Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges

Journal of Computer-Aided Molecular Design - We systematically tested the Autodock4 docking program for absolute binding free energy predictions using the host-guest systems from the recent SAMPL6,...     

Synthesis and preliminary biological evaluation of a new pyridocarbazole derivative covalently linked to a thymidine nucleoside as a potential targeted antitumoral agent. I

The therapy of human cancer is one of the more pursued goals by medicinal chemistry research. Most of the compounds clinically used as a treatment owe their efficacy to their cytotoxic interaction (direct or indirect) with nuclear DNA. This interaction results in the inhibition of DNA synthesis and the degradation of nucleic strands. Ellipticine is a naturally occurring 6H-pyrido[4,3-b]carbazole alkaloid endowed with antitumor activity, and several ellipticine derivatives have been used in clinical trials. We previously reported some 1,4-dimethyl-9H-carbazole derivatives structurally related to ellipticine. The purpose of our research was to transform the pyridocarbazole in a prodrug so that it would have more penetration in the tumor cells and block their replication. Our prodrug is slowly hydrolyzed in human plasma in the corresponding acid. From these preliminary results, we deduce that our compound can block cellular replication. Our hypothesis is that the antitumoral activity is probably related to the induction of damage to DNA, without cellular lysis in the short term.     

Methyl groups as probes for proteins and complexes in in-cell NMR experiments

Studying protein components of large intracellular complexes by in-cell NMR has so far been impossible because the backbone resonances are unobservable due to their slow tumbling rates. We describe a methodology that overcomes this difficulty through selective labeling of methyl groups, which possess more favorable relaxation behavior. Comparison of different in-cell labeling schemes with three different proteins, calmodulin, NmerA, and FKBP, shows that selective labeling with [(13)C]methyl groups on methionine and alanine provides excellent sensitivity with low background levels at very low costs.     

Co-ordination chemistry of amino pendant arm derivatives of 1,4,7-triazacyclononane

The binding properties of 1,4,7-triazacyclononane ([9]aneN3) to metal cations can be adapted through sequential functionalisation of the secondary amines with aminoethyl or aminopropyl pendant arms to generate ligands with increasing numbers of donor atoms. The new amino functionalised pendant arm derivative of 1,4,7-triazacyclononane ([9]aneN3), L1, has been synthesised and its salt [H2L1]Cl2 characterised by X-ray diffraction. The protonation constants of the ligands L1-L4 having one, two or three aminoethyl or three aminopropyl pendant arms, respectively, on the [9]aneN3 framework, and the thermodynamic stabilities of their mononuclear complexes with CuII and ZnII have been investigated by potentiometric measurements in aqueous solutions. In order to discern the protonation sites of ligands L1-L4, 1H NMR spectroscopic studies were performed in D2O as a function of pH. While the stability constants of the CuII complexes increase on going from L1 to L2 and then decrease on going from L2 to L3 and L4, those for ZnII complexes increase from L1 to L3 and then decrease for L4. The X-ray crystal structures of the complexes [Cu(L1)(Br)]Br, [Zn(L1)(NO3)]NO3, [Cu(L2)](ClO4)2, [Ni(L2)(MeCN)](BF4)2, [Zn(L4)](BF4)2.MeCN and [Mn(L4)](NO3)2.1/2H2O have been determined. In both [Cu(L1)(Br)]Br and [Zn(L1)(NO3)]NO3 the metal ion is five co-ordinate and bound by four N-donors of the macrocyclic ligand and by one of the two counter-anions. The crystal structures of [Cu(L2)](ClO4)2 and [Ni(L2)(MeCN)](BF4)2 show the metal centre in slightly distorted square-based pyramidal and octahedral geometry, respectively, with a MeCN molecule completing the co-ordination sphere around NiII in the latter. In both [Zn(L4)](BF4)2.MeCN and [Mn(L4)](NO3)2.1/2H2O the metal ion is bound by all six N-donors of the macrocyclic ligand in a distorted octahedral geometry. Interestingly, and in agreement with the solution studies and with the marked preference of CuII to assume a square-based pyramidal geometry with these types of ligands, the reaction of L4 with one equivalent of Cu(BF4)2.4H2O in MeOH at room temperature yields a square-based pyramidal five co-ordinate CuII complex [Cu(L6)](BF4)2 where one of the three propylamino pendant arms of the starting ligand has been cleaved to give L6.     

Euphohelioscopin A Is a PKC Activator Capable of Inducing Macrophage Differentiation

To identify small molecules that selectively control hematopoietic stem cell differentiation, we performed an unbiased screen using primary human CD34(+) cells. We identified a plant-derived natural product, euphohelioscopin A, capable of selectively differentiating CD34(+) cells down the granulocyte/monocytic lineage. Euphohelioscopin A also inhibits proliferation and induces differentiation of the myeloid leukemia cell lines THP-1 and HL-60. Mechanistic studies revealed that euphohelioscopin A is an activator of protein kinase C (PKC), and that the promonocytic effects of this natural product are mediated by PKC activation. In addition to shedding insights into normal hematopoiesis, this work may ultimately facilitate the application of stem cell therapies to a host of myeloid dysfunctions.     

