Solubility substrate-transporter interactions

The recent crystallization of the small water-soluble transcriptional regulator of Bacillus subtilis multidrug transporter Bmr, BmrR, which binds hydrophobic cations from the cytosol [64, 65] provides a good example for an interaction determined primarily by van der Waals interactions. Interestingly, the same drugs, which bind to the water-soluble BmrR are also substrates for the transmembrane multidrug transporter Bmr. As will be discussed below, the latter interactions could well be of different nature. 

It has recently been proposed that the Biopharmaceutical Classification System (BCS) can be used to predict intestinal drug disposition with regards to efflux transport and metabolism (339). Furthermore, on the basis of the key substrate BCS-related properties, permeability, and solubility, the system may be used to predict potential interactions mediated through changes in efflux and/or metabolism at the level of the intestine. 

The extent of oral absorption of a drug depends on physical properties of the drug (e.g., solubility and membrane permeability) and its interaction with various enzymatic processes of an organism. The two most prominent enzymatic systems are drug metabolic enzymes and drug transporters. Both metabolic enzymes and transporters exist as many related forms that generally have distinct, yet potentially overlapping, substrate specificities. 

In silico methods that are able to predict quantitative aspects of the interaction of a substrate with P-gp would be of great value. So far, modeling was applied mainly to lock-key-type reactions taking place in aqueous solution. The structural diversity and lipid solubility of P-gp substrates and the fact that their encounter with the transporter takes place in the lipid membrane and not in aqueous solution are new challenges for in silico predictions. Since all in silico models are based on experimental data, we first provide a short introduction to various P-gp assays and discuss their underlying principles (18.2). Secondly, we summarize the different in silico approaches (18.3), and, lastly, we discuss the parameters that are most relevant for the different in silico models (18.4). 

The absorption and transport of the majority of drugs across biological membranes occurs by passive diffusion, a process dependent upon physicochemical properties, i.e., lipophilicity, ionization, and molecular size. Since enantiomers have identical physicochemical properties, stereoselectivity would not be expected even though membrane phospholipids are chiral, the significance of lipophilieity appears to outweigh that of compound chirality. In contrast, differences between diastereoisomers may occur as a result of their differential solubility. However, in the case of compounds transported via earrier-mediated meehanisms, e.g., facilitated diffusion or active transport, proeesses involving a direct interaction between a substrate and a carrier maeromoleeule, stereoselectivity is expected. Preferential absorption of the l- eompared to the D-enantiomers of dopa [96] and methotrexate [97,98] have been reported. In the case of the above examples, enantioseleetivity in absorption is observed, whereas in the case of eephalexin, a eephalosporin antibiotic, diastereoselectivity for the L-epimer oeeurs. The L-epimer has shown a greater affinity than, and acted as a competitive inhibitor of o-eephalexin transport [99]. The L-epimer is also more suseeptible to enzyme-mediated hydrolysis, with the result that it cannot be detected in plasma [99]. 

A few variations to the original dip-pen lithography have been applied in separate studies. The results have fully demonstrated the potential of this technique [28,29]. For instance, Lim and Mirkin reported a patterning method in which the AFM tip was coated with a water-soluble CP by thermal evaporation or dip-coating and the charged water-soluble polymer was transported from the AFM tip to the pretreated oppositely charged substrate by electrostatic interactions (Figure 10.13 and 10.14) [28]. 

A second important limitation is associated with the fact that most zwitterionic compounds are water soluble. On the contrary, most designed receptors continue being soluble in organic solvents and having a much reduced solubility in water or aqueous solutions. Thus, it is not surprising that the analysis of the receptor-substrate interaction is carried out by means of extraction and/or transport experiments. Besides the interest of selective recognition for these kinds of processes, this fact also reflects, in many cases, the very different solubilities of both components, the zwitterionic substrate and the receptor. 

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