subject:(Chemical complementation)

1. Johnson, Kenyetta Alicia. Extending chemical complemenation to bacteria and furthering nuclear receptor based protein engineering and drug discovery.

Degree: PhD, Chemistry and Biochemistry, 2009, Georgia Tech

URL: http://hdl.handle.net/1853/29652

► Nuclear receptors (NRs) are modular ligand-activated transcription factors that control a broad range of physiological processes by regulating the expression of essential genes involved in… (more)

▼ Nuclear receptors (NRs) are modular ligand-activated transcription factors that control a broad range of physiological processes by regulating the expression of essential genes involved in cell physiology, differentiation, and metabolism. These receptors are implicated in a number of diseases and due to their profound role in development and disease progression and their modularity, much emphasis is being put forth into nuclear receptor based drug discovery and engineering these receptors to bind novel small molecules Chemical Complementation (CC) is a yeast three-hybrid genetic selection system that was developed to aid in the discovery of these engineered receptors by linking the survival of a yeast cell to a small molecules ability to activate the receptor. Due to several advantages, to include faster growth times and higher transformation efficiencies, we have attempted to extend chemical complementation from yeast to E. coli. The bacterial chemical complementation system (BCC) was designed, based on a bacterial two hybrid system, to parallel yeast CC system. However, bacterial chemical complementation did not produce ligand dependent activation due to heterologous protein expression. In a second project designed to further NR based protein engineering and drug discovery, CC was used to evaluate a library of charge reversal variants rationally designed to gain a better understanding of nuclear receptor function and structure and to produce orthogonal ligand receptor pairs. A library of retinoic acid receptor (RARα) variants were developed based on five residues in the binding pocket known to stabilize the natural negatively charged ligand, all-trans retinoic acid (atRA). We altered the binding selectivity of the receptor to bind positively charged retinoid ligands. We were able to engineer two triple variants capable of activating with the positively charged retinoid but not the natural atRA ligand, however they do not activate as well as RARα wild-type does with atRA. In a third project we characterized covalently linked tamoxifen and histone deacetylase inhibitor based dual inhibiting compounds as breast cancer therapeutics. Several dual inhibiting compounds were found to decrease the proliferation of ER positive breast cancer cells better than tamoxifen alone, the HDACi alone, or noncovalently linked HDACi and tamoxifen. Advisors/Committee Members: Doyle, Donald (Committee Chair), Barry, Bridgette (Committee Member), Bommarius, Andreas (Committee Member), Ledoux, Joe (Committee Member), Matsumura, Ichiro (Committee Member), Oyelere, Adegboyega (Committee Member).

Subjects/Keywords: Protein engineering; Nuclear receptor; Chemical complementation; Drug discovery; Nuclear receptors (Biochemistry); Developmental pharmacology; Protein engineering; Yeast Genetics

…Chemical Complementation Bacterial Two-Hybrid Systems Literature Cited CHAPTER 3 23 23 25 30 35… …41 BACTERIAL CHEMICAL COMPLEMENTATION: ELIMINATING BACKGROUND 47 3.3 Bacterial Chemical… …Complementation: Bacteria vs. Yeast 3.2 Developing Bacterial Chemical Complementation 3.3 Results of… …Eliminating Bacterial Chemical Complementation Background 3.3.1 Effects of Expression Vectors on… …63 67 CHAPTER 4 BACTERIAL CHEMICAL COMPLEMENTATION: LIGAND DEPENDENT ACTIVATION 70 4.1…

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APA (6^th Edition):

Johnson, K. A. (2009). Extending chemical complemenation to bacteria and furthering nuclear receptor based protein engineering and drug discovery. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/29652

Chicago Manual of Style (16^th Edition):

Johnson, Kenyetta Alicia. “Extending chemical complemenation to bacteria and furthering nuclear receptor based protein engineering and drug discovery.” 2009. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021. http://hdl.handle.net/1853/29652.

MLA Handbook (7^th Edition):

Johnson, Kenyetta Alicia. “Extending chemical complemenation to bacteria and furthering nuclear receptor based protein engineering and drug discovery.” 2009. Web. 23 Jan 2021.

Vancouver:

Johnson KA. Extending chemical complemenation to bacteria and furthering nuclear receptor based protein engineering and drug discovery. [Internet] [Doctoral dissertation]. Georgia Tech; 2009. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/1853/29652.

