between the two chelating N(imine)-Cu-N(pyrrolate) planes, is 33.13(5)° for 1f and 29.3° for 1g. X-band electron paramagnetic resonance (EPR) spectra for 1a-1h in glassy solutions (ca. 100 K) are approximately axial, with an inverse correlation between A _z and g _z . At room temperature in fluid solution there is an inverse correlation between A _iso and g _iso. Plots of A _z , A _iso, g _z , or g _iso as a function of the dihedral angles between the ligand planes in 1f and 1g, as well as the previously characterized 1a (R = H) and 1d (R = tert-butyl) were used to determine the dihedral angles of the four complexes of unknown geometry. A red-shift in the ligand field bands in the electronic absorption spectra in chloroform also correlates with increasing dihedral angle. For each of these correlations, the data point for the diphenylmethyl derivative 1g deviates slightly from the line based on the other complexes; this is attributed to crystal packing forces causing a smaller dihedral angle for 1g in the crystal than in solution.     

A homology-based model of the human 5-HT2A receptor derived from an in silico activated G-protein coupled receptor

A homology-based model of the 5-HT_2A receptor was produced utilizing an activated form of the bovine rhodopsin (Rh) crystal structure [1,2]. In silico activation of the Rh structure was accomplished by isomerization of the 11-cis-retinal (1) chromophore, followed by constrained molecular dynamics to relax the resultant high energy structure. The activated form of Rh was then used as a structural template for development of a human 5-HT_2A receptor model. Both the 5-HT_2A receptor and Rh are members of the G-protein coupled receptor (GPCR) super-family. The resulting homology model of the receptor was then used for docking studies of compounds representing a cross-section of structural classes that activate the 5-HT_2A receptor, including ergolines, tryptamines, and amphetamines. The ligand/receptor complexes that ensued were refined and the final binding orientations were observed to be compatible with much of the data acquired through both diversified ligand design and site directed mutagenesis.     

A copper(I) phosphine complex with 5,7-dinitro-2-methylquinolin-8-ol as co-ligand

5,7-Dinitro-2-methylquinolin-8-ol has been synthesized, and its copper(I) complex has been prepared. Both the free 2-MequinNO₂ ligand and its complex were characterized by IR, NMR, and UV–Vis spectra. The structure of the [Cu(2-MequinNO₂)(PPh₃)₂] complex has been determined by single-crystal X-ray analysis. The free 2-MequinNO₂ ligand reveals luminescence in contrast to the complex. For 2-MequinNO₂, the quantum yield, lifetime of the excited state, and the rate constants of both radiative and non-radiative decay have been determined. The lack of luminescence for the complex has been explained with the use of a quantum chemical study.     

A five-coordinate copper(II) perchlorate complex with tris(N-methylbenzimidazol-2-ylmethyl)amine and salicylate

A five-coordinate copper(II) complex with the tripod ligand tris(N-methylbenzimidazol-2-ylmethyl)amine (Mentb) and salicylate, with the composition [Cu(Mentb) (salicylate)](ClO₄) · 2DMF, was synthesized and characterized by elemental and thermal analyses, electrical conductivity, IR and UV-Vis spectral measurements. The crystal structure of the complex has been determined by single-crystal X-ray diffraction. The Cu(II) is five-coordinate with four N atoms from the Mentb ligand and an O atom of the monodentate salicylate ligand. The N₄O donors are in a distorted trigonal-bipyramid geometry. Cyclic voltammograms indicate a quasireversible Cu²⁺/Cu⁺ couple. The X-band EPR spectrum of the complex confirms the trigonal-bipyramidal structure with g_∥ < g _⊥ and a very small value of A_∥ (41 × 10^?4 cm^?1).     

A novel complex of copper(II) derived from symmetric five-dentate ligand: Synthesis,crystal structure,and characterization

A symmetric five-dentate Schiff-base ligand N,N-bis(pyridine-2-carboxaldehyde)diethylenetriamine (L) was prepared. An unusual copper(II) complex [CuCl₂ (L)] · H₂O was obtained, when copper chloride reacted with ligand L. In the course of the coordination reaction, a ring closure reaction happens to ligand L. So, the formation process of the complex can be used for reference to synthesize the ring compound. The complex has been characterized fully by elemental analysis, IR, absorption spectra, emission spectra, and single-crystal X-ray diffraction analysis. Moreover, a reasonable reaction mechanism for forming the complex was presumed. The complex was synthesized by treating an ethanolic solution of the appropriate ligand with an equimolar amount of metallic salt. In the complex, the copper atom is five-coordinated, which can be best described as a distorted square-pyramidal geometry with a N₃Cl₂ donor set, and two parallel one-dimensional chains are formed by packing of the complex.     

Ligand-, structure- and pharmacophore-based molecular fingerprints: a case study on adenosine A1, A2A, A2B, and A3 receptor antagonists

FLAP fingerprints are applied in the ligand-, structure- and pharmacophore-based mode in a case study on antagonists of all four adenosine receptor (AR) subtypes. Structurally diverse antagonist collections with respect to the different ARs were constructed by including binding data to human species only. FLAP models well discriminate ??active?? (=highly potent) from ??inactive?? (=weakly potent) AR antagonists, as indicated by enrichment curves, numbers of false positives, and AUC values. For all FLAP modes, model predictivity slightly decreases as follows: A_2BR?>?A_2AR?>?A₃R?>?A₁R antagonists. General performance of FLAP modes in this study is: ligand-?>?structure-?>?pharmacophore- based mode. We also compared the FLAP performance with other common ligand- and structure-based fingerprints. Concerning the ligand-based mode, FLAP model performance is superior to ECFP4 and ROCS for all AR subtypes. Although focusing on the early first part of the A_2A, A_2B and A₃ enrichment curves, ECFP4 and ROCS still retain a satisfactory retrieval of actives. FLAP is also superior when comparing the structure-based mode with PLANTS and GOLD. In this study we applied for the first time the novel FLAPPharm tool for pharmacophore generation. Pharmacophore hypotheses, generated with this tool, convincingly match with formerly published data. Finally, we could demonstrate the capability of FLAP models to uncover selectivity aspects although single AR subtype models were not trained for this purpose.