Fluorescent CXCR4 chemokine receptor antagonists: metal activated binding

The copper(II) complex of a novel rhodamine-azamacrocycle conjugate binds to the CXCR4 chemokine receptor and competes effectively against anti-CXCR4 monoclonal antibodies. The copper macrocycle unit adopts a trans-II configuration in the solid state.     

Imaging agents for the chemokine receptor 4 (CXCR4)

The interaction between the chemokine receptor 4 (CXCR4) and stromal cell-derived factor-1 (SDF-1, also known as CXCL12) is a natural regulatory process in the human body. However, CXCR4 over-expression is also found in diseases such as cancer, where it plays a role in, among others, the metastatic spread. For this reason it is an interesting biomarker for the field of diagnostic oncology, and therefore, it is gaining increasing interest for applications in molecular imaging. Especially "small-molecule" imaging agents based on T140, FC131 and AMD3100 have been extensively studied. SDF-1, antibodies, pepducins and bioluminescence have also been used to visualize CXCR4. In this critical review reported CXCR4 targeting imaging agents are described based on their affinity, specificity and biodistribution. The level wherein CXCR4 is up-regulated in cancer patients and its relation to the different cell lines and animal models used to evaluate the efficacy of the imaging agents is also discussed (221 references).     

Peptide and peptidomimetic ligands for CXC chemokine receptor 4 (CXCR4)

The development of novel peptide and peptidomimetic ligands for the CXC chemokine receptor 4 (CXCR4) as therapeutic agents for HIV-1 infection, cancer, and immune system diseases has grown over the last decade. In this perspective article, the design of CXCR4 agonists and antagonists from endogenous stromal cell-derived factor-1 (SDF-1)/CXCL12 and horseshoe crab-derived antimicrobial peptides and their therapeutic and diagnostic applications are described.     

Direct interaction between an allosteric agonist pepducin and the chemokine receptor CXCR4

Cell surface heptahelical G protein-coupled receptors (GPCRs) mediate critical cellular signaling pathways and are important pharmaceutical drug targets. (1) In addition to traditional small-molecule approaches, lipopeptide-based GPCR-derived pepducins have emerged as a new class of pharmaceutical agents. (2, 3) To better understand how pepducins interact with targeted receptors, we developed a cell-based photo-cross-linking approach to study the interaction between the pepducin agonist ATI-2341 and its target receptor, chemokine C-X-C-type receptor 4 (CXCR4). A pepducin analogue, ATI-2766, formed a specific UV-light-dependent cross-link to CXCR4 and to mutants with truncations of the N-terminus, the known chemokine docking site. These results demonstrate that CXCR4 is the direct binding target of ATI-2341 and suggest a new mechanism for allosteric modulation of GPCR activity. Adaptation and application of our findings should prove useful in further understanding pepducin modulation of GPCRs as well as enable new experimental approaches to better understand GPCR signal transduction.     

Application of affinity selection-mass spectrometry assays to purification and affinity-based screening of the chemokine receptor CXCR4

Affinity selection-mass spectrometry (AS-MS) is a sensitive technology for identifying small molecules that bind to target proteins, and assays enabled by AS-MS can be used to delineate relative binding affinities of ligands for proteins. 'Indirect' AS-MS assays employ size-exclusion techniques to separate target-ligand complexes from unbound ligands, and target-associated ligands are then specifically detected by liquid chromatography mass spectrometry. We report how indirect AS-MS binding assays with known reference control compounds were used as guideposts for development of an optimized purification method for CXCR4, a G-protein coupled chemokine receptor, for which we sought novel antagonists. The CXCR4 purification method that was developed was amenable to scale-up and enabled the screening of purified recombinant human CXCR4 against a large combinatorial library of small molecules by high throughput indirect AS-MS. The screen resulted in the discovery of new ligands that competed off binding of reference compounds to CXCR4 in AS-MS binding assays and that antagonized SDF1α-triggered responses and CXCR4-mediated HIV1 viral uptake in cell-based assays. This report provides a methodological paradigm whereby indirect AS-MS-based ligand binding assays may be used to guide optimal integral membrane protein purification methods that enable downstream affinity selection-based applications such as high throughput AS-MS screens.     

CXCR4 chemokine receptor antagonists: nickel(ii) complexes of configurationally restricted macrocycles

Tetraazamacrocyclic complexes of transition metals provide useful units for incorporating multiple coordination interactions into a single protein binding molecule. They can be designed with available sites for protein interactions via donor atom-containing amino acid side chains or labile ligands, such as H(2)O, allowing facile exchange. Three configurationally restricted nickel(ii) cyclam complexes with either one or two macrocyclic rings were synthesised and their ability to abrogate the CXCR4 chemokine receptor signalling process was assessed (IC(50) = 8320, 194 and 14 nM). Analogues were characterised crystallographically to determine the geometric parameters of the acetate binding as a model for aspartate. The most active nickel(ii) compound was tested in several anti-HIV assays against representative viral strains showing highly potent EC(50) values down to 13 nM against CXCR4 using viruses, with no observed cytotoxicity (CC(50) > 125 μM).     

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand‐protein complexes and a cross‐docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in analysis of covalently bound ligands, using both a grid‐based docking method and a modification of the flexible sidechain technique. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Hybrid cavitand-resorcin[4]arene receptor for the selective binding of choline and related compounds in protic media

[structure: see text] A hybrid cavitand-resorcin[4]arene receptor capable of displaying pH-modulated binding affinity toward trimethylalkylammonium ions is proposed as an alternative to the low selectivity exhibited by other receptors used in supramolecular fluorescent sensor systems for choline.     

