Structure-function studies of serine hydrolases: synthesis of a gene for ∝-lytic protease and the purification and characterization of a mutant β-lactamase

The author has constructed a synthetic gene for ∝-lytic protease. Since the DNA sequence of the protein is not known, the gene was designed by using the reverse translation of ∝-lytic protease's amino acid sequence. Unique restriction sites are carefully sought in the degenerate DNA sequence to aid in future mutagenesis studies. The unique restriction sites are designed approximately 50 base pairs apart and their appropriate codons used in the DNA sequence. The codons used to construct the DNA sequence of ∝-lytic protease are preferred codons in E-coli or used in the production of β-lactamase. Codon usage is also distributed evenly to ensure that one particular codon is not heavily used. The gene is essentially constructed from the outside in. The gene is built in a stepwise fashion using plasmids as the vehicles for the ∝-lytic oligomers. The use of plasmids allows the replication and isolation of large quantities of the intermediates during gene synthesis. The ∝-lytic DNA is a double-stranded oligomer that has sufficient overhang and sticky ends to anneal correctly in the vector. After six steps of incorporating ∝-lytic DNA, the gene is completed and sequenced to ensure that the correct DNA sequence is present and that no mutations occurred in the structural gene.

β-lactamase is the other serine hydrolase studied in this thesis. The author used the class A RTEM-1 β- lactamase encoded on the plasmid pBR322 to investigate the roll of the conserved threonine residue at position 71. Cassette mutagenesis was previously used to generate all possible amino acid substitutions at position 71. The work presented here describes the purification and kinetic characterization of a T71H mutant previously constructed by S. Schultz. The mutated gene was transferred into plasmid pJN for expression and induced with IPTG. The enzyme is purified by column chromatography and FPLC to homogeneity. Kinetic studies reveal that the mutant has lower k_(cat) values on benzylpenicillin, cephalothin and 6-aminopenicillanic acid but no changes in k_m except for cephalothin which is approximately 4 times higher. The mutant did not change siginificantly in its pH profile compared to the wild-type enzyme. Also, the mutant is more sensitive to thermal denaturation as compared to the wild-type enzyme. However, experimental evidence indicates that the probable generation of a positive charge at position 71 thermally stabilized the mutant.

Improving the biological activity of pyrrole-imidazole polyamides

DNA is nature’s blueprint, holding within it the genetic code that defines the structure and function of an organism. A complex network of DNA-binding proteins called transcription factors can largely control the flow of information from DNA, so modulating the function of transcription factors is a promising approach for treating many diseases. Pyrrole-imidazole (Py-Im) polyamides are a class of DNA-binding oligomers, which can be synthetically programmed to bind a target sequence of DNA. Due to their unique shape complementarity and a series of favorable hydrogen bonding interactions that occur upon DNA-binding, Py-Im polyamides can bind to the minor groove of DNA with affinities comparable to transcription factors. Previous studies have demonstrated that these cell-permeable small molecules can enter cell nuclei and disrupt the transcription factor-DNA interface, thereby repressing transcription. As the use of Py-Im polyamides has significant potential as a type of modular therapeutic platform, the need for polyamides with extremely favorable biological properties and high potency will be essential. Described herein, a variety of studies have been performed aimed at improving the biological activity of Py-Im polyamides. To improve the biological potency and cellular uptake of these compounds, we have developed a next-generation class of polyamides bearing aryl-turn moieties, a simple structural modification that allows significant improvements in cellular uptake. This strategy was also applied to a panel of high-affinity cyclic Py-Im polyamides, again demonstrating the remarkable effect minor structural changes can have on biological activity. The solubility properties of Py-Im polyamides and use of formulating reagents with their treatment have also been examined. Finally, we describe the study of Py-Im polyamides as a potential artificial transcription factor.