Council of Science Editors:

Johnson KA. Extending chemical complemenation to bacteria and furthering nuclear receptor based protein engineering and drug discovery. [Doctoral Dissertation]. Georgia Tech; 2009. Available from: http://hdl.handle.net/1853/29652

Georgia Tech

2. Schwimmer, Lauren J. Engineering ligand-receptor pairs for small molecule control of transcription.

Degree: PhD, Chemistry and Biochemistry, 2005, Georgia Tech

URL: http://hdl.handle.net/1853/11651

► Creating receptors for control of transcription with arbitrary small molecules has widespread applications including gene therapy, biosensors, and enzyme engineering. Using the combination of high… (more)

▼ Creating receptors for control of transcription with arbitrary small molecules has widespread applications including gene therapy, biosensors, and enzyme engineering. Using the combination of high throughput docking, codon randomization, and chemical complementation, we have created new receptors to control transcription with small molecules. Chemical complementation, a new method of protein engineering, was used to discover retinoid X receptors (RXR) variants that are activated by compounds that do not activate wild-type RXR. A first library of 32,768 RXR variants was designed for the synthetic retinoid-like compound LG335. The library produced ligand-receptor pairs with LG335 that have a variety of EC50s and efficacies. One engineered variant has essentially the reverse ligand specificity of wild-type RXR and is transcriptionally active at 10 and64979;fold lower LG335 concentration than wild-type RXR with 9cRA in yeast. The activity of this variant in mammalian cells correlates with its activity in yeast. A second library of 262,144 RXR variants was designed for two purposes: (i) to develop a high-throughput chemical complementation method to select variants that have high efficacies and low EC50s; and (ii) to find variants which are activated by small molecules not known to bind RXR variants. Selection conditions were manipulated to find only variants with high efficacies and low EC50s. This library was also selected for variants that activate transcription specifically in response to gamma-oxo-1-pyrenebutyric acid (OPBA), which is different from any known RXR ligand. OPBA was chosen as a potential ligand using high-throughput docking with the software program FlexX. Two variants are activated by OPBA with an EC50 of 5 mM. This is only ten-fold greater than the EC50 of wild type RXR with its ligand 9cRA (500 nM) in yeast. An improved method synthesizing LG335 and a method for quantifying intracellular ligand concentrations were developed. Although the LG335 synthetic method has an additional step, the overall yield was improved to 8% from 4% in the original publication. Liquid chromatography and mass spectrometry was used to quantify the intracellular concentration of LG335, which was found to be within four fold of the LG335 concentration in the media. Advisors/Committee Members: Doyle, Donald (Committee Chair), Bommarius, Andreas (Committee Member), Orville, Allen (Committee Member), Radhakrishna, Harish (Committee Member), Seley, Katherine (Committee Member).

Subjects/Keywords: Chemical complementation; Ligand-receptor pair; Protein engineering; Retinoid X receptor; Nuclear receptor; Codon randomized libraries; Transcription factors; Protein engineering; Nuclear receptors (Biochemistry); Genetic engineering

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APA (6^th Edition):

Schwimmer, L. J. (2005). Engineering ligand-receptor pairs for small molecule control of transcription. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/11651

Chicago Manual of Style (16^th Edition):

Schwimmer, Lauren J. “Engineering ligand-receptor pairs for small molecule control of transcription.” 2005. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021. http://hdl.handle.net/1853/11651.

MLA Handbook (7^th Edition):

Schwimmer, Lauren J. “Engineering ligand-receptor pairs for small molecule control of transcription.” 2005. Web. 23 Jan 2021.

Vancouver:

Schwimmer LJ. Engineering ligand-receptor pairs for small molecule control of transcription. [Internet] [Doctoral dissertation]. Georgia Tech; 2005. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/1853/11651.

Council of Science Editors:

Schwimmer LJ. Engineering ligand-receptor pairs for small molecule control of transcription. [Doctoral Dissertation]. Georgia Tech; 2005. Available from: http://hdl.handle.net/1853/11651

3. Shaffer, Hally A. Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation.

Degree: PhD, Chemistry and Biochemistry, 2011, Georgia Tech

URL: http://hdl.handle.net/1853/39620

► Nuclear receptors are ligand-activated transcription factors that play significant roles in various biological processes within the body, such as cell development, hormone metabolism, reproduction, and… (more)

Subjects/Keywords: Nuclear receptors; Chemical complementation; Negative chemical complementation; Yeast-two hybrid selection; Pregnane X receptor; Estrogen receptor; Pregnane; Protein engineering; Nuclear receptors (Biochemistry); Transcription factors; Yeast Genetics

