Pseudoreceptor

Fetal Hb transcription inducers TFIT pseudoreceptor, Similarity search of 630 candidate molecules 2 of 26 active [115]... 

It has not yet been clarified whether the ring substituents interact directly with the binding site or affect the molecular characteristics of the DHP molecules in common. A recently used atomistic pseudoreceptor model for a series of DHP indicated a putative charge-transfer interaction was stabilizing the DHP-binding site complex [19]. To prove this hypothesis qualitative and quantitative analysis of the molecular orbitals of nine DHP derivatives (Fig. 9.11) was performed [18]. Charge-transfer (or electron-donor-acceptor) interactions are indicative of electronic... 

Holtje and Sippl selected a representative training set of twelve superimposed structures. The aforementioned Y AK process resulted in a pseudoreceptor that consists of six amino acid residues (Figure 5). In this pseudoreceptor model, the imidazole ring of the ligands is bound to a tyrosine residue that donates a proton to the imidazole and an asparagine residue that accepts a proton from the imidazole. Hence, two distinct H-bond have been found, which explain the strict binding mode of the imidazole. It has to be noted that the position of these receptor residues relative towards the imidazole is a consequence of... 

Figure 5. Pseudoreceptor model for histamine H, agonists by Holtje and Sippl [25]. Four ligands are shown inside the binding region.

This chapter does not cover these classical approaches but rather focuses on basic principles, evolution and scientific applications based on specialized pseudoreceptor modeling software packages. 

In order to build up an atomistic pseudoreceptor model, the following basic steps have to be carried out ... 

If individually positioned residues are in close contact, the program evaluates the possibility of peptide-bond formation and thus links single residues to a peptide. Furthermore, ligand-independent extension (i.e. residues without direct contact to vectors) of the pseudoreceptor can be used in order to complete the peptidic receptor site (e.g. entirely closed shell around the ligand molecules). 

Internal ligand relaxation allows the removal of strain possibly imposed on the ligands by the receptor during correlation-coupled refinement but usually yields suboptimal models. Therefore, correlation-coupled receptor minimization followed by unconstrained ligand relaxation is repeated several times until a highly correlated pseudoreceptor model is obtained in the relaxed state (designated ligand equilibration). 

Fig. 5.2 Flowchart of a typical PrCen pseudoreceptor model construction and validation approach.

The pseudoreceptor modeling concept was utilized for (i) reconstruction of experimentally determined receptor sites, (ii) exploration of crucial ligand-receptor interaction sites and (iii) prediction of pharmacological activities of molecules, sometimes compared with results derived from other 3D-QSAR techniques. 

Although the orientations and calculated free binding energies of the sulfonamide ligands are not presented in the original paper, reconstruction of the receptor site via a pseudoreceptor approach was promising and stimulated further activities. 

The pseudoreceptor model was constructed with six amino acid residues. The imidazole ring of the ligands and the terminal basic function were saturated via... 

Fig. 5.5 (a) Binding site of human carbonic anhydrase I (pdb code 2CAB) with a bound zinc ion (sphere). Arrows indicate the directions of the pseudoreceptor model to rotate and shift amino acid residues, (b) Super-... 

Fig. 5.6 Part of the pseudoreceptor model for histamine H3-receptor antagonists [25] (one leucine beside the isoleucine residue is omitted for clarity). Hydrogen bonds from ligands to complementary functions of asparagine (Asn), tyrosine (Tyr) and aspartate (Asp) are located in the GR/D-...

Table 5.1 CoMFA statistics3 for 29 cannabinoids based on a pharmacophore (PA) and a pseudoreceptor (PrA) alignment...

The predictive powers of the two models are almost identical although, at first glance, deviation from experimental values is smaller making use of the classical pharmacophore-CoMFA approach [e.g. AAG° = 0.39 (PA) vs 0.70 kcal mol-1 (PrA)]. On closer inspection, one has to take into account that the pseudoreceptor-derived model shows a stronger internal correlation (higher r2 and r v values) and therefore the differences in the prediction are statistically not relevant. 

In a reversed type of approach, we used the pseudoreceptor modeling concept not to develop a tool for SAR predictions but to characterize two discrete ion channel modes on a molecular level [28]. For this purpose, a set of 13 well-characterized 1,4-dihydropyridine (DHP) derivatives with experimentally determined dissociation constants (Kf) for the voltage-gated calcium channel (VGCC) in the resting state (rs) and the open/inactivated state (is) were investigated (Table 5.2). 

Selectivity of the resting state pseudoreceptor model was checked with the same ligands via prediction of their binding behavior to the inactivated channel mode. 

For the construction of a pseudoreceptor model of the open/inactivated state, ligand-derived information was considered indicating the left-hand side of DHPs to be essential for binding [28]. 

Since all pseudoreceptor models are composed of the same six amino acid residues - Thr, Phe, Gly, Met, Tyr, Tyr - transition from resting to open/inactivated state could be described by one additional hydrogen-bond donor interaction (Thr) at the left-hand side of DHPs. 

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