Mechanistic aspects of the Ziegler-Natta polymerization

The isotope effect on propagation rate was determined for four homogeneous ethylene polymerization systems. The catalytic system Cp_2Ti(Et)Cl + EtA1Cl_2 has a k^H_p/k^D_p = 1.035 ± 0.03. This result strongly supports an insertion mechanism which does not involve a hydrogen migration during the rate determining step of propagation (Cossee mechanism). Three metal-alkyl free systems were also studied. The catalyst I_2 (PMe_3)_3Ta(neopentylidene)(H) has a k^H_p/k^D_p = 1.709. It is interpreted as a primary isotope effect involving a non-linear a-hydrogen migration during the rate determining step of propagation (Green mechanism). The lanthanide complexes Cp*_2LuMe•Et_2O and Cp*_2YbMe•Et_2O have a k^H_p/k^D_p = 1.46 and 1.25, respectively. They are interpreted as primary isotope effects due to a partial hydrogen migration during the rate determining step of propagation.

The presence of a precoordination or other intermediate species during the polymerization of ethylene by the mentioned metal-alkyl free catalysts was sought by low temperature NMR spectroscopy. However, no evidence for such species was found. If they exist, their concentrations are very small or their lifetimes are shorter than the NMR time scale.

Two titanocene (alkenyl)chlorides (hexenyl 1 and heptenyl 2 were prepared from titanocene dichloride and a THF solution of the corresponding alkenylmagnesium chloride. They do not cyclize in solution when alone, but cyclization to their respective titanocene(methyl(cycloalkyl) chlorides occurs readily in the presence of a Lewis acid. It is demonstrated that such cyclization occurs with the alkenyl ligand within the coordination sphere of the titanium atom. Cyclization of 1 with EtAlCl_2 at 0°C occurs in less than 95 msec (ethylene insertion time), as shown by the presence of 97% cyclopentyl-capped oligomers when polymerizing ethylene with this system. Some alkyl exchange occurs (3%). Cyclization of 2 is slower under the same reaction conditions and is not complete in 95 msec as shown by the presence of both cyclohexyl-capped oligomers (35%) and odd number α-olefin oligomers (50%). Alkyl exchange is more extensive as evidenced by the even number n-alkanes (15%).

Cyclization of 2-d_1 (titanocene(hept-6-en-1-yl-1-d_1)chloride) with EtA1Cl_2 demonstrated that for this system there is no α-hydrogen participation during said process. The cyclization is believed to occur by a Cossee-type mechanism. There was no evidence for precoordination of the alkenyl double bond during the cyclization process.

Targeting DNA repeat sequences with Py-Im polyamides

Hairpin pyrrole-imdazole polyamides are cell-permeable, sequence-programmable oligomers that bind in the minor groove of DNA. This thesis describes studies of Py-Im polyamides targeted to biologically important DNA repeat sequences for the purpose of modulating disease states. Design of a hairpin polyamide that binds the CG dyad, a site of DNA methylation that can become dysregulated in cancer, is described. We report the synthesis of a DNA methylation antagonist, its sequence specificity and affinity informed by Bind-n-Seq and iteratively designed, which improves inhibitory activity in a cell-free assay by 1000-fold to low nanomolar IC50. Additionally, a hairpin polyamide targeted to the telomeric sequence is found to trigger a slow necrotic-type cell death with the release of inflammatory molecules in a model of B cell lymphoma. The effects of the polyamide are unique in this class of oligomers; its effects are characterized and a functional assay of phagocytosis by macrophages is described. Additionally, hairpin polyamides targeted to pathologically expanded CTG•CAG triplet repeat DNA sequences, the molecular cause of myotonic dystrophy type 1, are synthesized and assessed for toxicity. Lastly, ChIP-seq of Hypoxia-Inducible Factor is performed under hypoxia-induced conditions. The study results show that ChIP-seq can be employed to understand the genome-wide perturbation of Hypoxia-Inducible Factor occupancy by a Py-Im polyamide.