Deorphanizing solute carriers in Saccharomyces cerevisiae for secondary uptake of xenobiotic compounds.

The exchange of small molecules between the cell and the environment happens through transporter proteins. Besides nutrients and native metabolic products, xenobiotic molecules are also transported, however it is not well understood which transporters are involved. In this study, by combining exo-metabolome screening in yeast with transporter characterization in Xenopus oocytes, we mapped the activity of 30 yeast transporters toward six small non-toxic substrates. Firstly, using LC-MS, we determined 385 compounds from a chemical library that were imported and exported by S. cerevisiae. Of the 385 compounds transported by yeast, we selected six compounds (viz. sn-glycero-3-phosphocholine, 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, acrylic acid, 2-benzoxazolol) for characterization against 30 S. cerevisiae xenobiotic transport proteins expressed in Xenopus oocytes. The compounds were selected to represent a diverse set of chemicals with a broad interest in applied microbiology. Twenty transporters showed activity toward one or more of the compounds. The tested transporter proteins were mostly promiscuous in equilibrative transport (i.e., facilitated diffusion). The compounds 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, and sn-glycero-3-phosphocholine were transported equilibratively by transporters that could transport up to three of the compounds. In contrast, the compounds acrylic acid and 2-benzoxazolol, were strictly transported by dedicated transporters. The prevalence of promiscuous equilibrative transporters of non-native substrates has significant implications for strain development in biotechnology and offers an explanation as to why transporter engineering has been a challenge in metabolic engineering. The method described here can be generally applied to study the transport of other small non-toxic molecules. The yeast transporter library is available at AddGene (ID 79999).

Engineering of CYP76AH15 can improve activity and specificity towards forskolin biosynthesis in yeast.

BACKGROUND: Forskolin is a high-value diterpenoid produced exclusively by the Lamiaceae plant Coleus forskohlii. Today forskolin is used pharmaceutically for its adenyl-cyclase activating properties. The limited availability of pure  forskolin is currently hindering its full utilization, thus a new environmentally friendly, scalable and sustainable strategy is needed for forskolin production. Recently, the entire biosynthetic pathway leading to forskolin was elucidated. The key steps of the pathway are catalyzed by cytochrome P450 enzymes (CYPs), which have been shown to be the limiting steps of the pathway. Here we study whether protein engineering of the substrate recognition sites (SRSs) of CYPs can improve their efficiency towards forskolin biosynthesis in yeast. RESULTS: As a proof of concept, we engineered the enzyme responsible for the first putative oxygenation step of the forskolin pathway: the conversion of 13R-manoyl oxide to 11-oxo-13R-manoyl oxide, catalyzed by the CYP76AH15. Four CYP76AH15 variants-engineered in the SRS regions-yielded at least a twofold increase of 11-oxo-13R-manoyl oxide when expressed in yeast cells grown in microtiter plates. The highest titers (5.6-fold increase) were observed with the variant A99I, mutated in the SRS1 region. Double or triple CYP76AH15 mutant variants resulted in additional enzymes with optimized performances. Moreover, in planta CYP76AH15 can synthesize ferruginol from miltiradiene. In this work, we showed that the mutants affecting 11-oxo-13R-manoyl oxide synthesis, do not affect ferruginol production, and vice versa. The best performing variant, A99I, was utilized to reconstruct the forskolin biosynthetic pathway in yeast cells. Although these strains showed increased 11-oxo-manoyl oxide production and higher accumulation of other pathway intermediates compared to the native CYP76AH15, lower production of forskolin was observed. CONCLUSIONS: As demonstrated for CYP76AH15, site-directed mutagenesis of SRS regions of plant CYPs may be an efficient and targeted approach to increase the performance of these enzymes. Although in this work we have managed to achieve higher efficiency and specificity of the first CYP of the pathway, further work is necessary in order to increase the overall production of forskolin in yeast cells.

Fragment-based discovery and optimization of BACE1 inhibitors.

