Selecting Agonists from Single Cells Infected with Combinatorial Antibody Libraries

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Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design

Use of solvent mapping, based on multiple-copy minimization (MCM) techniques, is common in structure-based drug discovery. The minima of small-molecule probes define locations for complementary interactions within a binding pocket. Here, we present improved methods for MCM. In particular, a Jarvis-Patrick (JP) method is outlined for grouping the final locations of minimized probes into physical clusters. This algorithm has been tested through a study of protein-protein interfaces, showing the process to be robust, deterministic, and fast in the mapping of protein "hot spots." Improvements in the initial placement of probe molecules are also described. A final application to HIV-1 protease shows how our automated technique can be used to partition data too complicated to analyze by hand. These new automated methods may be easily and quickly extended to other protein systems, and our clustering methodology may be readily incorporated into other clustering packages.     

The inverse sandwich complex [(K(18-crown-6))2Cp][CpFe(CO)2]--unpredictable redox reactions of [CpFe(CO)2]I with the silanides Na[SiRtBu2] (R = Me, tBu) and the isoelectronic phosphanyl borohydride K[PtBu2BH3

The dimeric iron carbonyl [CpFe(CO)(2)](2) and the iodosilanes tBu(2)RSiI were obtained from the reaction of [CpFe(CO)(2)]I with the silanides Na[SiRtBu(2)] (R = Me, tBu) in THF. By the reactions of [CpFe(CO)(2)]I and Na[SiRtBu(2)] (R = Me, tBu) the disilanes tBu(2)RSiSiRtBu(2) (R = Me, tBu) were additionally formed using more than one equivalent of the silanide. In this context it should be noted that reduction of [CpFe(CO)(2)](2) with Na[SitBu(3)] gives the disilanes tBu(3)SiSitBu(3) along with the sodium ferrate [(Na(18-crown-6))(2)Cp][CpFe(CO)(2)]. The potassium analogue [(K(18-crown-6))(2)Cp][CpFe(CO)(2)] (orthorhombic, space group Pmc2(1)), however, could be isolated as a minor product from the reaction of [CpFe(CO)(2)]I with [K(18-crown-6)][PtBu(2)BH(3)]. The reaction of [CpFe(CO)(2)](2) with the potassium benzophenone ketyl radical and subsequent treatment with 18-crown-6 yielded the ferrate [K(18-crown-6)][CpFe(CO)(2)] in THF at room temperature. The crown ether complex [K(18-crown-6)][CpFe(CO)(2)] was analyzed using X-ray crystallography (orthorhombic, space group Pna2(1)) and its thermal behaviour was investigated.     

An Unpredictable Reaction of <Emphasis Type="Italic">t</Emphasis>Bu<Subscript>2</Subscript>PHO·BCl<Subscript>3</Subscript> in the Presence of Water

Abstract  

When a benzene solution of tBu₂PHO·BCl₃ was exposed to air at room temperature, the phosphonium chloride [tBu₂PH₂]Cl was formed together with di-tert-butylphosphinic acid, tBu₂PO(OH). X-ray quality crystals of the hydrochloride [tBu₂PH₂]Cl·HCl were obtained from the reaction solution at room temperature. The hydrochloride [tBu₂PH₂]Cl·HCl crystallizes in the monoclinic space group P2₁ /m, a = 6.3012(7) ?, b = 6.8970(10) ?, c = 14.5011(15) ?, β = 99.376(9)°, V = 621.79(13) ?³, Z = 2, d _calcd = g cm⁻³ 1.165; R1 = 0.0510, wR2 = 0.1503 for 1,129 reflections with I > 2σ(I). The crystal was a non-merohedral twin with a contribution of 0.353(7) of the minor component. The structure is composed of discrete di-t-butylphosphonium cations and Cl anions. Both are located on a crystallographic mirror plane and are connected by P–H···Cl hydrogen bonds.     

The pentanuclear Fe(II) cluster [(C5H4)6Fe5]2-: bringing together ferrocene sandwiches and homoleptic Fe(II)-cyclopentadienyl sigma-complexes

Reaction of [(fc)3(Li)6.(TMEDA)2] with FeCl2 gives the pentanuclear iron complex [(fc)3(Fe)2(Li)2.(TMEDA)2] featuring two ferra[1]ferrocenophane moieties bridged by a 1,1'-ferrocenediyl unit; the non-ferrocene Fe(II) ions are tetra-coordinate and adopt a high-spin state.     

