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Quantitative structure activity relationship (QSAR) is the most frequently used modeling approach to explore the dependency of biological, toxicological, or other types of activities/properties of chemicals on their molecular features. In the past two decades, QSAR modeling has ...

Structure–activity relationship (SAR) and quantitative structure–activity relationship (QSAR) models are increasingly used in toxicology, ecotoxicology, and pharmacology for predicting the activity of the molecules from their physicochemical properties and/or t ...

Bibodies and tribodies are therapeutic antibody derivatives with sizes of approximately 75 and 100 kDa, respectively. This makes them smaller than full-size monoclonal antibodies, leading to better tissue penetration. Compared to the smaller scFv and Fab fragments, the bi- and tribo ...

Membrane proteins are notoriously difficult to produce at the high levels required for structural and biochemical characterization. Among the various expression systems used to date, the enteric bacterium Escherichia coli remains one of the best characterized and most versatil ...

E. coli has been widely used for recombinant protein production. Here, we introduce a novel expression method in E. coli, the Single Protein Production (SPP) system, in which E. coli is converted into a bioreactor producing only the target protein. In the SPP system, all E. coli cellular mRNAs are elimin ...

The dual variable domain immunoglobulin (DVD-IgTM) protein is a new type of dual-specific IgG. As a novel therapeutic class, the great potential of the DVD-Ig protein is to simultaneously target two mediators of disease by a single pharmaceutical entity. The molecule contains an Fc region and c ...

Proteins, especially antibodies, are widely used as therapeutic and diagnostic agents. Computational �protein design is a powerful tool for improving the affinity and stability of these molecules. We describe a protein design method which employs the dead-end elimination (DEE) and undefined ...

Affibody molecules are small and robust non-immunoglobulin affinity ligands capable of binding to a wide range of protein targets. They are selected from combinatorial libraries based on a 58 amino acid, three-alpha-helical Z-domain scaffold. They share no sequence or structural hom ...

Most of the FDA-approved therapeutic monoclonal antibodies are full-size IgG molecules with a molecular weight of about 150 kDa. A major problem for such large molecules is their poor penetration into tissues (e.g., solid tumors) and poor or absent binding to regions on the surface of some molecu ...

Yeast display is an efficient technology for selection of antibodies and other proteins with high affinity and thermal stability. Here, we describe a method for affinity maturation of engineered antibody domains (eAds) using yeast display. EAd yeast libraries of relatively large size ( ...

Ribosome display is a cell-free display technology which enables in vitro selection of antibodies from large recombinant DNA libraries. It also allows continuous introduction of mutations into the selected DNA pool by PCR-based mutagenesis in each cycle, enabling selection of antib ...

Phylomer libraries are made from random overlapping genome fragments of biodiverse bacteria and Archaea. They provide a rich source of high-affinity binders to protein interfaces, and can be used both for target-directed screening approaches and for phenotypic screens to discover n ...

Advances in antibody–drug conjugates (ADCs) will permit sensitive discrimination between healthy and cancer cells. Promising clinical results generated much hope that this targeted prodrug therapy will offer more effective treatment options to patients. Manufacturing su ...

Therapeutic proteins represent a significant part of the new pharmaceuticals coming on the market every year and are now widely spread in therapy to treat or relief symptoms related to many metabolic and oncologic diseases. The parenteral route remains as a primary strategy for protein adm ...

Protein aggregation is believed to be responsible for a number of human diseases and limits the yields of pharmaceutical proteins during production. Computer simulations can be used to develop novel experimentally testable hypotheses pertaining to aggregation. While all-atom s ...

Protein based biotherapeutics have emerged as a successful class of pharmaceuticals. However, these macromolecules endure a variety of physicochemical degradations during manufacturing, shipping, and storage, which may adversely impact the drug product quality. Of these de ...

In this chapter, application of size exclusion chromatography with inline multi-angle light scattering (SEC-MALS) to protein systems is reviewed, in particular for its use in elucidating mechanistic details of net-irreversible aggregation processes. After motivating why SEC ...

The unintended presence of particulate matter in injectable products is an indicator of the quality of the product. Subvisible particulates have historically been monitored through methods such as light obscuration and membrane microscopy, as outlined in the United States Pharma ...

Isomerization of aspartic acid (Asp) to isoaspartic acid (isoAsp) via succinimide intermediate is a common route of degradation for proteins that can affect their structural integrity. As Asp/isoAsp is isobaric in mass, it is difficult to identify the site of modification by LC-MS/MS pept ...

PEGylation of peptide and proteins is an important method of improving their pharmacokinetic, pharmacodynamic, and immunological profiles, and thus enhancing their therapeutic effect. However, PEGylation of peptides and proteins creates significant challenges for deta ...