Disruptive Strategies for Removing Drug Discovery Bottlenecks

Drug Discovery is shifting focus from the industry to outside partners and in the process creating new bottlenecks, suggesting the need for a more disruptive overhaul. Technologies like high throughput screening (HTS) have moved to a larger number of academic and institutional laboratories in the US, with little apparent coordination or consideration of the outputs and creating a translational gap. While there have been collaborative public private partnerships in Europe to share pharmaceutical data, the USA has lagged behind. Sharing precompetitive computational models may be the next frontier to provide more confidence in the quality of the leads produced and attract investment. We suggest there needs to be an awareness of what research is going on in the screening centers, more collaboration and coordination. These efforts will shift the focus to finding the best researchers to fund and require a rethink of how to reward their collaborative efforts

Dynamics of cognitive function in older patients after intravenous anestesia

To define the effect of various drugs for total intravenous anesthesia (TIVA) on cognitive function (CF) in older patients

Minireview PHARMACOPHORE AND THREE-DIMENSIONAL QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP METHODS FOR MODELING CYTOCHROME P450 ACTIVE SITES

This paper is available online at http://dmd.aspetjournals.org ABSTRACT: Structure activity relationships (SAR), three-dimensional structure activity relationships (3D-QSAR), and pharmacophores represent useful tools in understanding cytochrome P450 (CYP) active sites in the absence of crystal structures for these human enzymes. These approaches have developed over the last 30 years such that they are now being applied in numerous industrial and academic laboratories solely for this purpose. Such computational approaches have helped in understanding substrate and inhibitor binding to the major human CYPs 1A2, 2B6, 2C9, 2D6, 3A4 as well as other CYPs and additionally complement homology models for these enzymes. Similarly, these approaches may assist in our understanding of CYP induction. This review describes in detail the development of pharmacophores and 3D-QSAR techniques, which are now being more widely used for modeling CYPs; the review will also describe how such approaches are likely to further impact our active site knowledge of these omnipresent and important enzymes. By the end of the 1990s, several reviews had characterized the active site details and physicochemical properties of substrates for the major cytochrome P450 (CYP 1 ) enzymes. These reviews had been gathered from analysis of physicochemical data 1 Abbreviations used are: CYP or P450, cytochrome P450; CoMFA, comparative molecular field analysis; GOLPE, generating optimal linear PLS estimations; PLS, partial least squares; 3D-QSAR, three-dimensional quantitative structure-activity relationship; MS-WHIM, molecular surface weighted holistic invariant molecular. DMD 29:936-944, 2001 Printed in U.S.A. 936 intends to give an overview of the pharmacophore and 3D-QSAR models that have been used to describe P450s and indicate their varying degrees of success. 3D-QSAR and Pharmacophores The development of computational tools has paralleled that of in vitro approaches to understanding and characterizing CYPs. One of the first visual 3D-QSAR computational approaches was comparative molecular field analysis (CoMFA) Until recently, few CYP binding or active site models had been generated using enzyme kinetic data, and these focused primarily on inhibition. Now, however, a considerable number of CYP pharmacophores have appeared in the literature, which presents us with the opportunity to review what is known about several CYPs based on such computational analyses. CYP Models CYP1A2. CYP1A2 is an inducible member of the CYP superfamily, which can be inhibited by some selective serotonin reuptake inhibitors With regard to predicting substrates for CYP1A2, one study has suggested that they are generally neutral or protonated and that they possess a total interaction energy greater than Ϫ40 kcal/mol and a molecular volume lower than 200 Å 3 CYP2A6. To date there has been no published CYP2A6 QSAR; however, the related mouse form, CYP2A5, has been studied. One group analyzed substrate requirements using a graphical method and concluded that bicyclic ring systems with an electron-rich moiety were essential for the 11 molecules analyzed CYP2B6. Many examples of xenobiotics metabolized in part by CYP2B6 have been identified and described in more detail This challenge was answered by The first quantitative QSAR for CYP2C9 was published in 1996 This model was validated by testing 14 new compounds that had K i values ranging from 0.1 to 48 M (Rao et al., 2000). While the initial training set contained mostly coumarin-containing compounds, this validation set contained mostly sulfonamides. Interestingly, the initial model predicted the affinity of the validation set reasonably well, predicting 13 of the 14 compounds within 1 log residual. Finally, when these compounds where included in the training set, the pharmacophore remained essentially the same. In separate experiments, conducted at the same time as the validation study described above, pharmacophore and PLS predictive models where constructed using Catalyst and PLS MS-WHIM, respectively To gain confidence in the pharmacophores generated for CYP2C9, an attempt was made to determine the specific amino acid residues that might be involved in establishing the