Manufacturing immunity to disease in a test tube: the magic bullet realized

Although it took over one hundred years, Ehrlich's concept of the magic bullet is now a reality. Today, therapeutic antibodies are, arguably, the most important class of new drugs for the treatment of illnesses ranging from Alzheimer's disease to cancer. The emergence of therapeutic antibodies had to wait for advances in immunochemistry that allowed construction of antibodies in vitro. The centerpiece of the new technology is the combinatorial antibody library, which essentially allows one to synthesize an artificial immune system with a diversity that exceeds that of the natural repertoire. The construction of such libraries was perceived to be difficult because, if the natural immune system was to be used as the starting material, construction of the libraries would entail protocols that are the opposite of usual cloning. In gene cloning one starts with complexity and reduces it to a singularity. In the generation of diversity by construction of combinatorial antibody libraries, one starts with a collection of clones, randomly expands their complexity, and then returns them to recoverable singularities. The methods developed to accomplish this seemingly formidable task now allow construction of antibodies in a test tube to any antigen. These synthetic antibodies may be qualitatively and quantitatively superior to those of nature.     

A polymorph of tetrakis(acetonitrile‐κN)copper(I) tetrafluoridoborate

A P2₁2₁2₁ polymorph of the title compound, [Cu(CH₃CN)₄]BF₄, is reported. The crystal structure is very similar to the structure of the Pna2₁ polymorph reported by Jones & Crespo [Acta Cryst. (1998), C 54 , 18–20]. The anions and one of the three independent cations occupy similar positions in both polymorphs. Two of the four symmetry‐related positions of the other two cations are also identical in the two polymorphs, and the other two positions are related by mirror symmetry. The crystal used for the structure determination contained a volume fraction of 0.088 (7) of the Pna2₁ polymorph.     

Polymorphism of 2,5‐[(diphenylphosphanyl)methyl]‐1,1,2,4,4,5‐hexaphenyl‐1,4‐diphospha‐2,5‐diboracyclohexane

2,5‐[(Diphenylphosphanyl)methyl]‐1,1,2,4,4,5‐hexaphenyl‐1,4‐diphospha‐2,5‐diboracyclohexane shows polymorphism as two tetrahydrofuran (THF) disolvates [C₆₄H₅₈B₂P₄·2C₄H₈O, (Ia) and (Ib)] and pseudo‐polymorphism as its toluene monosolvate [C₆₄H₅₈B₂P₄·C₇H₈, (Ic)]. In each of polymorphs (Ia) and (Ib), the diphosphadiboracyclohexane molecule is located on a centre of inversion. The THF molecule of (Ib) is disordered over two sites, with a site‐occupation factor of 0.612 (8) for the major‐occupied site. Both structures crystallize in the same space group (P2₁/n), but they display a different crystal packing. For pseudo‐polymorph (Ic), although the space group is P2₁/c, which is just a different setting of the P2₁/n space group of (Ia) and (Ib), the crystal packing is completely different. Although the crystal packing in these three structures is significantly different, their molecular conformations are surprisingly the same.     

Study of the lumiescence properties of a new series of quinolizinium salts and their interaction with DNA

The spectrofluorimetric characteristic of a new group of benzo- and methyl- quinolizinium salts at room temperature and 77 LK are reported. At room temperature, linear calibration is wide; 10^-9 M 9-cyanobenzo [a] phenathro [9,10-g] quinolizinium chloride can be detected in methanolic solution and 10^-7 M in aqueous solution. The polynuclear compounds show the most intense luminescence bands, and a significant hypsochromic shift of the fluorenscence emission maximum was observed at 77 K compared with room temperature. For the 2,3-diphenyl derivatives, the presence of a methoxy substituent produces a marked Stoke's shift, because it causes a decrease in the planarity of the molecule. The benzo compounds are similar in structure to the alkaloid coralyne, which has significant antileuikemic activity. The fused planar aromatic compounds are shown to bind with DNA.