…Complementation 12 1.4 Applications of Chemical Complemenation 15 1.4.1 Drug Discovery 15 1.4.2… …Promiscuous Activity of PXR 27 2.3 PXR in Chemical Complementation 32 2.4 PXR Library for… …Chemical Complementation 41 2.5 PXR in HEK293T Mammalian Cells 50 2.6 Summary and Future Work… …Complementation 99 ix 4.3.2 hERα Variants in Chemical Complementation 103 4.3.3 Random Mutagenesis… …COMPLEMENTATION WITH ANTAGONISTS 159 6.1 Genetic Selection and Negative Chemical Complementation 159…

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Shaffer, H. A. (2011). Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/39620

Chicago Manual of Style (16^th Edition):

Shaffer, Hally A. “Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation.” 2011. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021. http://hdl.handle.net/1853/39620.

MLA Handbook (7^th Edition):

Shaffer, Hally A. “Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation.” 2011. Web. 23 Jan 2021.

Vancouver:

Shaffer HA. Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation. [Internet] [Doctoral dissertation]. Georgia Tech; 2011. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/1853/39620.

Council of Science Editors:

Shaffer HA. Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation. [Doctoral Dissertation]. Georgia Tech; 2011. Available from: http://hdl.handle.net/1853/39620

INP Toulouse

4. Bacha, Nafees. Caractérisation des polycétones synthases intervenant dans la biosynthèse d’ochratoxine A, d’acide pénicillique, d’asperlactone et d’isoasperlactone chez aspergillus westerdijkiae : Caracterization of the polyketide synthases involved in biosynthesis of ochratoxin A, penicillic acid, asperlactone and isoasperlactone in aspergillus westerdijkiae (a molecular approach).

Degree: Docteur es, Microbiologie et biocatalyse industrielles, 2009, INP Toulouse

URL: http://www.theses.fr/2009INPT004A

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Aspergillus westerdijkiaem qui est récemment démembré d'A. ochraceus est un producteur principal de plusieurs composés de type polycétone d'importance économique. Ces composés incluent l’ochratoxin A,… (more)

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Aspergillus westerdijkiaem qui est récemment démembré d'A. ochraceus est un producteur principal de plusieurs composés de type polycétone d'importance économique. Ces composés incluent l’ochratoxin A, mellein, l'acide penicillique, asperlactone et l’isoasperlactone et quelques intermédiaires comme l'acide 6- methylsalicylique et l’acide orsellinique. La biosynthèse de ces métabolites est catalysée par un groupe d'enzymes connues comme la polycétone synthases (PKSs). Ce travail a été visé pour cloner et a caractérisé fonctionnellement les différentes genes des PKS i.e. aoks1, aolc35-12 et aomsas, et de genes de polyketide synthases-non ribosomal peptide synthase (PKS-NRPS) i.e. aolc35-6, chez A. westerdijkiae. Ces gènes ont été inactivés par l'insertion du gène d’hygromycine B phosphotransferase d’Escherichia coli dans le génome d'A. westerdijkiae, pour obtenir les mutantes ao?ks1, ao?lc35-12, ao?msas et ao?lc35-6. Les mutants ao?ks1 et ao?lc35-12 ont été trouvés déficients dans la biosynthèse d’ochratoxin A, mais produisaient encore mellein. À notre connaissance, c’est la première fois que nous avons caractérisé les gènes impliquées dans la biosynthèse d’OTA, sachant que mellein, qui était proposé dans la littérature comme un intermédiaire, joue a cune role dans la biosynthesis de l'OTA. Ensuite le mutant ao?msas n'a pas seulement perdu la capacité de produire isoasperlactone et asperlactone, mais aussi il ne produit pas l’intermédiaire acide 6-methylsalicylique. Basé sur les expériences de la caractérisation génétique et de complémentation chimiques, nous avons proposé un shéma hypothétique de la biosynthèse d’asperlactone et isoasperlactone dans lequel l'acide 6-methylsalicylique, diepoxide et aspyrone jouent le rôle d’intermédiaires. La techniques de gène knock-out et de la reverse transcription PCR (RT-PCR) ont montré que seulle gène de type PKS-NRPS « aolc35-6 » identifié chez A. westerdijkiae codant pour un intermédiaire inconnu(s) qui pourrait inciter l'expression de gène aomsas et un gène impliqué dans la biosynthèse d'acide orsellinique et d'acide penicillique.