pharmacophore. Initial docking of the 9(R)-11(S)-cyclocoumarol and visualizing the CoMFA field in a CYP2C9 homology model indicated that two phenylalanine residues, Phe 110 EKINS ET AL CYP2C19. One group has focused on obtaining substrate structure activity relationships for the polymorphic CYP2C19 using inhibitors of omeprazole 5-hydroxylation (Lock et al., 1998a,b). Using mainly benzodiazepines which are N-dealkylated and 3-hydroxylated, it was suggested that these sites and the carbonyl group were important for inhibition. Electron-withdrawing groups were found to further decrease inhibition. As yet, the data for the 14 compounds used in these two studies have not been used to produce a published 3D-QSAR. CYP2D6. Human CYP2D6 is a polymorphic member of the CYP superfamily and is absent in 5 to 9% of the Caucasian population as a result of a recessive inheritance of gene mutations The first substrate models were manual alignments based on substrates containing a basic nitrogen atom at either 5 Å Another small-molecule model for CYP2D6 was derived by The actual positions of the heme moiety and the I-helix containing Asp 301 [derived from a protein homology model of CYP2D6 Recently, a combined pharmacophore and homology model for CYP2D6 has been derived (de Groot et al., 1999a,b). This model consists of a set of two pharmacophores (one for O-dealkylation and oxidation reactions and a second one for N-dealkylation reactions catalyzed by CYP2D6) embedded in a protein homology model based on bacterial CYP crystal structures (de Groot et al., 1999a,b). This model for the first time combines the strengths of pharmacophore models (atom-atom overlap and reproducible starting points) and homology models (steric interactions and the possibility to identify amino acids involved in binding). This model correctly predicted the metabolism of a wide variety of compounds (de Groot et al., 1999a,b). An inhibitor model for CYP2D6 has also been derived. The template of this model was derived by fitting six strong reversible inhibitors of CYP2D6 onto each other . The basic nitrogen atoms were superimposed and the aromatic planes of these inhibitors were fitted coplanar. Consecutively, other inhibitors, such as derivatives of ajmalicine and quinidine, were fitted onto the derived template. The derived preliminary pharmacophore model consisted of a tertiary nitrogen atom (protonated at physiological pH) and a flat hydrophobic region. There also appeared to be two regions in which functional groups with lone pairs were allowed. In one of these regions, these groups caused enhanced inhibitory potency, which was not the case in yet another region . The overall criteria derived for this inhibitor-based small-molecule model were very similar to the criteria for the proposed substrate models of CYP2D6 P450 PHARMACOPHORE AND QSAR MODELS A set of 3D/4D-QSAR pharmacophore models has also been created for competitive inhibitors of CYP2D6 in a manner similar to that described for CYP2B6 and CYP2C9 using Catalyst CYP2E1. CYP2E1 is involved in the metabolism of many toxic and carcinogenic molecules such as low molecular weight solvents and anesthetics. Early on, it was suggested that the active site was restricted due to the limited size of known substrates. A graphical model of the active site topology was derived from reactions of human CYP2E1 with phenyldiazene, 2-naphthyl, and p-biphenylhydrazine. This work indicated that the active site was open above the pyrrole rings A and D of the heme for a height of 10 Å CYP3A4. Smith et al. have described in detail the CYP3A4 active site characteristics (as well as those of the other major mammalian CYPs) based on homology models built using soluble bacterial CYP structures as a template More recently, a pharmacophore for inhibitors of CYP3A4-mediated midazolam 1Ј-hydroxylase was developed that consisted of four features necessary for the inhibition of CYP3A4 To evaluate these 3D-QSAR models, the activity of molecules excluded from the training set was predicted and then compared with those observed by means of a 1 log residual. Eight molecules were selected from the literature with K i (apparent) values. Both of the CYP3A4 K i (apparent) Catalyst models predicted the K i values similarly. Seven of eight best fit predictions were within 1 log unit residual, for both models, and the correct rank ordering of three protease inhibitors was observed Using the same commercially available software, a Catalyst hypothesis for 38 CYP3A4 substrates was generated using literature K m data Analyses of the likely features of activators of CYP3A4 have also been undertaken, as three substrates (carbamazepine, nifedipine, and testosterone) within the 38-molecule training set used in the CYP3A4 pharmacophore were known CYP3A4 autoactivators. A common features analysis of these molecules using the HipHop function within Catalyst generated a pharmacophore illustrating three hydrophobic areas and one hydrogen bond acceptor. The hydrophobic areas were located 4.4 to 7.6 Å from the hydrogen bond acceptor feature, and the sites of metabolism were colocated. Therefore, hydrophobic interactions with the CYP3A4 active site may be more important than hydrogen bonding for these same CYP3A4 substrates CYP19 (Aromatase). The importance of CYPs that metabolize endogenous substrates can be demonstrated by aromatase, which catalyzes the metabolism of androstenedione to estrone, 16␣-hy- EKINS ET AL droxyandrostenedione to estriol, and testosterone to estradiol via the aromatization of the A ring and the removal of the C19 methyl group CYP51 (14␣-Demethylase)

