"Inject-mix-react-separate-and-quantitate" (IMReSQ) method for screening enzyme inhibitors

Many regulatory enzymes are considered attractive therapeutic targets, and their inhibitors are potential drug candidates. Screening combinatorial libraries for enzyme inhibitors is pivotal to identifying hit compounds for the development of drugs targeting regulatory enzymes. Here, we introduce the first inhibitor screening method that consumes only nanoliters of the reactant solutions and is applicable to regulatory enzymes. The method is termed inject-mix-react-separate-and-quantitate (IMReSQ) and includes five steps. First, nanoliter volumes of substrate, candidate inhibitor, and enzyme solutions are injected by pressure into a capillary as separate plugs. Second, the plugs are mixed inside this capillary microreactor by transverse diffusion of laminar flow profiles. Third, the reaction mixture is incubated to form the enzymatic product. Fourth, the product is separated from the substrate inside the capillary by electrophoresis. Fifth, the amounts of the product and substrate are quantitated. In this proof-of-principle work, we applied IMReSQ to study inhibition of recently cloned protein farnesyltransferase from parasite Entamoeba histolytica. This enzyme is a potential therapeutic target for antiparasitic drugs. We identified three previously unknown inhibitors of this enzyme and proved that IMReSQ could be used for quantitatively ranking the potencies of inhibitors.     

Mixtures of interacting particles with well-defined composition field coupling chi parameters

This article proposes a systematic, quantitative treatment of the problem of associating a scalar Flory-Huggins-like chi parameter directly with the interaction potentials in a binary mixture of point particles. This work fulfills the need for a general, quantitative way to compare chi values in explicitly simulated ensembles of lattice and off-lattice polymer models with field theoretic calculations. Emphasis is placed on constructing particle models where chi is relatively well defined. In general, chi is defined through pair correlation functions, whose thermal fluctuations are coupled to local average composition and composition gradients. This implies that chi is composition dependent even in the simplest particle models. At the same time, by quantifying this effect, it is found that composition-independent chi may be defined to within a few percent for cases where the range of the potential is large relative to the interparticle distance. An explicit formula for chi in terms of interaction potentials is given.     

Configurational assignment of N-arylsulfonylimines of alpha-polychloroaldehydes

Configurational assignment of seven synthesized N-arylsulfonylimines of alpha-polychloroaldehydes has been carried out by means of experimental measurements and high-level ab initio calculations of their (13)C--(13)C, (13)C--(1)H and (15)N--(1)H spin-spin coupling constants. The title compounds were shown to exist in solution solely in the form of E isomers, in line with thermodynamic reasoning.     

para-Hydrogen-induced polarization in heterogeneous hydrogenation reactions

We demonstrate the creation and observation of para-hydrogen-induced polarization in heterogeneous hydrogenation reactions. Wilkinson's catalyst, RhCl(PPh3)3, supported on either modified silica gel or a polymer, is shown to hydrogenate styrene into ethylbenzene and to produce enhanced spin polarizations, observed through NMR, when the reaction was performed with H2 gas enriched in the para spin isomer. Furthermore, gaseous phase para-hydrogenation of propylene to propane with two catalysts, the Wilkinson's catalyst supported on modified silica gel and Rh(cod)(sulfos) (cod = cycloocta-1,5-diene; sulfos = -O3S(C6H4)CH2C(CH2PPh2)3) supported on silica gel, demonstrates heterogeneous catalytic conversion resulting in large spin polarizations. These experiments serve as a direct verification of the mechanism of heterogeneous hydrogenation reactions involving immobilized metal complexes and can be potentially developed into a practical tool for producing catalyst-free fluids with highly polarized nuclear spins for a broad range of hyperpolarized NMR and MRI applications.     

Effect of Inertial Terms on Fluid–Porous Medium Flow Coupling

The study considers an effect of the nonlinear inertial terms in the Brinkman filtration equation on the characteristics of coupled flows in a pure fluid and porous medium in the frameworks of two independent problems. The first problem is the forced boundary-layer flow overlying the Darcy–Brinkman porous medium. The Prandtl theory is used, and the self-similar equations are built to describe it. It is shown that the inertial terms have a valuable effect on the boundary-layer structure because of the large velocity gradient in the transition zone. The boundary-layer thickness in a porous medium rapidly grows at large Reynolds numbers. The velocity magnitude and gradient at the interface also change. The second independent problem is an analysis of the inertial terms effect on the flow stability. The neutral curves of the full and linearized flow models are built using the shooting method. They have different short-wave asymptotic, but there are no significant changes in the critical Reynolds numbers and corresponding wave numbers.     

