OptiDock: virtual HTS of combinatorial libraries by efficient sampling of binding modes in product space

Products from combinatorial libraries generally share a common core structure that can be exploited to improve the efficiency of virtual high-throughput screening (vHTS). In general, it is more efficient to find a method that scales with the total number of reagents (Sigma growth) rather with the number of products (Pi growth). The OptiDock methodology described herein entails selecting a diverse but representative subset of compounds that span the structural space encompassed by the full library. These compounds are docked individually using the FlexX program (Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. J. Mol. Biol. 1995, 251, 470-489) to define distinct docking modes in terms of reference placements for combinatorial core atoms. Thereafter, substituents in R-cores (consisting of the core structure substituted at a single variation site) are docked, keeping the core atoms fixed at the coordinates dictated by each reference placement. Interaction energies are calculated for each docked R-core with respect to the target protein, and energies for whole compounds are calculated by finding the reference core placement for which the sum of corresponding R-core energies is most negative. The use of diverse whole compounds to define binding modes is a key advantage of the protocol over other combinatorial docking programs. As a result, OptiDock returns better-scoring conformers than does serially applied FlexX. OptiDock is also better able to find a viable docked pose for each library member than are other combinatorial approaches.     

PHOTOINHIBITION OF PHOTOSYNTHESIS IN NATURAL WATERS*

Abstract— A quantitative analysis of the wavelength-dependent influence of solar irradiance on natural phytoplankton photosynthesis has been made. The effect on productivity due to several different UV radiation regimes has been measured. In the course of this analysis, it has been shown that the biological weighting function for photoinhibition of chloroplasts (Jones and Kok, 1966) allows the calculation of a biologically effective dose which is consistent with the measured photoinhibition in natural phytoplankton populations. The ecological implications of a change in available UV radiation, possibly due to anthropogenic altering of the ozone layer, are explored and it is found that the present static bottle ^l4C technique of measuring in situ phytoplankton productivity does not lend itself to assessing accurately the potential ecological consequences of possible increased MUV (middle ultraviolet radiation in the 280–340 nm region) on phytoplankton populations. A small change in MUV has a relatively minor effect on photoinhibition dose rates whereas it has a large potential effect on DNA dose rates.     

Irreversible enzyme inhibitors. CXI. Candidate active-site-directed irreversible inhibitors of dihydrofolic reductase derived from 4,6-diamino-1,2-dihydro-l-phenyl-s-triazines. V.

Condensation of 5-(p-nitrophenyl)-2-pentanone with phenylbiguanide hydrochloride (V) gave a 2-methyl-2-(p-nitrophenylpropyl)-1,2-dihydro-s-triazine (IX); hydrogenation of the nitro group to amino followed by bromoacetylation afforded the candidate irreversible inhibitor of dihydrofolic reductase, namely, 2-(p-bromoacetamidophenylpropyl)-4,6-diamino-1,2-dihydro-2-methyl-s-triazine hydrochloride (VIII). Similarly, the o, m, and p-isomers of 5-nitrophenoxy-2-pentanone were converted to the corresponding 2-(bromoacetamidophenoxypropyl)-1,2-dihydro-s-triazines (XI). The four candidate irreversible inhibitors were evaluated on the dihydrofolic reductases from pigeon liver, Walker-256 rat tumor, and L-1210/FR8 mouse leukemia. Only VIII was an irreversible inhibitor; VIII slowly inactivated the L-121-/FR8 mouse leukemia enzyme with a half-life of 2–3 hours at 37°, but VIII showed no inactivation of the other two dihydrofolic reductases—a species specific inactivation.     

The synthesis and spectroscopic properties of some but-2-yne tungsten complexes of the type [WIX(CO){Ph2P(CH2)PPh2}(η-MeC2Me)] (X = Cl, Br, I, NO2, NO3, NCS or OH)

Reaction of the cationic complex [WI(CO)(NCMe){Ph₂P(CH₂)PPh₂}(η²-MeC₂ME)][BF₄] with an equimolar amount of MX (MX = NaCl, NaBr, NaI, KNO₂, KNO₃, NaNCS or KOH) in acetone at room temperature gave the neutral complex [WIX(CO){Ph₂P(CH₂)PPh₂}(η²-MeC₂Me)] (1–7) in good yield. Complexes 1–7 have been characterized by elemental analysis (C, H and N), IR and ¹H NMR spectroscopy.     

A convenient and inexpensive conversion of an aziridine to an oxazolidinone

The conversion of an aziridine to the corresponding oxazolidinone using only carbon dioxide and a catalytic amount of lithium iodide is discussed. In all cases, either no reaction occurred or a high yield of product was obtained. HMPA has been added to the reaction mixture, as needed, to drastically improve the regioselectivity. Net retention of stereochemistry between the starting aziridine and the product oxazolidinone was observed.     

Synthesis and applications of C2-symmetric guanidine bases

The preparation of the tetracyclic C₂-symmetric guanidinium salts 5 and 11-13 is reported together with their application to enantioselective transformations.     

Optimization and development of a high-performance liquid chromatography-based one-site immunometric assay with chemiluminescence detection

Various practical and theoretical considerations were examined in the creation and optimization of a high-performance liquid chromatography (HPLC)-based one-site immunometric assay. This method used an HPLC analyte analog column and post-column chemiluminescence detection. The specific analyte chosen as the model for this study was l-thyroxine (also known as T₄). In this technique, a sample containing thyroxine was first combined with an excess of anti-T₄ antibody Fab fragments that had earlier been conjugated with chemiluminescent acridinium ester labels. After incubation, the mixture was injected onto a column that contained immobilized T₄. The amount of thyroxine in the original sample was then determined by measuring the labeled Fab fragments that appeared in the non-retained fraction, or the decrease in excess Fab fragments that were bound to and later eluted from the column. Items considered in creating this assay included the preparation of acridinium ester-labeled Fab fragments, the detection of these fragments with a post-column reactor, and the creation of a suitable immobilized analog column for capturing excess labeled Fab fragments. The final method could measure T₄ in standards at clinically-relevant concentrations and provided a response within 1.5 min of sample injection, following a 20-45 min incubation with the labeled Fab fragments. Possible applications of this method include its use in clinical chemistry and the screening of proteomic or combinatorial libraries.     

Remarkable tris(trimethylsilyl)silyl group for diastereoselective [2 + 2] cyclizations

[reaction: see text] Diastereoselective [2 + 2] cyclizations of aldehyde- and ketone-derived silyl enol ethers with acrylates is described. The use of the tris(trimethylsilyl)silyl group allows for unprecedented reactivity, yields, and selectivity for these cyclizations. The presence of silicon-silicon bonds proved to be important for this transformation, where typical silyl groups (TBS and TIPS) failed to give any desired product. The bulky bis(2,6-diphenylphenoxide) aluminum triflimide catalyst was essential for high diastereoselectivity.     

Amide bond formation using an air-stable source of AlMe3

Synthesis of amides from coupling esters with a range of primary amines can be conveniently achieved in moderate to excellent yields (69-99%) using an air-stable adduct of trimethylaluminium (AlMe₃)₂·DABCO (DABCO is 1,4-diazobicyclo[2.2.2]octane), referred to as DABAL-Me₃. Reactions can be run without requiring the exclusion of atmospheric oxygen or the drying of solvents.