Flexible ligand docking without parameter adjustment across four ligand–receptor complexes

Understanding molecular recognition is one of the fundamental problems in molecular biology. Computationally, molecular recognition is formulated as a docking problem. Ideally, a molecular docking algorithm should be computationally efficient, provide reasonably thorough search of conformational space, obtain solutions with reasonable consistency, and not require parameter adjustments. With these goals in mind, we developed DIVALI (Docking wIth eVolutionary AlgorIthms), a program which efficiently and reliably searches for the possible binding modes of a ligand within a fixed receptor. We use an AMBER-type potential function and search for good ligand conformations using a genetic algorithm (GA). We apply our system to study the docking of both rigid and flexible ligands in four different complexes. Our results indicate that it is possible to find diverse binding modes, including structures like the crystal structure, all with comparable potential function values. To achieve this, certain modifications to the standard GA recipe are essential. © 1995 John Wiley & Sons, Inc.     

Stereoselective synthesis of the cyclic ether core of (+)-laurenyne

A concise enantioselective synthesis of the cyclic ether core of the marine natural product (+)-laurenyne has been accomplished using ring-closing metathesis for medium-ring construction.     

Nonaqueous biocatalytic synthesis of new cytotoxic doxorubicin derivatives: exploiting unexpected differences in the regioselectivity of salt-activated and solubilized subtilisin

Two enzymes, Mucor javanicus lipase and subtilisin Carlsberg (SC), catalyzed the nonaqueous acylation of doxorubicin (DOX). Compared to the untreated enzyme the rate of DOX acylation at the C-14 position with vinyl butyrate in toluene was 25-fold higher by lipase ion-paired with Aerosol OT (AOT) and 5-fold higher by lipase activated by 98% (w/w) KCl co-lyophilization (3.21 and 0.67 mumol/min g-lipase, respectively, vs 0.13 mumol/min g-lipase). Particulate subtilisin Carlsberg (SC) was nearly incapable of DOX acylation, but ion-paired SC (AOT-SC) catalyzed acylation at a rate of 2.85 mumol/min g-protease. The M. javanicus formulations, AOT-SC, and SC exclusively acylated the C14 primary hydroxyl group of DOX. Co-lyophilization of SC with 98% (w/w) KCl expanded the enzyme's regiospecificity such that KCl-SC additionally acylated the C4' hydroxyl and C3' amine groups. The total rate of DOX conversion with KCl-SC was 56.7 mumol/min g-protease. The altered specificity of KCl-SC is a new property of the enzyme imparted by the salt activation, and represents the first report of unnatural regioselectivity exhibited by a salt-activated enzyme. Using AOT-SC catalysis, four unique selectively acylated DOX analogues were generated, and KCl-SC was used to prepare DOX derivatives acylated at the alternative sites. Cytotoxicities of select derivatives were evaluated against the MCF7 breast cancer cell line (DOX IC50 = 27 nM) and its multidrug-resistant sub-line, MCF7-ADR (DOX IC50 = 27 muM). The novel derivative 14-(2-thiophene acetate) DOX was relatively potent against both cell lines (IC50 of 65 nM and 8 muM, respectively) and the 14-(benzyl carbonate) DOX analogue was as potent as DOX against the MCF7 line (25 nM). Activated biocatalysts and their novel regioselectivity differences thus enabled single-step reaction pathways to an effective collection of doxorubicin analogues.     

Thermally induced ortho-metalation of dicarbomethoxyacetylenebis(triphenylphosphine)platinum

Heating a toluene solution of dicarhomethoxyacetylenebis(triphenylphosphine)platinum(0) at 130°C gives the ortho-metalated complex (Ph₃P)(Ph₂$\text{PC}{}_6\text{H}{}_4\text{)P}$t-trans-(COOMe)CCHCOOMe.     

Rapid method for the determination of alachlor, atrazine and metolachlor in groundwater by solid-phase extraction

A solid-phase extraction method is described for the separation of alachlor, atrazine and metolachlor from groundwater using solid-phase disposable columns. The method is rapid, reproducible and uses considerably fewer reagents than classical liquid-liquid methods. The average recoveries were greater than 90% for all three compounds.     

A novel regiodivergent resolution reaction mediated by a homochiral lithium amide base

The reaction of a racemic perhydroisoquinolene derivative 9 with the homochiral lithium amide basse 3 in the presence of Me₃SiCl in an regiodivergent fashion to give the two non-racemic regioisomeric enol silanes 10 and 11. Conversion of 10 into enone 15, an intermediate useful in the synthesis of the alkaloid (+)-yohimbine, was also possible.     

Plasma polymerization. V. A systematic investigation of the inductively coupled RF plasma polymerization of the isomeric tetrafluorobenzenes

A systematic investigation has been made of the composition, gross structural features, and rates of deposition of plasma polymer films produced from the excitation of inductively coupled RF plasmas in the isomeric tetrafluorobenzenes. ESCA data reveal that the dominant reaction involves rearrangement such that under a wide variety of experimental conditions the composition of the crosslinked products remains essentially the same as that of the starting material. Small differences in rates of deposition are observed for the different isomers, and theoretical SCF MO studies at the MNDO level provides a basis for discussion of the experimental data.     

A theoretical investigation of molecular core binding and relaxation energies in a series of oxygen-containing organic molecules of interest in the study of surface oxidation of polymers

Nonempirical LCAO MO SCF computations (in the ΔSCF formalism) have been carried out of binding energies and relaxation energies for an extensive series of oxygen-containing organic systems encompassing most of the common functionalities. The molecules for which experimental data are available for comparison demonstrate the adequacy of the treatment for describing the relative binding energies for both the C_ls and O_ls core levels. A sound basis is therefore provided for the discussion of relative core binding energies (C_ls and O_ls) for functionalities for which experimental data are not available, that is, hydroperoxides, peroxides, peroxyacids, and peroxyesters, a knowledge of which is essential for investigations of the surface oxidation of polymers by means of ESCA. C_ls shifts are discussed in terms of primary and secondary substituent effects of oxygen, which greatly simplify the analysis of complex unresolved spectra, whereas for the O_ls levels a similar but less straightforward situation exists. The relaxation energies associated with both C_ls and O_ls core ionization follow a dependence on the binding energy for a given structural type.