Transition state docking: a probe for noncovalent catalysis in biological systems. Application to antibody-catalyzed ester hydrolysis

A strategy for pinpointing favorable noncovalent interactions between transition states and active sites of biological catalysts is described. This strategy combines high-level quantum mechanical calculations of transition state geometries with an automated docking procedure using AutoDock. By applying this methodology to antibody-catalyzed hydrolyses of aryl esters (by the 48G7, CNJ206, and 17E8 families of antibodies), varying levels of catalysis are explained in terms of specific hydrogen bonding interactions between combining site residues and transition states. Although these families of antibodies were produced in separate experiments by different researchers using related but different haptens, the mechanism of transition state stabilization appears to be highly conserved. Despite being elicited in response to anionic phosphonate haptens, the best catalysts often utilize hydrogen bond acceptors to stabilize transition states. A mutant of antibody CNJ206, designed based on this observation and predicted to be a better catalyst, is proposed. In the case of antibody 48G7, affinity maturation is shown to produce a catalyst that is highly selective for one of two enantiomeric transition states from a nonselective germline precursor.     

Synthesis and luminescence studies of aryl substituted tetraamide complexes of europium(III): a new approach to pH responsive luminescent europium probes

DOTA-tetraamide ligands having extended phenol or pyridine substituents have been synthesized. The (5)D(0) --> (7)F(J) deltaJ = 1 and 2 emission bands in the corresponding europium(III) complexes differ in their sensitivity to solution pH. This offers the potential for developing pH responsive probes for in vivo imaging that are independent of probe concentration.     

Catalysis on the coastline: theozyme,molecular dynamics,and free energy perturbation analysis of antibody 21D8 catalysis of the decarboxylation of 5-nitro-3-carboxybenzisoxazole

Antibody 21D8 catalyzes the decarboxylation of 5-nitro-3-carboxybenzisoxazole. The hapten used was designed to induce an antibody binding site with anion binders for the carboxylate, plus a nonpolar environment to accelerate decarboxylation. A recent X-ray crystal structure of 21D8 has shown that the binding pocket contains an array of both polar and charged residues. Nevertheless, 21D8 is able to catalyze a reaction that involves a decrease in polarity from reactant to transition state. The origins of this phenomenon were explored using various computational strategies-quantum mechanics, theozyme models, docking, molecular dynamics, free energy perturbation, and linear interaction energy-the combination of which has produced a consistent picture of catalysis. By partially desolvating the charged carboxylate, 21D8 manages to effect "catalysis on the coastline," without burying the carboxylate in a nonpolar region of the binding pocket. The results have implications for that broad class of enzyme and antibody catalyzed reactions that involve the conversion of a substrate with a relatively localized charge into a transition state with a highly dispersed charge.     

Synthesis of 1,3,4-oxadiazol-2-ones with aliphatic groups at N-3

A series of 3-substituted-5-methoxy-1,3,4-oxadiazol-2-ones were prepared from aldehydes, ketones, phenylacetic acids, and 1,2- and 1,3-diketones. Conditions for the formation of these oxadiazolones from the precursor N-carbamoyl chlorides depended on the structure, and varied from spontaneous ring closure to those requiring bases. Variation in the N-3 substituents sometimes produced mixtures of isomers which were separated and identified. These molecules were prepared in order to study the effect of the N-3 substituent variation on the biological properties of oxadiazolones.     

Particle circulation and oxygen mass transfer in an immobilized cell bioreactor

Two important considerations in the design of an aerobic particulate immobilized cell bioreactor are the provision of sufficient oxygen to maintain the desired metabolism of the immobilized organism, and the biomass holdup (which is proportional to the number of immobilized cell particles in the reactor). The Circulating Bed Reactor, a reactor developed for use with those forms of immobilization that result in particles of essentially neutral buoyancy, operates with an expanded bed of circulating particles. The particle number density attainable in such a reactor has been found to be dependent upon the circulation cell aspect ratio, the individual particle properties, the static bed voidage of the particles, and the superficial gas velocity. The oxygen mass transfer characteristics have been found to be dependent upon the circulatory nature of the system, the particle (solids) holdup, the particle porosity, and the superficial gas velocity.     

Sequential ortho effects: characterization of novel [M - 35]+ fragment ions in the mass spectra of 2-alkyl-4, 6-dinitrophenols

High-resolution mass spectrometry (HRMS), hybrid tandem mass spectrometry (MS/MS) (EBqQ), and photoelectron-photoion coincidence (PEPICO) experiments were conducted to examine a possible ortho-ortho effect resulting in a novel [M - 35]⁺ fragment ion in 2-alkyl-4, 6-dinitrophenols. For compounds having ethyl or larger alkyl substituents, [M35]⁺ was observed only when [M - 18]⁺ ions were present, with the ortho nitro group being involved in the reaction to [M- 35]⁺. For [M - 18]⁺ and [M - 35]⁺, HRMS results were consistent with losses of H₂O and H₂O + OH, respectively, whereas MS/MS results indicated a sequential reaction due to metastable dissociations. The appearance energy determined by PEPICO for [M - 35]⁺ was found to be greater than the appearance energy for [M - 18]⁺, thus supporting a sequential reaction. 69–75).     

