Identification and Affinity Determination of Protein-Antibody and Protein-Aptamer Epitopes by Biosensor-Mass Spectrometry Combination

Analytical methods for molecular characterization of diagnostic or therapeutic targets have recently gained high interest. This review summarizes the combination of mass spectrometry and surface plasmon resonance (SPR) biosensor analysis for identification and affinity determination of protein interactions with antibodies and DNA-aptamers. The binding constant (K_D) of a protein–antibody complex is first determined by immobilizing an antibody or DNA-aptamer on an SPR chip. A proteolytic peptide mixture is then applied to the chip, and following removal of unbound material by washing, the epitope(s) peptide(s) are eluted and identified by MALDI-MS. The SPR-MS combination was applied to a wide range of affinity pairs. Distinct epitope peptides were identified for the cardiac biomarker myoglobin (MG) both from monoclonal and polyclonal antibodies, and binding constants determined for equine and human MG provided molecular assessment of cross immunoreactivities. Mass spectrometric epitope identifications were obtained for linear, as well as for assembled (“conformational”) antibody epitopes, e.g., for the polypeptide chemokine Interleukin-8. Immobilization using protein G substantially improved surface fixation and antibody stabilities for epitope identification and affinity determination. Moreover, epitopes were successfully determined for polyclonal antibodies from biological material, such as from patient antisera upon enzyme replacement therapy of lysosomal diseases. The SPR-MS combination was also successfully applied to identify linear and assembled epitopes for DNA–aptamer interaction complexes of the tumor diagnostic protein C-Met. In summary, the SPR-MS combination has been established as a powerful molecular tool for identification of protein interaction epitopes.     

Removing of light hydrocarbons from gas mixtures using polymeric composite membranes based on poly(1-trimethylsilylpropyne)

Usually the methodologies used to analyse the feasibility of water reuse projects are focused on the internal costs. The aim of this paper is to show a methodology to assess the feasibility of a water reuse project taking into account not just the internal impact, but also the external impact (environmental and social, for example) and the opportunity cost derived from the project. Internal benefit is obtained from the difference between internal income and internal costs. Internal income is obtained by multiplying the selling price of reclaimed water and the volume obtained. Internal costs are made up of the sum of investment costs, operating costs, financial costs and taxes. While some of these factors identified can be calculated directly in terms of money, biophysical and social aspects demand the definition of units of measurement. In order to homogenize results, an annual reference is proposed. A monetary value can be obtained from the calculation of each impact. However, there are a series of externalities for which no explicit market exists. In these cases economic valuation methods are used, based on hypothetical scenarios or patterns observed in related markets.     

Hyaluronan/Diethylaminoethyl Chitosan Polyelectrolyte Complexes as Carriers for Improved Colistin Delivery

Improving the therapeutic characteristics of antibiotics is an effective strategy for controlling the growth of multidrug-resistant Gram-negative microorganisms. The purpose of this study was to develop a colistin (CT) delivery system based on hyaluronic acid (HA) and the water-soluble cationic chitosan derivative, diethylaminoethyl chitosan (DEAECS). The CT delivery system was a polyelectrolyte complex (PEC) obtained by interpolymeric interactions between the HA polyanion and the DEAECS polycation, with simultaneous inclusion of positively charged CT molecules into the resulting complex. The developed PEC had a hydrodynamic diameter of 210–250 nm and a negative surface charge (ζ-potential = −19 mV); the encapsulation and loading efficiencies were 100 and 16.7%, respectively. The developed CT delivery systems were characterized by modified release (30–40% and 85–90% of CT released in 15 and 60 min, respectively) compared to pure CT (100% CT released in 15 min). In vitro experiments showed that the encapsulation of CT in polysaccharide carriers did not reduce its antimicrobial activity, as the minimum inhibitory concentrations against Pseudomonas aeruginosa of both encapsulated CT and pure CT were 1 μg/mL.     

Investigation of Bemethyl Biotransformation Pathways by Combination of LC–MS/HRMS and In Silico Methods

Bemethyl is an actoprotector, an antihypoxant, and a moderate psychostimulant. Even though the therapeutic effectiveness of bemethyl is well documented, there is a gap in knowledge regarding its metabolic products and their quantitative and qualitative characteristics. Since 2018, bemethyl is included to the Monitoring Program of the World Anti-Doping Agency, which highlights the challenge of identifying its urinary metabolites. The objective of the study was to investigate the biotransformation pathways of bemethyl using a combination of liquid chromatography-high-resolution mass spectrometry and in silico studies. Metabolites were analyzed in a 24 h rat urine collected after oral administration of bemethyl at a single dose of 330 mg/kg. The urine samples were prepared for analysis by a procedure developed in the present work and analyzed by high performance liquid chromatography–tandem mass spectrometry. For the first time, nine metabolites of bemethyl with six molecular formulas were identified in rat urine. The most abundant metabolite was a benzimidazole–acetylcysteine conjugate; this biotransformation pathway is associated with the detoxification of xenobiotics. The BioTransformer and GLORY computational tools were used to predict bemethyl metabolites in silico. The molecular docking of bemethyl and its derivatives to the binding site of glutathione S-transferase has revealed the mechanism of bemethyl conjugation with glutathione. The findings will help to understand the pharmacokinetics and pharmacodynamics of actoprotectors and to improve antihypoxant and adaptogenic therapy.     