Inertial and Darcy’s Terms Ratio in Boundary Layer at Fluid–Porous Medium Interface

The study considers the forced boundary-layer flow overlying the Darcy–Brinkman porous medium and gives a quantitative analysis of the nonlinear inertial terms in the Brinkman filtration equation. The inertial terms are shown to be larger than the Darcy’s drag near the porous medium interface. The applicability range of boundary-layer approach is determined. It is suitable in high-permeable media with moderate velocities of an external flow. If it is slow enough, the inertial terms can be omitted in spite of interface effect. On the other hand, fast external flow produces the filtration with large pore-scale Reynolds number; therefore, the Forchheimer’s drag should be taken into account. It is shown the Brinkman term as well as inertial terms have a significant role in boundary-layer formation within the porous medium.     

Diels-Alder ligation of peptides and proteins

The development of the Diels-Alder cycloaddition as a new method for the site-specific chemoselective ligation of peptides and proteins under mild conditions is reported. Peptides equipped with a 2,4-hexadienyl ester and an N-terminal maleimide react in aqueous media to give cycloadducts in high yields and depending on the amino acid sequence with high stereoselectivity. Except for the cysteine SH group the transformation is compatible with all amino acid side chain functional groups. For ligation to proteins the hexadienyl group was attached to avidin and streptavidin noncovalently by means of complex formation with a biotinylated peptide or by covalent attachment of a hexadienyl ester-containing label to lysine side chains incorporated into the proteins. Site-specific attachment of the hexadienyl unit into a Rab protein was achieved by means of expressed protein ligation followed by protection of the generated cysteine SH by means of Ellman's reagent. The protein reacted with different maleimido-modified peptides under mild conditions to give the fully functional cycloadducts in high yield. The results demonstrate that the Diels-Alder ligation offers an advantageous and technically straightforward new opportunity for the site-specific equipment of peptides and proteins with further functional groups and labels. It proceeds under very mild conditions and is compatible with most functional groups found in proteins. Its combination with other ligation methods, in particular expressed protein ligation is feasible.     

Formation mechanisms and properties of semifluorinated molecular gradients on silica surfaces

The goal of this study is to elucidate the formation of molecular gradients made of semifluorinated organosilanes (SFOs) on flat substrates by using a methodology developed by Chaudhury and Whitesides (Science 1992, 256, 1539). We use surface-sensitive combinatorial near-edge X-ray absorption fine structure (combi-NEXAFS) spectroscopy to measure the position-dependent concentration and orientation of SFO molecules in SFO molecular gradients on flat silica surfaces. Using the combi-NEXAFS data, we establish the correlation between the fraction of the F(CF(2))(8)(CH(2))(2)- species on the substrate and the average tilt angle of the -(CF(2))(8)F group in the SFO as a function of the deposition gas medium (air vs nitrogen) and the end group around the silicon atom (monofunctional vs trifunctional). In addition, we utilize the gradient geometry to comprehend the mechanism of formation of SFO self-assembled monolayers (SAMs). Specifically, we provide evidence that depending on the nature of the end group in the SFO and the vapor phase the SFO molecules add themselves into the existing SAMs either as individual molecules or as multimolecular complexes.     

Nonempirical calculations of NMR indirect spin-spin coupling constants. Part 14: azomethines of the alpha, beta-unsaturated aldehydes

Configurational assignment of seven azomethines obtained from the alpha-functionally substituted and nonsubstituted alpha,beta-unsaturated aldehydes has been performed on the basis of experimental measurements and the high-level ab initio calculations of their 1J(C,C) and 1J(C,H), involving the alpha-imino carbon that demonstrated the marked stereochemical dependence of both coupling constants upon the orientation of the nitrogen lone pair in the diverse isomers of the title azomethines.