Current Topics in Medicinal Chemistry - Volume 4, Issue 16, 2004

Motivation: No details on P2X receptor architecture had been known at the atomic resolution level. Using comparative homology-based molecular modelling and threading, it was attempted to predict the three-dimensional structure of P2X receptors. This prediction could not be carried out, however, because important properties of the P2X family differ considerably from that of the potential template proteins. This paper reviews an alternative approach consisting of three research fields: bioinformatics, structural modelling, and a variety of the results of biological experiments. Model: Starting point is the amino acid sequence. Using the sequential data, the first step is a secondary structure prediction. The resulting secondary structure is converted into a three-dimensional geometry. Then, the secondary and tertiary structures are optimized by using the quantum chemistry RHF / 3-21G minimal basic set and the allatom molecular mechanics AMBER96 force field. The fold of the membrane-embedded protein is simulated by a suitable dielectricum. The structure is refined using a conjugate gradient minimizer (Fletcher-Reeves modification of the Polak-Ribiere method). The results of the geometry optimization were checked by a Ramanchandran plot, rotamer analysis, all-atom contact dots, and the C(β) deviation. As additional tools for the model building, multiple alignment analysis and comparative sequence-function analysis were used. The approach is exemplified on the membrane-embedded, ligand-gated P2X3 receptor subunit, a monovalent-bivalent cation channel-forming glycoprotein that is activated by extracellular adenosine 5'-triphosphate. From these results, a topology of the pore-forming motif of the P2X3 receptor subunit was proposed. It is believed that a fully functional P2X channel requires a precise coupling between (i) two distinct peptide modules, an extracellularly occuring ATP-binding module and a pore module that includes a long transmembrane and short intracellular part, (ii) an interaction surface with membranes, and (iii) hydrogen bonding forces of the residues and hydrated cations. Furthermore, this paper demonstrates the role of quantitative structure-activity relationships (QSARs) in P2X research (calcium ion permeability of the wild-type and after site-directed mutagenesis of the rat P2X2 receptor protein, KN-62 analogs as competitive antagonists of the human P2X7 receptor). Experimental proofs: The predictions are experimentally testable and may provide an additional interpretation of experimental observations published in literature. In particular, there is the good agreement of the geometry optimized P2X3 structure with experimentally proposed P2X receptor models obtained by neurophysiological, biochemical, pharmacological, and mutation experiments. Although the rat P2X3 receptor subunit is more complex (397 amino acids) than the KcsA protein (160 amino acids), the overall folds of the peptide backbone atoms are similar. Limitations: To avoid semantic confusion, it should be noted that “;prediction”; is defined in a probabilistic sense. Matches to generic rules do not mean “;this is true“; but rather ”;this might be true”;. Only biological and chemical knowledge can determine whether or not these predictions are meaningful. Thus, the results from the computational tools are probabilistic predictions and subject to further experimental verification. Availability: The geometry optimized P2X3 receptor subunit is freely available for academic researchers on e-mail request (PDB format).

The P2X7 receptor is involved in several processes relevant to inflammation (cytokine release, NO generation, killing of intracellular pathogens, cytotoxicity), thus, it may be an appealing target for pharmacological intervention. The characterisation of native and recombinant P2X7 receptor continues to be hindered by the lack of specific and subtypeselective agonists and antagonists. BzATP is currently the most potent agonist known at the endogenous and recombinant P2X7 receptor A tyrosine derivative named KN-62 exhibits selective P2X7 receptor-blocking properties. In this review article we have reported novel series of KN-62-related compounds of the general structure R1-Tyr(OR2)-piperazinyl-R3, in which three positions (R1, R2 and R3) were systematically varied. Two recent articles published by AstraZeneca have reported that novel series of cyclic imides and adamantane amides are potent P2X7 receptor antagonists.

Purinergic P2X1 and P2X7 receptors are co-expressed in several cell types such as lymphocytes or epithelial cells. Here we examined whether these two P2X subtypes interact with each other in a manner that results in a mutual alteration of their electrophysiologic behaviour. Furthermore, since specific pharmacological tools are needed to assign distinct effects to a particular receptor subtype in native cells, we assessed a series of compounds for their capacity to separate individual current components in cells that co-expressed both receptor subtypes. In Xenopus oocytes, coexpression neither changed the time courses of activation, desensitization and deactivation nor recovery from desensitization when compared to oocytes that express either hP2X1 or hP2X7 receptors alone. A selective activation of hP2X7 receptors was achieved with benzoyl-benzoyl-ATP, which did not activate P2X1 receptor currents. P2X7 receptors could also be selectively activated by ATP when co-applied with 1 μM NF449, a suramin derivative, which is 100,000 fold more potent in blocking P2X1 than P2X7 receptors. ab-methylene-ATP, a reportedly hP2X1 receptor-specific agonist, as well as oxidized-ATP, brilliant blue or KN62, reported hP2X7 receptor antagonists, were found to be ineffective in separating hP2X1 receptor current from the P2X7 current. The best way for a selective activation of the hP2X1 receptor component in cells co-expressing the P2X7 receptor is the application of low concentrations of ATP (< 1 μM) or the addition of Mg2+ when using higher concentrations of ATP.

