Targeting drug transporters - combining in silico and in vitro approaches to predict in vivo.

Transporter proteins are expressed throughout the human body in different vital organs. They play an important role to various extents in determining absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) properties of therapeutic molecules. Over the past decade, numerous drug transporters have been cloned and considerable progress has been made toward understanding the molecular characteristics of individual transporters. In this chapter several in vitro and in silico techniques are described with applications to understand transporter behavior. These include employing new techniques to rapidly identify novel ligands for transporters. Ultimately these methods should lead to a greater overall appreciation of the role of transporters in vivo.

Bacterial peptide recognition and immune activation facilitated by human peptide transporter PEPT2.

Microbial detection requires the recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs) that are distributed on the cell surface and within the cytosol. The nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) family functions as an intracellular PRR that triggers the innate immune response. The mechanism by which PAMPs enter the cytosol to interact with NLRs, particularly muropeptides derived from the bacterial proteoglycan cell wall, is poorly understood. PEPT2 is a proton-dependent transporter that mediates the active translocation of di- and tripeptides across epithelial tissues, including the lung. Using computational tools, we initially established that bacterial dipeptides, particularly gamma-D-glutamyl-meso-diaminopimelic acid (gamma-iE-DAP), are suitable substrates for PEPT2. We then determined in primary cultures of human upper airway epithelia and transiently transfected CHO-PEPT2 cell lines that gamma-iE-DAP uptake was mediated by PEPT2 with an affinity constant of approximately 193 microM, whereas muramyl dipeptide was not transported. Exposure to gamma-iE-DAP at the apical surface of differentiated, polarized cultures resulted in activation of the innate immune response in an NOD1- and RIP2-dependent manner, resulting in release of IL-6 and IL-8. Based on these findings we report that PEPT2 plays a vital role in microbial recognition by NLR proteins, particularly with regard to airborne pathogens, thereby participating in host defense in the lung.

Design of high-affinity peptide conjugates with optimized fluorescence quantum yield as markers for small peptide transporter PEPT1 (SLC15A1).

We employed a computational approach to design and synthesize a series of fluorescently labeled hPEPT1 substrates. Five Alexa Fluor-350-labeled peptides were assessed for their in vitro inhibitory activity in hPEPT1-transfected CHO cells. At least four labeled peptides show potent inhibitory activity toward hPEPT1-mediated uptake of [(3)H]-GlySar and three compounds displayed a significant cellular uptake specifically mediated by hPEPT1.

Computational models to assign biopharmaceutics drug disposition classification from molecular structure.

PURPOSE: We applied in silico methods to automatically classify drugs according to the Biopharmaceutics Drug Disposition Classification System (BDDCS). MATERIALS AND METHODS: Models were developed using machine learning methods including recursive partitioning (RP), random forest (RF) and support vector machine (SVM) algorithms with ChemDraw, clogP, polar surface area, VolSurf and MolConnZ descriptors. The dataset consisted of 165 training and 56 test set molecules. RESULTS: RF model 3, RP model 1, and SVM model 1 can correctly predict 73.1, 63.6 and 78.6% test compounds in classes 1, 2 and 3, respectively. Both RP and SVM models can be used for class 4 prediction. The inclusion of consensus analysis resulted in improved test set predictions for class 2 and 4 drugs. CONCLUSIONS: The models can be used to predict BDDCS class for new compounds from molecular structure using readily available molecular descriptors and software, representing an area where in silico approaches could aid the pharmaceutical industry in speeding drugs to the patient and reducing costs. This could have significant applications in drug discovery to identify molecules that may have future developability issues.

Rapid identification of P-glycoprotein substrates and inhibitors.

Identifying molecules that interact with P-glycoprotein (P-gp) is important for drug discovery but is also generally reliant on time-consuming in vitro and in vivo studies. As an alternative approach, the current study applied pharmacophore models and database screening to rapidly retrieve molecules that bind as substrates or inhibitors for P-gp from commercial databases and then confirmed their affinity as inhibitors in vitro. Seven molecules (acitretin, cholecalciferol, misoprostol, nafcillin, repaglinide, salmeterol, and telmisartan) with no published details for P-gp affinity, one positive control inhibitor (miconazole), and two negative control molecules (phenelzine and zonisamide) were selected for testing. The MDCK-MDR1 in vitro cell model was used to confirm their inhibitory effect on [3H]digoxin transport, and the ATPase assay was used as an additional in vitro tool to indicate P-gp activation. All seven test drugs were confirmed to have P-gp affinity. Additionally, our experimental results provided plausible explanations for the published pharmacokinetic profiles of the tested drugs and their classification according to the biopharmaceutics and drug disposition classification system. In this study, we showed the successful application of pharmacophore models to accurately predict P-gp binding, which holds promise to anticipate drug-drug interactions from screening drug databases and a priori prediction of novel P-gp inhibitors or substrates.

Functional characterization of the peptide transporter PEPT2 in primary cultures of human upper airway epithelium.

This study characterizes the expression and function of the peptide transporter hPepT2 (SLC15A2) in differentiated primary cultures of human upper airway lung epithelia obtained from six human donors. Genotype analysis of a SNP in exon 15 of hPepT2 genotypes in six donors revealed an expected distribution of the two main variants present at similar frequency (two AA homozygotes, two BB homozygotes, and two AB heterozygotes). Real-time PCR analysis of the hPepT2 mRNA message revealed no significant differences among genotypes. hPEPT2 was expressed on the apical membrane in all donor specimens, demonstrated by cell surface biotinylation and Western analysis (104 kD). We then compared transepithelial transport of the prototypical substrate (3)H-glycylsarcosine in all donor cultures in the absence and presence of known inhibitors of hPEPT2 to ascertain the phenotype of functionally expressed hPepT2 in the upper airway epithelium. An array of inhibitors included dipeptides, beta-lactam antibiotics, bestatin, and ACE inhibitors. hPEPT2 exhibited saturable Michaelis-Menten-type kinetic parameters for GlySar, corroborating previously reported values for K(T) and J(max). Donor-to-donor variation of transport for different substrates did not correlate with hPepT2 haplotypes in this sample cohort. These findings demonstrate functional hPEPT2 transporter expression in primary cultures of human lung epithelial cells. hPEPT2-mediated transport could serve as a strategy for noninvasive systemic delivery of peptides and peptidomimetics drugs.