Dependence of electrical performance on structural organization in polymer field effect transistors

Organic semiconductors (OSCs) are strong contenders for use in printed, flexible electronics. Although organic electronic materials have been studied for many years, the physics of charge transport is still under investigation. This is in part due to variability resulting from the large variety of molecules that can be synthesized and inconsistency in electrical characterization due to device and processing conditions. Molecular ordering in OSCs is known to alter the charge transport characteristics and attention to long range and short range ordering provides clues as to the nature of transport pathways. Here, we study ordered regioregular poly(3‐hexylthiophene‐2,5‐diyl) films carefully prepared to obtain a set of three samples with incrementally increasing order on identical transistor architectures. Ordering was characterized using a variety of short and long range techniques to probe the coherence and number of crystallites formed during processing, and the correlation between these different measures of order are quantified. We observe three changes in transistor behavior that show a shift from non‐ideal to more textbook‐like characteristics with increasing order: reduction of the contact resistance, shift to field‐independent mobility, and a shift from a diode‐like (S‐shaped) to linear response at low lateral fields. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 1063–1074     

Determination of a novel antifibrotic small molecule GDC‐3280 in human plasma and urine by liquid chromatography tandem mass spectrometry to support its first‐in‐human clinical trial

A specific and robust LC–MS/MS method was developed and validated for the quantitative determination of GDC‐3280 in human plasma and urine. The nonspecific binding associated with urine samples was overcome by the addition of CHAPS. The sample volume was 25 μL for either matrix, and supported liquid extraction was employed for analyte extraction. d6‐GDC‐3280 was used as the internal standard. Linear standard curves (R² > 0.9956) were established from 5.00 to 5000 ng/mL in both matrices with quantitation extended to 50,000 ng/mL through dilution. In plasma matrix, the precision (RSD) ranged from 1.5 to 9.9% (intra‐run) and from 2.4 to 7.2% (inter‐run); the accuracy (RE) ranged from 96.1 to 107% (intra‐run) and from 96.7 to 104% (inter‐run). Similarly, in urine the precision was 1.5–6.2% (intra‐run) and 1.9–6.1% (inter‐run); the accuracy was 83.1–99.3% (intra‐run) and 87.1–98.3% (inter‐run). Good recovery (>94%) and negligible matrix effect were achieved in both matrices. Long‐term matrix stability was established for at least 703 days in plasma and 477 days in urine. Bench‐top stability of 25 h and five freeze–thaw cycles were also confirmed in both matrices. The method was successfully implemented in GDC‐3280's first‐in‐human trial for assessing its pharmacokinetic profiles.     

Non-Template-Centered, Closed Tetravanadium Phosphate and Phosphonate Clusters

Tetranuclear V(III) complexes, [HB(pz)(3)](4)V(4)(&mgr;-C(6)H(5)OPO(3))(4) (I), its acetonitrile solvate (I.4CH(3)CN), and [HB(pz)(3)](4)V(4)(&mgr;-O(2)NC(6)H(4)OPO(3))(4).4C(7)H(8).H(2)O (II), and tetranuclear vanadyl complexes, (t-Bupz)(4)V(4)O(4)(&mgr;-C(6)H(5)PO(3))(4).2H(2)O (III) and (t-Bupz)(5)V(4)O(4)(&mgr;-C(6)H(5)PO(3))(4).4CH(3)CN.0.6 H(2)O (IV), have been prepared and characterized by spectroscopic, magnetic, and electrochemical methods (pz = pyrazole, t-Bupz = tert-butylpyrazole). The use of organic solvents and bulky organic groups as ancillary ligands leads to formation of neutral species instead of the anionic clusters commonly found in the hydrothermal synthesis of vanadium organophosphate/phosphonate systems. Complexes I.4CH(3)CN and IV have also been characterized by single-crystal X-ray diffraction. Crystal data: I.4CH(3)CN, triclinic, P&onemacr;, a = 15.495(3) ?, b = 17.000(3) ?, c = 17.949(4) ?, alpha = 89.17(3) degrees, beta = 86.00(3) degrees, gamma = 78.60(3) degrees, Z = 2; IV, triclinic, P&onemacr;, a = 15.541(3) ?, b = 16.340(2) ?, c = 19.069(5) ?, alpha = 83.58(2) degrees, beta = 79.67(2) degrees, gamma = 63.68(1) degrees, Z = 2. Both are closed clusters, the core structure of the first consisting of a cubane-like arrangement of metal octahedra and phosphate tetrahedra and the core structure of the second consisting of a distorted, collapsed variant of the first. Unlike other vanadium phosphate clusters, these compounds form in the absence of a central, templating agent. As such they represent the simplest form of a closed cluster in which steric forces and cluster connectivity requirements play the primary role in organizing the cluster framework.     

Design criteria for molecular mimics of fragments of the β-turn. 1. Cα atom analysis

Peptides represent an extensive class of biologically active molecules. They may be used as leads in the development of novel therapeutic agents provided the pharmacophoric information present within them can be translated into non-peptide analogs that lack the peptide backbone and are stable to proteolysis. This is the rationale for peptidomimetic drug design. Frequently, the -turn has been implicated as a conformation important for biological recognition of peptides. Empirical evidence from known peptidomimetics, coupled with a theoretical model of peptide binding and the observation that glycine and proline residues are common within the -turn, has suggested the design of molecules to mimic placement of between two and four of the side-chains. The moderate number of different -turn conformations, combined with the combinatoric nature of side-chain selection complicates the procedure. In this paper, cluster analysis has been used to classify the arrangement of C_{_} atoms about the various fragments of the -turn. Recombination of the observed patterns provides a general model for the -turn which may be used as an effective screen for potential peptidomimetic scaffolds in chemical databases.