Profiling protein binding

A similar strategy was employed to identify a DPP-IV inhibitor (6) with good in vivo potency in a mouse model of diabetes [44], Plasma protein binding, as assessed by shift assay (50% serum), was presented for all final compounds. The compound selected as having the best overall profile was active in vivo at 0.1 mg/kg. The activity at 1 h post-dose was consistent with the free drug principle - total plasma concentration 269 nM murine-free fraction 4% unbound plasma concentration 11 nM in vitro potency versus murine DPP-IV 6nM. 

Additional assays used in early pharmaceutical property profiles usually include plasma protein binding, individual cytochrome P450 assays, stability in the presence of serum, production of metabolites likely to be involved in covalent binding to biomolecules, and interaction with efflux pumps ... 

Zyomyx chip technology is based upon an atomically flat gold surface to which is attached a proprietary SAM (self-assembled monolayer) surface for optimal protein binding (Peluso et al., 2003). The company launched its Protein Profiling Biochip System and Human Cytokine Biochip products in February 2003. 

The analysis was completed for 12 compounds for which protein binding, renal and hepatic clearances and microsomal data were available. Plasma concentration versus time profiles in the rat were also available for these compounds. The approach taken was to simulate the individual processes (metabolic clearance, renal clearance, distribution, pharmacological activity). The ability of the PBPK model to simulate the in vivo behavior of the compound was verified in the rat. Thus, the metabolic clearance of the compounds could be reasonably well simulated, based on microsomal data and assuming no binding to microsomes less than twofold deviation between the observed and predicted clearance was achieved for about eight of the... 

In the study by Parrott et al. [7], a generic PBPK model was applied to predict plasma profiles after intravenous and oral dosing to the rat for a set of 68 compounds from six different chemical classes. The compounds were selected without particular bias and so are considered representative of current Roche discovery compounds. The physicochemical properties of the compounds are rather different from those of marketed compounds in particular they have higher lipophilicity (mean logP = 4) and lower aqueous solubility as well as a tendency to be neutral at physiological pH. The more extreme property values can present experimental determination challenges and so for consistency all predictions were made on the basis of calculated lipophilicity and protein binding while in vitro... 

The quinolones have long enjoyed a favorable pharmacokinetic profile. They are well absorbed and distributed in body tissues and fluids. A typical dose is between 100 mg and 1 g. The older agents have half-lives under 3 h, but a more typical value is between 4 and 14 h. Protein binding tends to be low to moderate (15-65%), but there are some exceptions such as nahdixic acid (90%) and garenoxacin (80%) (Howe and MacGowan, 2004). Bioavailability ranges from 55 to 100% (Dudley, 2003b). It has been well estabhshed in the hterature that the effectiveness of quinolones can be dramatically reduced if the medication is taken with an antacid. Many antacids are salts of divalent and trivalent cations such as Al " , Ca, and Mg " ". In addition, Fe " , Cu " , Ni " ", Zn " ", and also reduce quinolone activity. All these cations form a chelate with... 

It has a favorable pharmacokinetic profile with 90-100% oral absorption. Effective concentrations are reached in the CSF and also in prostatic tissue. Protein binding is about 45%. 

The protein binding of compounds with such low partition coefficients is virtually non-existent as demonstrated by MRI and pharmacokinetic studies. The low protein binding of the extracellular gadolinium complexes currently used in clinical practice correlates very well with their excellent safety profile. 

When the rotation of the Gd(III) chelate is substantially slowed down, one observes the typical high field peak around 20-60 MHz in the NMRD profiles. As an example, Fig. 10 shows the effect of non-covalent protein binding on the relaxivity under the experimental conditions applied, the small molecular weight chelate MP2269 is totally bound to bovine serum albumin which results in an increase in the rotational correlation time, and consequently in proton relaxivity [50]. 

Fig. 10. Effect of non-covalent protein binding on proton relaxivity NMRD profiles obtained for the small molecular weight Gd(III) complex, MP2269 (empty squares) and for its fully bound protein adduct (filled squares) at t = 37°C. The high field peak in the NMRD profile of the protein-bound chelate is the consequence of slow rotation...

Clemons PA, Bodycombe NE, Carrinski HA, Wilson JA, Shamji AF, Wagner BK, Koehler AN, Schreiber SL (2010) Small molecules of different origins have distinct distributions of structural complexity that correlate with protein-binding profiles. Proc Natl Acad Sci USA 107 18787-18792... 

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