Aspects of antibody-catalyzed primary amide hydrolysis

Because there are many known C-terminally amidated peptides of biological importance, there is great potential in medicine and organic synthesis for antibodies that catalyze primary amide bond hydrolysis or formation. We characterized a catalytic antibody, 13D11, raised to a phosphinate hapten, that hydrolyzed the primary amide of a dansyl-alkylated derivative of (R)-phenylalaninamide (DNS-(R)F-NH₂). At pH 9.0, 13D11 hydrolyzed DNS-(R)F-NH₂ with a k_cat of 1.65 × 10^-7 s^-1 (k_cat/k_uncat = 132) and a K_m of 432 μM, and was stereospecifically hapten-inhibited (K_i = 14.0 μM). Control experiments indicated that the catalytic activity was not the result of a contaminating protease. In accordance with the hapten being a transition-state analog of base hydrolysis, the rate of DNS-(R)F-NH₂ hydrolysis increased with hydroxide concentration to an optimum pH of 9.5. Above pH 9.5, activity declined rapidly suggesting the antibody was inactivated during the long incubation period. This work demonstrates the feasibility of generating catalytic antibodies to hydrolyze unactivated amide bonds without cofactor assistance.     

Structural analysis of regular copolymers of Butadiene and methylene with repeat unit [But-(CH2)n-But] by the use of model compounds—III. An analysis of the factors which influence the ratio of cis and trans 1,4 addition

In previous papers the 1,2 to total 1,4 ratios in copolymers of butadiene of repeat unit-[But-But-R]¹, where R is an alkyl ligand, have been determined by preparing model compounds HR-But-But-RH under identical conditions. Use of capillary column GLC enables the cis and trans isomers to be separated and the effect of varying experimental parameters on the cis/trans ratio is examined. This ratio is shown to be more sensitive to reaction temperature than the 1,2 to total 1,4 ratios previously studied. Results indicate that when R = (CH₂)_n the cis/trans ratio is independent of n for values of n > 1.     

Multivalent drug design. Synthesis and in vitro analysis of an array of vancomycin dimers

The design, synthesis, and in vitro microbiological analysis of an array of forty covalently linked vancomycin dimers are reported. This work was undertaken to systematically probe the impact of linkage orientation and linker length on biological activity against susceptible and drug-resistant Gram-positive pathogens. To prepare the array, monomeric vancomycin synthons were linked through four distinct positions of the glycopeptide (C-terminus (C), N-terminus (N), vancosamine residue (V), and resorcinol ring (R)) in 10 unique pairwise combinations. Amphiphilic, peptide-based linkers of four different lengths (11, 19, 27, and 43 total atoms) were employed. Both linkage orientation and linker length were found to affect in vitro antibacterial potency. The V-V series displayed the greatest potency against vancomycin-susceptible organisms and vancomycin-resistant Enterococcus faecalis (VRE) of VanB phenotype, while the C-C, C-V, and V-R series displayed the most promising broad-spectrum activity that included VRE of VanA phenotype. Dimers bearing the shortest linkers were in all cases preferred for activity against VRE. The effects of linkage orientation and linker length on in vitro potency were not uniform; for example, (1) no single compound displayed activity that was superior against all test organisms to that of vancomycin or the other dimers, (2) linker length effects varied with test organism, and (3) whereas one-half of the dimers were more potent than vancomycin against methicillin-susceptible Staphylococcus aureus (MSSA), only one dimer was more potent against methicillin-resistant S. aureus (MRSA) and glycopeptide-intermediate susceptible S. aureus (GISA). In interpreting the results, we have considered the potential roles of multivalency and of other phenomena.     

Optimal control of harvesting coupled with boundary control in a predator—prey system

We consider boundary control and control via harvesting in a parabolic predator—prey system for a bounded region. The boundary control depicts the relationship between the boundary environment and the possibly harmful species. In addition, a proportion of the predator is harvested for profit. We choose to maximize the objective functional which incorporates the amount of the prey and the revenue of harvesting of the predator less the economic cost of sustaining a satisfactory boundary habitat and the cost due to the harvesting component. Moreover, we characterize the unique optimal control in terms of the solution to the optimality system, which is the state system coupled with the adjoint system.     

Redox-Neutral Metal-Free Three-Component Carbonylative Dearomatization of Pyridine Derivatives with CO2

The TBD (1,3,5-triazabicyclodec-5-ene) assisted three-component carbonylation of pyridine-2-methanamines is documented by means of CO₂ as a benign CO surrogate. The redox-neutral methodology enables the realization of densely functionalized imidazo-pyridinones in high yields (up to 93 %) and excellent chemoselectivity. Combined computational and experimental investigations revealed an unprecedented RCOCl/TBD concerted electrophilic activation of carbon dioxide.     

Computational chemistry at Janssen

Computer-aided drug discovery activities at Janssen are carried out by scientists in the Computational Chemistry group of the Discovery Sciences organization. This perspective gives an overview of the organizational and operational structure, the science, internal and external collaborations, and the impact of the group on Drug Discovery at Janssen.     

Effect of steam on structure and mechanical properties of biomedical block copolymers

The effect of steam on the micro‐phase structure and mechanical properties of different block copolymers used in biomedical devices is investigated via FT‐IR, tensile tests and dynamic mechanical analysis (DMA). Steam sterilization, commonly performed on medical devices and simulated in this work, affects the copolymers' morphology, due to high temperature and humidity conditions. FT‐IR analysis reveals that steam induces a modification in the crystalline conformations of copolymers with a pre‐existing hydrogen bonding network, that is, thermoplastic polyurethanes (TPU) and poly(ether‐block‐amide) (PEBA), while it does not significantly affect the domain conformation in styrenic block copolymers (SEBS), due to weak interaction with water. As a consequence, relevant changes of the mechanical properties, closely related to the microdomain structure, are found for TPU and PEBA after sterilization, while SEBS mechanical behavior remains stable, as demonstrated by tensile tests and DMA results. For this reason, SEBS is suggested as the best choice in terms of durability in biomedical applications. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014 , 52, 1337–1346