Binding property classes

A fuzzier atom type participating in these descriptors has been defined that is pharmacologically relevant - the physicochemical type at near-neutral pH [24], which is one of the following seven binding property classes 1 = cation 2 = anion 3 = neutral hydrogen-bond donor 4 = neutral H-bond acceptor ... 

In this respect, the CUE domain is not a isolated case. There are a number of other domain families, each of them only defined in the bioinformatical sense, that have significant matches within established UBA or CUE domain regions. Based on this similarity and on secondary-structure predictions, it can be expected that all of those domain types assume the typical UBA-like three-helix bundle fold. However, it is not clear if all of those domains also bind to ubiquitin, or if they have evolved to different binding properties. Many of the UBA-like domain classes are unpublished. Nevertheless, they should be briefly discussed here, as they are a logical extension of the UBA/CUE paradigm. 

Horton et al. analyzed the Mn -binding properties of hammerhead ribozyme-substrate complexes by EPR [81]. The results are consistent with the two-phase folding model. They found two classes of metal-binding sites with higher affinity and lower affinity, by monitoring the number of bound Mn + ions per hammerhead ribozyme-substrate complex at various concentrations of NaCl. They observed, in the presence of a constant concentration of Mn + ions, a sudden decrease in the number of bound low-affinity Mn ions at a lower concentration of NaCl, followed by a slow decrease or a plateau value of the number of bound high-affinity Mn ions at a higher concentration of NaCl. For example, in the absence of NaCl and in the presence of either 0.3 mmol/1 or 1 mmol/1 Mn + ions, the number of bound Mn ions per hammerhead ribozyme-substrate complex was approximately 14. Addition... 

The cause of the cell cycle specificity of the bisindole alkaloids may be associated with the ability of these compounds to interact with the protein tubulin and thereby inhibit the polymerization (and depolymerization) of microtubules (16,17). In this respect the cellular pharmacology of vinca alkaloids is similar to that of other cytotoxic natural products such as colchicine or podophyllotoxin. On closer inspection, however, Wilson determined that the specific binding site on tubulin occupied by vinblastine or vincristine is chemically distinct from the site occupied by the other natural products (18). Subsequent experiments have determined that the maytansinoids, a class of ansa-macrocycles structurally distinct from the bisindoles, may bind to tubulin at an adjacent (or overlapping) site (19). A partial correlation of the antimitotic activity of these compounds with their tubulin binding properties has been made, but discrepancies in cellular uptake probably preclude any quantitative relationship of these effects (20). 

Poly(ethylene oxide) (PEO) macromonomers constitute a new class of surface active monomers which give, by emulsifier-free emulsion polymerization or copolymerization, stable polymer dispersions and comb-like materials with very interesting properties due to the exceptional properties of ethylene oxide (EO) side chains. They are a basis for a number of various applications which take advantage of the binding properties of PEO [39], its hydrophilic and amphipathic behavior [40], as well as its bio compatibility and non-absorbing character towards proteins [41]. Various types of PEO macromonomers have been proposed and among them the most popular are the acrylates and methacrylates [42]. 

Calixarenes provided the main inspiration for the artifidal receptors studied in my group. We wanted to develop a new class of macrocyclic host with binding properties and structural variability similar to calixarenes but a closer relationship to natural systems. The obvious choice was, of course, to base such receptors on cyclopeptides, macrocydic compounds that are composed of the same subunits as the natural systems. 

Biopharmaceuticals represent a broad but discrete class of large molecular weight therapeutic entities that are characterized by their specific pharmacological activities and distinctive pharmacokinetics. The selection of an appropriate animal model is dependent on a combination of PD and PK factors. As described in this chapter, it is essential to understand the relationship of the basic pharmacology of a biopharmaceutical (signaling, receptor presence, binding properties, etc.) and the associated PK properties to that expected in humans, in order to select animal species that will have the most predictive value in safety assessments. 

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