Traditionally, post-translational modifications have been difficult to study in native environments due to their inherent small size and recent efforts have focused on developing new strategies to identify both the substrate and specific location of these modifications on complex biological surfaces. While a variety of approaches are currently being pursued by others, we are developing a novel set of small molecules that exploit cellular machinery to transfer unique chemical functionalities to biological substrates. This approach utilizes both cellular enzymes and non-native cofactor mimics as biochemical tools to identify and isolate modified substrates. Instead of generating the native modification depicted here, a ligatable handle (R) is enzymatically transferred to the substrate. Once incorporated, this non-native, chemical functionality can be modified through various chemoselective ligations, such as the Staudinger ligation or Hüisgen [2+3] cycloaddition, to permit visualization of the modified substrate and hasten substrate isolation and identification from complex environments.
Utilizing this enzyme-based approach, two independent projects unified by the common theme of exploring post-translational modifications through cofactor mimics bearing ligatable handles, such as azides and alkynes, is being pursued. The first project incorporates the synthesis of modified analogs of adenosine triphosphate (ATP) and their subsequent biochemical evaluation as cofactors for cellular kinases. The second project entails generating synthetic analogs of S-adenosyl-L-methionine (SAM) bearing ligatable functionalities and evaluating their methyltransferase-dependent modification of biological targets.
Ligatable Analogs of ATP as Probes of Cellular Kinases and Their Substrates
Phosphorylation has been demonstrated to be the most universal regulatory mechanism of protein function. Carried out by kinases, phosphorylation occurs primarily on either a serine, threonine, or tyrosine residue and results in a functional change of the target protein by altering enzyme activity, cellular location, or its association with other proteins. Aberrant expression of kinases has been linked to a variety of cancers, leukemias, and neurodegenerative diseases and challenges still remain in identifying the role of phosphorylation defects in these altered states. With more than 500 known kinases in the human genome, one of the largest tasks has been to identify the substrates of specific kinases and the pathways in which they are involved. While chemical genetics has emerged at the forefront in developing new methodologies to investigate the role of cellular kinases in physiological function, this methodology typically lacks generality amongst a wide variety of kinases.
To circumvent this, an alternate approach is taken here to develop a more universal analog of ATP that bears the ligatable handle and is tolerated by several classes of kinases. As depicted in the crystal structure of CK2, a tyrosine kinase, the g-phosphate of ATP is solvent accessible and the incorporation of a small functionality at this position is well-tolerated. Thus, ATP analogs bearing a ligatable handle on the g-phosphate would not only bind in the active site, but also transfer the modified phosphate to substrate. A small library of cofactor mimics is being synthesized bearing modified linker structures and/or lengths between the g-phosphate and either alkynes or azides, creating a diverse library of compounds to explore phosphorylation biology.
Development and Biochemical Evaluation of Ligatable Analogs of S-adenosyl-L-Methionine
Methylation of nucleic acids has been shown to play a pivotal role in controlling cellular function through gene silencing, and protein methylation, specifically on histones, is essential for transcriptional regulation via chromatin remodeling. Aberrant methylation of proteins/DNA is often responsible for the onset of disease states, including carcinogenesis. Catalyzing the transfer of a methyl group from the naturally-occurring cofactor SAM, methyltransferases function in either a site- or sequence-specific fashion. Although this modification is highly efficient, the incorporation of a methyl group onto a DNA base or amino acid can often traditionally been difficult to detect due to its small size. While strategies for detecting methylated proteins and DNA have improved, the advent of cofactor mimics that utilize naturally occurring enzymes may hold tremendous value in future research efforts.
A novel approach in exploring methyltransferases using synthetic cofactor mimics is illustrated in the following reaction scheme. Highlighting the utility of DNA methyltransferase M.TaqI, cofactor mimics containing an aziridine ring in lieu of the methyl-sulfonium (2) undergo enzyme-dependent DNA alkylation. Instead of generating the N6-methylated adenine residue, substrate adenylation results from ring-opening of the aziridine to form the modified-DNA complex. While chemical modifications (i.e. attachment of biotin or fluorophore) of aziridine 2 have been carried out to improve its utility for biological imaging, such agents are synthetically difficult to obtain. Recent efforts introduce small ligatable functionalities to the aziridine base of 2 and demonstrate their versatility in undergoing chemoselective ligations on DNA. Interestingly, synthetic cofactors of SAM are not restricted to 5'-aziridines, as N-mustard containing analogs generate the aziridinium in situ prior to methyltransferase-dependent transfer. The structural core of these N-mustards serve as the basis for creating a diverse library of second generation cofactor mimics bearing alkynes or azides to continue recent efforts in exploring methylation biology.
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