Antibacterial agents and cystic fibrosis: synthesis and antimicrobial evaluation of a series of N-thiomethylazetidinones

The increasing emergence of multidrug-resistant microorganisms is one of the greatest challenges in the clinical management of infectious disease. New antimicrobial agents are therefore urgently required, particularly in the treatment of chronic and recurrent infections often associated with antibiotic-resistant pathogens, as in the case of cystic fibrosis (CF) patients. This study reports the antibacterial activity of a series of monocyclic β-lactams with an alkylidenecarboxyl chain or electron-withdrawing groups such as 4-OAc, 4-SAc, and 4-SO(2)Ph at the C4 position of the ring. N-Unsubstituted and N-thiomethyl derivatives were compared. A total of 33 azetidinones were tested for their activity against Gram-positive and Gram-negative bacterial clinical isolates. The combination of an N-thiomethyl group and a benzyl ester on the 4-alkylidene side chain were found to increase the potency against Gram-positive bacteria. The N-thiomethyl group clearly elevated the activity of 4-acetoxyazetidinones relative to the corresponding NH derivatives. The most active compounds showed minimum inhibitory concentration (MIC) values of 4 and 8 mg L(-1) against methicillin-resistant Staphylococcus aureus isolated from pediatric patients with CF.     

Mass spectrometry and the cellular surfaceome

The collection of exposed plasma membrane proteins, collectively termed the surfaceome, is involved in multiple vital cellular processes, such as the communication of cells with their surroundings and the regulation of transport across the lipid bilayer. The surfaceome also plays key roles in the immune system by recognizing and presenting antigens, with its possible malfunctioning linked to disease. Surface proteins have long been explored as potential cell markers, disease biomarkers, and therapeutic drug targets. Despite its importance, a detailed study of the surfaceome continues to pose major challenges for mass spectrometry-driven proteomics due to the inherent biophysical characteristics of surface proteins. Their inefficient extraction from hydrophobic membranes to an aqueous medium and their lower abundance compared to intracellular proteins hamper the analysis of surface proteins, which are therefore usually underrepresented in proteomic datasets. To tackle such problems, several innovative analytical methodologies have been developed. This review aims at providing an extensive overview of the different methods for surfaceome analysis, with respective considerations for downstream mass spectrometry-based proteomics.     

Balancing–sequencing procedure for a mixed model assembly system in case of finite buffer capacity

In the last decades, the necessity to make production more versatile and flexible has forced assembly line production systems to change from fixed assembly lines to mixed model assembly lines, where the output products are variations of the same base product and only differ in specific customizable attributes. Such assembly lines allow reduced setup time, since products can be jointly manufactured in intermixed sequences (Boysen, Flieder, Scholl. Jena Research Papers in Business and Economics, Friedrich-Schiller-Universitat Jena, 1;1–11, 2007a; Boysen, Flieder, Scholl. Jena Research Papers in Business and Economics, Friedrich-Schiller-Universitat Jena, 2;1–33, 2007b). Unfortunately, the installation of customization options typically leads to variations in process times, and when the cycle is exceeded within a certain station, an overload is created, forcing other stations to wait and idle. Normally, process time variation in an un-paced line are absorbed by buffers, but in some industrial application the buffer dimensions are critical not only for the reduction of work in progress but also in reducing other constrains (space, technology, model dimensions, etc.). The problem of balancing mixed model assembly lines (MALBP), in the long term, and that of sequencing mixed model assembly lines (MMS), in the short term (Merengo, Nava, Pozetti. Int J Prod Res 37:2835–2860, 1999), are the two major problems to solve. The object of this paper is to illustrate an innovative balancing–sequencing step-by-step procedure that aims to optimize the assembly line performance and at the same time contain the buffer dimensions in function of different market demand and production mix. The model is validated using a simulation software and an industrial application is presented.     

Order picking system design: the storage assignment and travel distance estimation (SA&TDE) joint method

Of all the warehouse activities, order picking is one of the most time-consuming and expensive. In order to improve the task, several researches have pointed out the need to consider jointly the layout of the warehouse, the storage assignment strategy and the routing policy to reduce travelled distances and picking time. This paper presents the storage assignment and travel distance estimation (SA&TDE) joint method, a new approach useful to design and evaluate a manual picker-to-parts picking system, focusing on goods allocation and distances estimation. Starting from a set of picking orders received in a certain time range, this approach allows to evaluate the combinations of product codes assigned to storage locations, aisles, sections or warehouse areas and to assess the most relevant ones, for the best location and warehouse layout, with the aim of ensuring optimal picking routes, through the application of the multinomial probability distribution. A case study is developed as well, in order to clarify the concept that underlies the SA&TDE joint method, and to show the validity and the flexibility of the approach, through the calculation of the saving at different levels of detail.