The cytochromes P450 are a family of heme-containing proteins with a major role in the oxidation of both xenobiotics (including prescribed drugs) and endogenous compounds. There are at least 57 human P450s (termed isoforms) which are all encoded by separate genes but only 10 of these contribute to drug metabolism, with the major contribution coming from only 3 isoforms, CYP3A4, CYP2D6 and CYP2C9. It is now well recognised that most cytochrome P450 genes are subject to genetic polymorphism and that therefore some individuals have sequence changes present that result in the production of an enzyme with altered catalytic activity or give rise to abnormal gene expression. This article describes the range of genetic polymorphisms now known to occur in the drug metabolizing cytochromes P450 with particular reference to their functional effects and the influence of ethnic origin on the frequency of variant alleles. The relevance of the various polymorphisms to drug response and toxicity is considered as well as the possibility that genotype for these polymorphisms may be a determinant for “personalized prescribing” in the future.

The induction of cytochromes P450 (CYPs) has been appreciated for some time but an understanding of the mechanisms involved has been poorly understood until recently. The discovery of the role of nuclear receptors such as the pregnane X receptor (PXR) and the constitutive androstane receptor (CAR) has provided a major trigger for research in this area. This work has provided an explanation for species differences in hepatic induction. The production of a PXR crystal structure in the presence and absence of known high affinity ligands has offered the possibility of predicting structures which may bind to the receptor and hence act as inducing agents in man. An improvement in the technology of hepatocyte culture, access to good quality human hepatocytes and the miniaturisation of cultured preparations has meant that the potential of this technique to predict induction in man has been realised. Molecular biological techniques have also proved essential in both the science and the quantitation of CYP induction. The use of transient transfection cell based systems coupled with reporter gene assays have meant that dose response curves can be generated for many chemicals. Assays have been developed to measure the increase of the corresponding CYP mRNAs in primary hepatocytes and some cell lines with a high degree of sensitivity and specificity (allowing the quantitation of closely related CYPs). Although CYP induction is not usually considered as a major drawback in drug development, the aim should be to eliminate or reduce the inducing effects of a new drug to a minimum. Thus, it is essential to increase our understanding of the complex mechanisms that regulate induction and to pay attention to both the dose and the physicochemical and structural properties of CYP inducing agents.

The initial view that the cytochrome P450 enzyme system functions simply in the deactivation of xenobiotics is anachronistic on the face of mounting evidence that this system can also transform many innocuous chemicals to toxic products. However, not all xenobiotic-metabolising cytochrome P450 subfamilies show the same propensity in the bioactivation of chemicals. For example, the CYP2C, 2B and 2D subfamilies play virtually no role in the bioactivation of toxic and carcinogenic chemicals, whereas the CYP1A, 1B and 2E subfamilies are responsible for the bioactivation of the majority of xenobiotics. Electronic and molecular structural features of organic chemicals appear to predispose them to either bioactivation by one cytochrome P450 enzyme or deactivation by another. Consequently, the fate of a chemical in the body is largely dependent on the cytochrome P450 profile at the time of exposure. Any factor that modulates the enzymes involved in the metabolism of a certain chemical will also influence its toxicity and carcinogenicity. For example, many chemical carcinogens bioactivated by CYP1, on repeated administration, selectively induce this family, thus exacerbating their carcinogenicity. CYP1 induction potency by chemicals appears to be determined by a combination of their molecular shape and electron activation. The function of cytochromes P450 in the bioactivation of chemicals is currently being exploited to design systems that can be used clinically to facilitate the metabolic conversion of prodrugs to their biologically-active metabolites in cells that poorly express them, such as tumour cells, in the so-called gene-directed prodrug therapy.

Our understanding of structure-function relationships have made considerable advances owing to the increasing number of new P450 crystal structures. This is especially true with mammalian P450s. As always, the main bottleneck in a structure determination project is crystallization. While the crystallization techniques used for P450 crystal growth are not much different from that utilized for other proteins, special protein engineering strategies have been developed in order to generate soluble, homogeneous membrane-bound P450 samples amendable for crystallization. Newly determined P450 structures also provide convincing evidence that P450 enzymes are highly dynamic and flexible. Common structural elements found in all P450s have been identified that undergo large conformational changes to allow substrate access and product release. In addition, flexible regions may enable the active site to adapt to the binding of substrates of different size, shape, and polarity. This review will focus on the successful membrane P450 crystallization techniques and the new structural insights based on the growing P450 structure database.

A large number of computational methodologies have been used to predict, and thus help explain, the metabolism catalysed by the enzymes of the cytochrome P450 superfamily (P450s). A summary of the methodologies and resulting models is presented. This shows that investigations so far have focused on just a few of the many P450s, mainly those that are involved in drug metabolism. The models have evolved from simple comparisons of known substrates to more elaborate models requiring considerable computer power. These help to explain and, more importantly, predict the involvement of P450s in the metabolism of specific compounds.

J. Balzarini, Current Status of the Non-nucleoside Reverse Transcriptase Inhibitors of Human Immunodeficiency Virus Type 1, Curr. Top. Med. Chem. 2004, 4, 921-944. The correct generic name for TMC125 listed in the abstract, Table 1 and Figure 1 is etravirine, and not dapivirine as listed.