The evolution of farnesoid X, vitamin D, and pregnane X receptors: insights from the green-spotted pufferfish (Tetraodon nigriviridis) and other non-mammalian species

<p>Abstract</p> <p>Background</p> <p>The farnesoid X receptor (FXR), pregnane X receptor (PXR), and vitamin D receptor (VDR) are three closely related nuclear hormone receptors in the NR1H and 1I subfamilies that share the property of being activated by bile salts. Bile salts vary significantly in structure across vertebrate species, suggesting that receptors binding these molecules may show adaptive evolutionary changes in response. We have previously shown that FXRs from the sea lamprey (<it>Petromyzon marinus</it>) and zebrafish (<it>Danio rerio</it>) are activated by planar bile alcohols found in these two species. In this report, we characterize FXR, PXR, and VDR from the green-spotted pufferfish (<it>Tetraodon nigriviridis</it>), an actinopterygian fish that unlike the zebrafish has a bile salt profile similar to humans. We utilize homology modelling, docking, and pharmacophore studies to understand the structural features of the <it>Tetraodon </it>receptors.</p> <p>Results</p> <p><it>Tetraodon </it>FXR has a ligand selectivity profile very similar to human FXR, with strong activation by the synthetic ligand GW4064 and by the primary bile acid chenodeoxycholic acid. Homology modelling and docking studies suggest a ligand-binding pocket architecture more similar to human and rat FXRs than to lamprey or zebrafish FXRs. <it>Tetraodon </it>PXR was activated by a variety of bile acids and steroids, although not by the larger synthetic ligands that activate human PXR such as rifampicin. Homology modelling predicts a larger ligand-binding cavity than zebrafish PXR. We also demonstrate that VDRs from the pufferfish and Japanese medaka were activated by small secondary bile acids such as lithocholic acid, whereas the African clawed frog VDR was not.</p> <p>Conclusions</p> <p>Our studies provide further evidence of the relationship between both FXR, PXR, and VDR ligand selectivity and cross-species variation in bile salt profiles. Zebrafish and green-spotted pufferfish provide a clear contrast in having markedly different primary bile salt profiles (planar bile alcohols for zebrafish and sterically bent bile acids for the pufferfish) and receptor selectivity that matches these differences in endogenous ligands. Our observations to date present an integrated picture of the co-evolution of bile salt structure and changes in the binding pockets of three nuclear hormone receptors across the species studied.</p