Structure flexibility of the Cu2ZnSnS4 absorber in low-cost photovoltaic cells: from the stoichiometric to the copper-poor compounds

Here we present for the very first time a single-crystal investigation of the Cu-poor Zn-rich derivative of Cu(2)ZnSnS(4). Nowadays, this composition is considered as the one that delivers the best photovoltaic performances in the specific domain of Cu(2)ZnSnS(4)-based thin-film solar cells. The existence of this nonstoichiometric phase is definitely demonstrated here in an explicit and unequivocal manner on the basis of powder and single-crystal X-ray diffraction analyses coupled with electron microprobe analyses. Crystals are tetragonal, space group I ?4, Z = 2, with a = 5.43440(15) ? and c = 10.8382(6) ? for Cu(2)ZnSnS(4) and a = 5.43006(5) ? and c = 10.8222(2) ? for Cu(1.71)Zn(1.18)Sn(0.99)S(4).     

Synthesis and dopamine receptor binding affinity of 4H-thiochromenoapomorphines

Abstract  The synthesis of 4H-thiochromene derivatives of apomorphines, a novel class of isoquinoline alkaloid-related compounds, has been achieved by different O-dealkylation methods applied on previously published heteroring-fused aporphinoids. Detailed DFT study has been presented regarding the mechanism of the L-selectride-mediated multiple O-dealkylation of a seven-ring aporphine analogue. Dopamine-binding tests confirmed the essential function of 11-hydroxy moiety of the aporphine skeleton and revealed a remarkable D₁ over D₂ specificity for the derivative having the 4H-thiochromene ring system attached to positions 2 and 3 of the aporphine backbone. Graphical Abstract  

Conformational flexibility of pyrimidine ring in adenine and related compounds

The structural non-rigidity of aromatic pyrimidine rings in adenine and selected related compounds has been investigated by quantum chemical non-empirical methods of calculation at the MP2 and DFT levels of theory. The results of the calculations demonstrate that the pyrimidine ring possesses a notable degree of conformational flexibility despite its aromatic character. The transition of the heterocycle from a planar equilibrium geometry to a non-planar structure with an endocyclic torsion angle of ±20° results in an energy increase of less than 2.8 kcal/mol. An analysis of the population of ground and excited vibrational levels for the lowest out-of-plane vibration of the ring indicates that in adenine 45% of the molecules have a non-planar pyrimidine ring with relevant torsion angle up to ±17° at any moment of time.     

Molecular modelling prediction of ligand binding site flexibility

We have investigated the efficacy of generating multiple sidechain conformations using a rotamer library in order to find the experimentally observed ligand binding site conformation of a protein in the presence of a bound ligand. We made use of a recently published algorithm that performs an exhaustive conformational search using a rotamer library to enumerate all possible sidechain conformations in a binding site. This approach was applied to a dataset of proteins whose structures were determined by X-ray and NMR methods. All chosen proteins had two or more structures, generally involving different bound ligands. By taking one of these structures as a reference, we were able in most cases to successfully reproduce the experimentally determined conformations of the other structures, as well as to suggest alternative low-energy conformations of the binding site. In those few cases where this procedure failed, we observed that the bound ligand had induced a high-energy conformation of the binding site. These results suggest that for most proteins that exhibit limited backbone motion, ligands tend to bind to low energy conformations of their binding sites. Our results also reveal that it is possible in most cases to use a rotamer search-based approach to predict alternative low-energy protein binding site conformations that can be used by different ligands. This opens the possibility of incorporating alternative binding site conformations to improve the efficacy of docking and structure-based drug design algorithms.     

Tuning the photophysical behavior of luminescent cyclam derivatives by cation binding and excited state redox potential

The emission from two photoactive 14-membered macrocyclic ligands, 6-((naphthalen-1-ylmethyl)-amino)-trans-6,13-dimethyl-13-amino-1,4,8,11-tetraaza-cyclotetradecane (L1) and 6-((anthracen-9-ylmethyl)-amino)-trans-6,13-dimethyl-13-amino-1,4,8,11-tetraaza-cyclotetradecane (L2) is strongly quenched by a photoinduced electron transfer (PET) mechanism involving amine lone pairs as electron donors. Time-correlated single photon counting (TCSPC), multiplex transient grating (TG), and fluorescence upconversion (FU) measurements were performed to characterize this quenching mechanism. Upon complexation with the redox inactive metal ion, Zn(II), the emission of the ligands is dramatically altered, with a significant increase in the fluorescence quantum yields due to coordination-induced deactivation of the macrocyclic amine lone pair electron donors. For [ZnL2]2+, the substituted exocyclic amine nitrogen, which is not coordinated to the metal ion, does not quench the fluorescence due to an inductive effect of the proximal divalent metal ion that raises the ionization potential. However, for [ZnL1]2+, the naphthalene chromophore is a sufficiently strong excited-state oxidant for PET quenching to occur.     

Efficient inclusion of receptor flexibility in grid-based protein-ligand docking

Accounting for receptor flexibility is an essential component of successful protein-ligand docking but still marks a major computational challenge. For many target molecules of pharmaceutical relevance, global backbone conformational changes are relevant during the ligand binding process. However, popular methods that represent the protein receptor molecule as a potential grid typically assume a rigid receptor structure during ligand-receptor docking. A new approach has been developed that combines inclusion of global receptor flexibility with the efficient potential grid representation of the receptor molecule. This is achieved using interpolation between grid representations of the receptor protein deformed in selected collective degrees of freedom. The method was tested on the docking of three ligands to apo protein kinase A (PKA), an enzyme that undergoes global structural changes upon inhibitor binding. Structural variants of PKA were generated along the softest normal mode of an elastic network representation of apo PKA. Inclusion of receptor deformability during docking resulted in a significantly improved docking performance compared with rigid PKA docking, thus allowing for systematic virtual screening applications at small additional computational cost.