Multiple ligand simultaneous docking: Orchestrated dancing of ligands in binding sites of protein

Present docking methodologies simulate only one single ligand at a time during docking process. In reality, the molecular recognition process always involves multiple molecular species. Typical protein–ligand interactions are, for example, substrate and cofactor in catalytic cycle; metal ion coordination together with ligand(s); and ligand binding with water molecules. To simulate the real molecular binding processes, we propose a novel multiple ligand simultaneous docking (MLSD) strategy, which can deal with all the above processes, vastly improving docking sampling and binding free energy scoring. The work also compares two search strategies: Lamarckian genetic algorithm and particle swarm optimization, which have respective advantages depending on the specific systems. The methodology proves robust through systematic testing against several diverse model systems: E. coli purine nucleoside phosphorylase (PNP) complex with two substrates, SHP2NSH2 complex with two peptides and Bcl‐xL complex with ABT‐737 fragments. In all cases, the final correct docking poses and relative binding free energies were obtained. In PNP case, the simulations also capture the binding intermediates and reveal the binding dynamics during the recognition processes, which are consistent with the proposed enzymatic mechanism. In the other two cases, conventional single‐ligand docking fails due to energetic and dynamic coupling among ligands, whereas MLSD results in the correct binding modes. These three cases also represent potential applications in the areas of exploring enzymatic mechanism, interpreting noisy X‐ray crystallographic maps, and aiding fragment‐based drug design, respectively. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

K2B12F12: A rare A2X structure for an ionic compound at ambient conditions

The anhydrous salt K₂B₁₂F₁₂ crystallized from aqueous solution and its structure was determined by single crystal X-ray diffraction. The Ni₂In-type structure it exhibits is rare for an A₂X ionic compound at 25 °C and 1 atm., consisting of an expanded hexagonal close-packed array of B₁₂F₁₂²⁻ centroids (cent?cent distances: 7.204-8.236 Å) with half of the K⁺ ions filling all of the O_h holes and half of the K⁺ ions filling all of the D_3h trigonal holes in the close-packed layers that are midway between two “empty” T_d holes. The structure is also unusual in that the bond-valence sum for the K⁺ ions in O_h holes is less than or equal to 0.73 (the bond-valence sum for the other type of K⁺ ion is 1.16). A variation of the Ni₂In structure is exhibited by the previously published monohydrate Cs₂(H₂O)B₁₂F₁₂, for which an improved structure is also reported here. For K₂B₁₂F₁₂: monoclinic, C2/c, a = 8.2072(8), b = 14.2818(7), c = 11.3441(9) Å, β = 92.832(5)°, Z = 4, T = 120(2) K. For Cs₂(H₂O)B₁₂F₁₂: orthorhombic, P2₁2₁2₁, a = 9.7475(4), b = 10.2579(4), c = 15.0549(5) Å, Z = 4, T = 110(1) K.     

The use of trehalose in the preparation of specimens for molecular electron microscopy

Biological specimens have to be prepared for imaging in the electron microscope in a way that preserves their native structure. Two-dimensional (2D) protein crystals to be analyzed by electron crystallography are best preserved by sugar embedding. One of the sugars often used to embed 2D crystals is trehalose, a disaccharide used by many organisms for protection against stress conditions. Sugars such as trehalose can also be added to negative staining solutions used to prepare proteins and macromolecular complexes for structural studies by single-particle electron microscopy (EM). In this review, we describe trehalose and its characteristics that make it so well suited for preparation of EM specimens and we review specimen preparation methods with a focus on the use of trehalose.     

Two New Meroterpenes from the Mangrove Endophytic Fungus Aspergillus sp. 085241B

Two new meroterpenes, ‘acetoxydehydroaustin B’ ( 1 ) and ‘1,2‐dihydro‐acetoxydehydroaustin B’ ( 2 ) were isolated in the form of a mixed crystal from the mangrove endophytic fungus Aspergillus sp. 085241B. Their structures and absolute configurations were determined by extensive analysis of their spectra and X‐ray diffraction data. In a preliminary bioassay, the mixed crystal did not exhibit activities against cancer cell lines of MDA‐MB‐435, SKBR3, HepG2, HEP3B, PC‐3, and A549, as well as against α‐glucosidase and tyrosinase.     

Diastereoselective ortho-lithiation of [5]ferrocenophanes

Planarly chiral ferrocene derivatives with bridged cyclopentadienyl rings are interesting ligands in asymmetric catalysis. A planar stereogenic unit is conveniently introduced by diastereoselective ortho-lithiation. The directed lithiation of several [5]ferrocenophane derivatives followed by quenching with chlorodiphenylphosphane led to planarly chiral ligands. The sense of diastereoselection was studied by computational methods. Absolute configuration of methoxy phosphane was determined by single crystal X-ray diffraction study.     

Solutions for the storage and handling of SPINE standard pucks

Currently there is no rack system for the long‐term storage of SPINE pucks in spite of their commercial availability and heavy usage at the ESRF. The only way to store pucks is in transport dewar canisters which presents a number of limitations and drawbacks. Here a simple affordable rack for storing SPINE pucks is described, which we believe is accessible to not only synchrotrons but also both academic and industrial research laboratories.     

Two New Daphniphyllum Alkaloids from Daphniphyllum calycinum

Two new daphniphyllum alkaloids named 2‐hydroxyyunnandaphnine D ( 1 ) and methyl 7‐hydroxyhomodaphniphyllate ( 2 ), together with eight known alkaloids, daphnioldhanin D, calyciphylline F, calyciphylline B, deoxycalyciphylline B, daphnicyclidin H, macropodumine C, 9,10‐epoxycalycine A, and yunnandaphnine A, were isolated from the stems and leaves of Daphniphyllum calycinum. Their structures and relative configurations were established on the basis of spectral evidence (including 2D‐NMR) and subsequently confirmed by a single‐crystal X‐ray crystallographic diffraction analysis.     

Synthesis and structural characterization of new polynuclear complexes of 1-hydroxymethyl-3,5-dimethylpyrazole with Ni(II) and Fe(II)

The complexation of the simple 1-hydroxymethyl-3,5-dimethylpyrazole (HL) ligand with Fe and Ni salts leads to interesting polynuclear complexes in good yield. X-ray diffraction reveals that the resulting complexes (μ₄-L)₄Ni₄Cl₄(H₂O)₄ and (μ₂-L)₄(μ₃-L)₂Fe₈Cl₁₆(μ₄-O)₆ adopt cubane-type and open-cubane-type structures in the solid state.