Randall L. Halcomb

Exploration of factors driving incorporation of unnatural dNTPS into DNA by Klenow fragment (DNA polymerase I) and DNA polymerase α

In order to further understand how DNA polymerases discriminate against incorrect dNTPs, we synthesized two sets of dNTP analogues and tested them as substrates for DNA polymerase α (pol α) and Klenow fragment (exo−) of DNA polymerase I (Escherichia coli). One set of analogues was designed to test the importance of the electronic nature of the base. The bases consisted of a benzimidazole ring with one or two exocyclic substituent(s) that are either electron-donating (methyl and methoxy) or electron-withdrawing (trifluoromethyl and dinitro). Both pol α and Klenow fragment exhibit a remarkable inability to discriminate against these analogues as compared to their ability to discriminate against incorrect natural dNTPs. Neither polymerase shows any distinct electronic or steric preferences for analogue incorporation. The other set of analogues, designed to examine the importance of hydrophobicity in dNTP incorporation, consists of a set of four regioisomers of trifluoromethyl benzimidazole. Whereas pol α and Klenow fragment exhibited minimal discrimination against the 5- and 6-regioisomers, they discriminated much more effectively against the 4- and 7-regioisomers. Since all four of these analogues will have similar hydrophobicity and stacking ability, these data indicate that hydrophobicity and stacking ability alone cannot account for the inability of pol α and Klenow fragment to discriminate against unnatural bases. After incorporation, however, both sets of analogues were not efficiently elongated. These results suggest that factors other than hydrophobicity, sterics and electronics govern the incorporation of dNTPs into DNA by pol α and Klenow fragment.

RECENT DEVELOPMENTS IN TECHNOLOGY FOR GLYCOSYLATION WITH SIALIC ACID

Sialic acids are a class of nine-carbon monosaccharides found at the termini of oligosaccharides in many mammalian cellular systems [1]. This class is represented by the prototypical congener N-acetylneuraminic acid (NeuAc, 1, Scheme 1). These unique sugars are ubiquitous, and they are present as components of both glycolipids and glycoproteins. Some examples of sialic acid containing oligosaccharides are shown in Scheme 2. Sialic acids are found in variety of glycosidic linkages, some more common of which are α-2,3or α-2,6-linkages to galactose residues. Additionally, they frequently exist as α-2,8-linked oligomers or polymers. The lack of efficient technology to accomplish glycosylations with sialic acid is one of the long-standing deficiencies in carbohydrate chemistry [2]. Owing to the central role of sialic acids in carbohydrate recognition events, the development of high-yielding and operable methods to synthesize sialic acid glycosides has been the subject of considerable research. The development of such methods allows the construction of complex sialic acid containing glycoconjugates for the investigation of their roles in biochemical and cellular processes. Most classical methods for synthesizing sialic acid glycosides are based on the reaction of an activated sialic acid such as 2 with an oligosaccharide glycosyl acceptor bearing a hydroxyl group nucleophile (Scheme 3) [2]. The leaving group is typically a halogen, such as a chloride or bromide, and the activator is typically a heavy metal salt [3,4]. A regioselective union of the two reacting partners of course relies on appropriate protecting group patterns for both the glycosyl donor and acceptor components. Many of the early methods are generally plagued with side reactions, low yields, and poor stereoselectivity. There are several reasons for

Synthesis and evaluation of phosphoramidate amino acid-based inhibitors of sialyltransferases.

Several phosphoramidate analogues of CMP-N-acetylneuraminic acid were prepared for evaluation as inhibitors of alpha-2,3- and alpha-2,6-sialyltransferase. Central to the synthesis was the oxidative coupling of an amino acid ester with an H-phosphonate to construct the phosphoramidate linkage. All compounds synthesized were weak inhibitors of both of the sialyltransferases as determined by an HPLC-based inhibition assay.

Synthesis of CMP-sialic acid conjugates: Substrates for the enzymatic synthesis of natural and designed sialyl oligosaccharides

Abstract The syntheses of several congeners of CMP-NeuAc are described. These compounds are substrates for enzymatic glycosylation.

Synthesis of bicyclic ketals related to zaragozic acid by a novel photoannulation

Abstract The 2,8-dioxabicyclo[3.2.1]octane ring system of the zaragozic acids was synthesized by a Norrish Type II photochemical reaction. This reaction occured through an unusual 1,6-hydrogen abstraction to generate a 1,5-biradical. A solvent study found that using benzene provides the best yield of the desired cyclized product.

New design concepts for constraining glycosylated amino acids

Abstract In an effort to probe the mechanism by which glycosyltransferases recognize glycoproteins and assemble the core structures of O-linked oligosaccharides, two constrained glycopeptides based on the α- N -acetylgalactosaminyl serine substructure were chosen for synthesis. These compounds representing one of the two possible gauche conformations of the d -serine and l -serine configurations of the parent substructure were successfully prepared in reasonable overall yield through a convergent strategy.

MILD OXIDATION OF CYTIDINE-SIALIC ACID PHOSPHITE DERIVATIVES USING DIMETHYLDIOXIRANE

Abstract The dimethyldioxirane oxidation of several Cytidine-Neu5Ac phosphite analogs is described.

A symmetry-based approach to zaragozic acid: Synthesis and end-differentiation of an advanced intermediate

Abstract Reported is a novel, symmetry-based strategy for the synthesis of the zaragozic acids. Two enantioselective dihyroxylations are used to set the absolute stereochemistry of a C-2 symmetric intermediate. A sequence of a furan photo-oxidation followed by a diastereoselective dihydroxylation breaks the symmetry and sets two quaternary stereocenters. Finally, a group selective lactonization is used to protect one of two secondary hydroxyls. This accomplishes the critical end-differentiation of this intermediate. An approach to protecting group removal and oxidation is also presented.

Functional Label-Free Assays for Characterizing the in Vitro Mechanism of Action of Small Molecule Modulators of Capsid Assembly

HIV capsid protein is an important target for antiviral drug design. High-throughput screening campaigns have identified two classes of compounds (PF74 and BI64) that directly target HIV capsid, resulting in antiviral activity against HIV-1 and HIV-2 laboratory strains. Using recombinant proteins, we developed a suite of label-free assays to mechanistically understand how these compounds modulate capsid activity. PF74 preferentially binds to the preassembled hexameric capsid form and prevents disruption of higher-order capsid structures by stabilizing capsid intersubunit interactions. BI64 binds only the monomeric capsid and locks the protein in the assembly incompetent monomeric form by disrupting capsid intersubunit interactions. We also used these assays to characterize the interaction between capsid and the host protein cleavage and polyadenylation specific factor 6 (CPSF6). Consistent with recently published results, our assays revealed CPSF6 activates capsid polymerization and preferentially binds to the preassembled hexameric capsid form similar to the small molecule compound, PF74. Furthermore, these label-free assays provide a robust method for facilitating the identification of a different class of small molecule modulators of capsid function.