Aspergillus westerdijkiaem which is recently dismembered from A. ochraceusm is the principal producer of several economically important polyketide metabolites. These metabolites include ochratoxin A, mellein, penicillic acid, asperlactone and isoasperlactone and some intermediates like orsellinic acid and 6-methylsalicylic acid. The biosynthesis of these metabolites is catalyzed by a group of enzymes known as polyketide synthases (PKSs). This work was aimed to clone and functionally characterized various PKS i.e. aoks1, aolc35-12 and aomsas, and polyketide synthasesnon ribosomal peptide synthase (PKS-NRPS) genes i.e. aolc35-6, in A. westerdijkiae. These genes were inactivated by the insertion of Escherichia coli hygromycin B phosphotransferase gene in the genome of A. westerdijkiae to obtain ao?ks1, ao?lc35-12, ao?msas and ao?lc35-6 mutants. ao?ks1, ao?lc35-12 mutants were found deficient in ochratoxin A biosynthesis but are still producing…

Advisors/Committee Members: Lebrihi, Ahmed (thesis director), Mathieu, Florence (thesis director).

Subjects/Keywords: Aspergillus westerdijkiae; Polycétone synthase gènes; Caractérisation génétique; Genome walking; Transformation; Complémentation chimique; Ochratoxine A; Acide penicillique; Aspyrone; Acide 6-methylsalicylique; Isoasperlactone; Asperlactone; Aspergillus westerdijkiae; Polyketide synthase genes; Genetic characterization; Genome calking; Transformation; Chemical complementation; Ochratoxin A; Penicillic acid; Aspyrone; 6-methylsalicylic acid; Isoasperlactone; Asperlactone

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Bacha, N. (2009). Caractérisation des polycétones synthases intervenant dans la biosynthèse d’ochratoxine A, d’acide pénicillique, d’asperlactone et d’isoasperlactone chez aspergillus westerdijkiae : Caracterization of the polyketide synthases involved in biosynthesis of ochratoxin A, penicillic acid, asperlactone and isoasperlactone in aspergillus westerdijkiae (a molecular approach). (Doctoral Dissertation). INP Toulouse. Retrieved from http://www.theses.fr/2009INPT004A

Chicago Manual of Style (16^th Edition):

Bacha, Nafees. “Caractérisation des polycétones synthases intervenant dans la biosynthèse d’ochratoxine A, d’acide pénicillique, d’asperlactone et d’isoasperlactone chez aspergillus westerdijkiae : Caracterization of the polyketide synthases involved in biosynthesis of ochratoxin A, penicillic acid, asperlactone and isoasperlactone in aspergillus westerdijkiae (a molecular approach).” 2009. Doctoral Dissertation, INP Toulouse. Accessed January 23, 2021. http://www.theses.fr/2009INPT004A.

MLA Handbook (7^th Edition):

Bacha, Nafees. “Caractérisation des polycétones synthases intervenant dans la biosynthèse d’ochratoxine A, d’acide pénicillique, d’asperlactone et d’isoasperlactone chez aspergillus westerdijkiae : Caracterization of the polyketide synthases involved in biosynthesis of ochratoxin A, penicillic acid, asperlactone and isoasperlactone in aspergillus westerdijkiae (a molecular approach).” 2009. Web. 23 Jan 2021.

Vancouver:

Bacha N. Caractérisation des polycétones synthases intervenant dans la biosynthèse d’ochratoxine A, d’acide pénicillique, d’asperlactone et d’isoasperlactone chez aspergillus westerdijkiae : Caracterization of the polyketide synthases involved in biosynthesis of ochratoxin A, penicillic acid, asperlactone and isoasperlactone in aspergillus westerdijkiae (a molecular approach). [Internet] [Doctoral dissertation]. INP Toulouse; 2009. [cited 2021 Jan 23]. Available from: http://www.theses.fr/2009INPT004A.

Council of Science Editors:

Bacha N. Caractérisation des polycétones synthases intervenant dans la biosynthèse d’ochratoxine A, d’acide pénicillique, d’asperlactone et d’isoasperlactone chez aspergillus westerdijkiae : Caracterization of the polyketide synthases involved in biosynthesis of ochratoxin A, penicillic acid, asperlactone and isoasperlactone in aspergillus westerdijkiae (a molecular approach). [Doctoral Dissertation]. INP Toulouse; 2009. Available from: http://www.theses.fr/2009INPT004A

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