Extension of the Coulomb–Hole–Hartree–Fock theory to molecules

The Coulomb–Hole–Hartree–Fock method introduced by E. Clementi in the early 1960s and reparametrized more recently by S. Chakraworty and E. Clementi to compute the correlated electronic energy in atomic systems, is here extended to compute molecules. The new parametrization is obtained empirically by fitting first and second atomic ionization potentials from He to Ca and a few diatomic molecules. The present formulation makes use of either one or more determinants in order to ensure proper dissociation products, following the early proposal of G.C. Lie and E. Clementi in the context of density functional computations for molecular systems. The new formulation is tested against the dissociation energies of a large number of molecules and it is found satisfactory. © 1995 John Wiley & Sons, Inc.     

Graphene from electrochemical exfoliation and its direct applications in enhanced energy storage devices

Graphite was electrochemically exfoliated in mixtures of room temperature ionic liquids and deionized water containing lithium salts to produce functionalized graphenes and such an electrochemical exfoliation technique can be directly used in making primary battery electrodes with significantly enhanced specific energy capacity.     

Equilibrium and NMR relaxometric studies on the s-triazine-based heptadentate ligand PTDITA showing high selectivity for Gd3+ ions

A complete potentiometric and NMR relaxometric solution study on the heptadentate 2,2',2″,2'″-[(6-piperidinyl-1,3,5-triazine-2,4-diyl)dihydrazin-2-yl-1-ylidene]tetraacetic acid (PTDITA) ligand has been carried out. This ligand is based on the 1,3,5-triazine ring with two hydrazine-N,N-diacetate groups in positions 2 and 4 and a piperidine moiety in position 6. The introduction of the triazine ring into the ligand backbone is expected to modify its flexibility and then to affect the stability of the corresponding complexes with transition-metal and lanthanide ions. Thermodynamic stabilities have been determined by pH potentiometry, UV spectrophotometry, and (1)H NMR spectroscopy for formation of the complexes with Mg(2+), Ca(2+), Cu(2+), Zn(2+), La(3+), Gd(3+), and Lu(3+) ions. PTDITA shows a good binding affinity for Gd(3+) (logK = 18.49, pGd = 18.6) and an optimal selectivity for Gd(3+) over the endogenous Ca(2+), Zn(2+), and Cu(2+) (K(sel) = 6.78 × 10(7)), which is 3 orders of magnitude higher that that reported for Gd(DTPA) (K(sel) = 2.85 × 10(4)). This is mainly due to the lower stability of the Cu(II)- and Zn(II)(PTDITA) complexes compared to the corresponding DTPA complexes, which suggests an important role of the triazine ring on the selectivity for the Gd(3+) ion. The relaxometric properties of Gd(PTDITA) have been investigated in aqueous solution by measuring the (1)H relaxivity as a function of the pH, temperature, and magnetic field strength (nuclear magnetic relaxation dispersion profile). Variable-temperature (17)O NMR data have provided direct information on the kinetic parameters for exchange of the coordinated water molecules. A simultaneous fit of the data suggests that the high relaxivity value (r(1) = 10.2 mM(-1) s(-1)) is a result of the presence of two inner-sphere water molecules along with the occurrence of relatively slow rotation and electronic relaxation. The water residence lifetime, (298)τ(M) = 299 ns, is quite comparable to that of clinically approved magnetic resonance imaging contrast agents. The displacement of the inner-sphere water molecules by bidentate endogeneous anions (citrate, phosphate, and carbonate) has also been evaluated by (1)H relaxometry. In general, the binding interaction is markedly weak, and only in the case of citrate, a ca. 35% decrease in relaxivity was observed in the presence of 60 equiv of the anion. Phosphate and carbonate also interact with the paramagnetic ion, likely as monodentate ligands, but formation of the ternary complex is accompanied by a modest increase of r(1) due to the contribution of second-sphere water molecules.     

Dinuclear Cu(II) complexes of isomeric bis-(3-acetylacetonate)benzene ligands: synthesis, structure, and magnetic properties

Highly versatile coordinating ligands are designed and synthesized with two β-diketonate groups linked at the carbon 3 through a phenyl ring. The rigid aromatic spacer is introduced in the molecules to orient the two acetylacetone units along different angles and coordination vectors. The resulting para, meta, and ortho bis-(3-acetylacetonate)benzene ligands show efficient chelating properties toward Cu(II) ions. In the presence of 2,2'-bipyridine, they promptly react and yield three dimers, 1, 2, and 3, with the bis-acetylacetonate unit in bridging position between two metal centers. X-ray single crystal diffraction shows that the compounds form supramolecular chains in the solid state because of intermolecular interactions. Each of the dinuclear complexes shows a magnetic behavior which is determined by the combination of structural parameters and spin polarization effects. Notably, the para derivative (1) displays a moderate antiferromagnetic coupling (J = -3.3 cm(-1)) along a remarkably long Cu···Cu distance (12.30 ?).