A novel series of 2-aminobenzimidazole inhibitors of BACE1 has been discovered using fragment-based drug discovery (FBDD) techniques. The rapid optimization of these inhibitors using structure-guided medicinal chemistry is discussed.

An in silico method for predicting Ames activities of primary aromatic amines by calculating the stabilities of nitrenium ions.

In this paper, we describe an in silico first principal approach to predict the mutagenic potential of primary aromatic amines. This approach is based on the so-called "nitrenium hypothesis", which was developed by Ford et al. in the early 1990s. This hypothesis asserts that the mutagenic effect for this class of molecules is mediated through the transient formation of a nitrenium ion and that the stability of this cation is correlated with the mutagenic potential. Here we use quantum mechanical calculations at different levels of theory (semiempirical AM1, ab initio HF/3-21G, HF/6-311G(d,p), and DFT/B3LYP/6-311G(d,p)) to compute the stability of nitrenium ions. When applied to a test set of 257 primary aromatic amines, we show that this method can correctly differentiate between Ames active and inactive compounds, and furthermore that it is able to rationalize and predict SAR trends within structurally related chemical series. For this test set, the AM1 nitrenium stability calculations are found to provide a good balance between speed and accuracy, resulting in an overall accuracy of 85%, and sensitivity and specificity of 91% and 72%, respectively. The nitrenium-based predictions are also compared to the commercial software packages DEREK, MULTICASE, and the MOE-Toxicophore descriptor. One advantage of the approach presented here is that the calculation of relative stabilities results in a continuous spectrum of activities and not a simple yes/no answer. This allows us to observe and rationalize subtle trends due to the different electrostatic properties of the organic molecules. Our results strongly indicate that nitrenium ion stability calculations should be used as a complementary approach to assist the medicinal chemist in prioritizing and selecting nonmutagenic primary aromatic amines during preclinical drug discovery programs.

Involvement of water in carbohydrate-protein binding: concanavalin A revisited.

Ordered water molecules bound to protein surfaces, or in protein-ligand interfaces, are frequently observed by crystallography. The investigation of the impact of such conserved water molecules on protein stability and ligand affinity requires detailed structural, dynamic, and thermodynamic analyses. Several crystal structures of the legume lectin concanavalin A (Con A) bound to closely related carbohydrate ligands show the presence of a conserved water molecule that mediates ligand binding. Experimental thermodynamic and theoretical studies have examined the role of this conserved water in the complexation of Con A with a synthetic analog of the natural trisaccharide, in which a hydroxyethyl side chain replaces the hydroxyl group at the C-2 position in the central mannosyl residue. Molecular modeling earlier indicated (Clarke, C.; Woods, R. J.; Glushka, J.; Cooper, A.; Nutley, M. A.; Boons, G.-J. J. Am. Chem. Soc. 2001, 123, 12238-12247) that the hydroxyl group in this synthetic side chain could occupy a position equivalent to that of the conserved water, and thus might displace it. An interpretation of the experimental thermodynamic data, which was consistent with the displacement of the conserved water, was also presented. The current work reports the crystal structure of Con A with this synthetic ligand and shows that even though the position and interactions of the conserved water are distorted, this key water is not displaced by the hydroxyethyl moiety. This new structural data provides a firm basis for molecular dynamics simulations and thermodynamic integration calculations whose results indicate that differences in van der Waals contacts (insertion energy), rather than electrostatic interactions (charging energy) are fundamentally responsible for the lower affinity of the synthetic ligand. When combined with the new crystallographic data, this study provides a straightforward interpretation for the lower affinity of the synthetic analog; specifically, that it arises primarily from weaker interactions with the protein via the positionally perturbed conserved water. This interpretation is fully consistent with the experimental observations that the free energy of binding is enthalpy driven, that there is both less enthalpic gain and less entropic penalty for binding the synthetic ligand, relative to the natural trisaccharide, and that the entropic component does not arise from releasing an ordered water molecule from the protein surface to the bulk solvent.