Elucidating the ‘Jekyll and Hyde’ Nature of PXR: The Case for Discovering Antagonists or Allosteric Antagonists

The pregnane X receptor belongs to the nuclear hormone receptor superfamily and is involved in the transcriptional control of numerous genes. It was originally thought that it was a xenobiotic sensor controlling detoxification pathways. Recent studies have shown an increasingly important role in inflammation and cancer, supporting its function in abrogating tissue damage. PXR orthologs and PXR-like pathways have been identified in several non-mammalian species which corroborate a conserved role for PXR in cellular detoxification. In summary, PXR has a multiplicity of roles in vivo and is being revealed as behaving like a “Jekyll and Hyde” nuclear hormone receptor. The importance of this review is to elucidate the need for discovery of antagonists of PXR to further probe its biology and therapeutic applications. Although several PXR agonists are already reported, virtually nothing is known about PXR antagonists. Here, we propose the development of PXR antagonists through chemical, genetic and molecular modeling approaches. Based on this review it will be clear that antagonists of PXR and PXR-like pathways will have widespread utility in PXR biology and therapeutics

Challenges Predicting Ligand-Receptor Interactions of Promiscuous Proteins: The Nuclear Receptor PXR

Transcriptional regulation of some genes involved in xenobiotic detoxification and apoptosis is performed via the human pregnane X receptor (PXR) which in turn is activated by structurally diverse agonists including steroid hormones. Activation of PXR has the potential to initiate adverse effects, altering drug pharmacokinetics or perturbing physiological processes. Reliable computational prediction of PXR agonists would be valuable for pharmaceutical and toxicological research. There has been limited success with structure-based modeling approaches to predict human PXR activators. Slightly better success has been achieved with ligand-based modeling methods including quantitative structure-activity relationship (QSAR) analysis, pharmacophore modeling and machine learning. In this study, we present a comprehensive analysis focused on prediction of 115 steroids for ligand binding activity towards human PXR. Six crystal structures were used as templates for docking and ligand-based modeling approaches (two-, three-, four- and five-dimensional analyses). The best success at external prediction was achieved with 5D-QSAR. Bayesian models with FCFP_6 descriptors were validated after leaving a large percentage of the dataset out and using an external test set. Docking of ligands to the PXR structure co-crystallized with hyperforin had the best statistics for this method. Sulfated steroids (which are activators) were consistently predicted as non-activators while, poorly predicted steroids were docked in a reverse mode compared to 5α-androstan-3β-ol. Modeling of human PXR represents a complex challenge by virtue of the large, flexible ligand-binding cavity. This study emphasizes this aspect, illustrating modest success using the largest quantitative data set to date and multiple modeling approaches

Computational drug discovery for the Zika virus

Few Zika virus (ZIKV) outbreaks had been reported since its first detection in 1947, until the recent epidemics occurred in South America (2014/2015) and expeditiously became a global public health emergency. This arbovirus reached 0.5-1.3 million cases of ZIKV infection in Brazil in 2015 and rapidly spread in new geographic areas such as the Americas. Despite the mild symptoms of the Zika fever, the major concern is related to the related severe neurological disorders, especially microcephaly in newborns. Advances in ZIKV drug discovery have been made recently and constitute promising approaches to ZIKV treatment. In this review, we summarize current computational drug discovery efforts and their applicability to discovery of anti-ZIKV drugs. Lastly, we present successful examples of the use of computational approaches to ZIKV drug discovery