Photoaffinity capture compounds to profile the Magic Spot Nucleotide interactomes

Magic Spot Nucleotides (MSN) regulate the stringent response, a highly conserved bacterial stress adaptation mechanism, enabling survival when confronted with adverse external challenges. In times of antibiotic crisis, a detailed understanding of the stringent response is of critical importance, as potentially new targets for pharmacological intervention could be identified. In this study, we delineate the MSN interactome in Escherichia coli and Salmonella typhimurium cell lysates applying a family of trifunctional photoaffinity capture compounds. We introduce different MSN probes covering diverse phosphorylation patterns, such as pppGpp, ppGpp, and pGpp. Our chemical proteomics approach provides datasets of diverse putative MSN receptors both from cytosolic and membrane fractions that, upon validation, unveil new MSN targets. We find, for example, that the dinucleoside polyphosphate hydrolase activity of the non-Nudix hydrolase ApaH is potently inhibited by pppGpp, which itself is converted to pGpp by ApaH. The photoaffinity capture compounds described herein will be useful to identify MSN interactomes under varying conditions and across bacterial species.

Development and validation of inducible protein degradation and quantitative phosphoproteomics to identify kinase-substrate relationships.

Phosphorylation signaling is an essential post-translational regulatory mechanism that governs almost all eukaryotic biological processes and is controlled by an interplay between protein kinases and phosphatases. Knowledge of direct substrates of kinases provides evidence of mechanisms that relate activity to biological function. Linking kinases to their protein substrates can be achieved by inhibiting or reducing kinase activity and quantitative comparisons of phosphoproteomes in the presence and absence of kinase activity. Unfortunately, most of the human kinases lack chemical inhibitors with selectivity required to unambiguously assign protein substrates to their respective kinases. Here, we develop and validate a chemical proteomics strategy for linking kinase activities to protein substrates via targeted protein degradation and quantitative phosphoproteomics and apply it to the well-studied, essential mitotic regulator polo-like kinase 1 (Plk1). We leveraged the Tir1/auxin system to engineer HeLa cells with endogenously homozygous auxin-inducible degron (AID)-Plk1). We used HeLa cells and determined the impact of AID-tagging on Plk1 activity, localization, protein interactors, and substrate motifs. Using quantitative proteomics, we show that of over 8,000 proteins quantified, auxin addition is highly selective for degrading AID-Plk1 in mitotic cells. Comparison of phosphoproteome changes in response to chemical Plk1 inhibition to auxin-induced degradation revealed a striking degree of correlation. Finally, we explored basal protein turnover as a potential basis for clonal differences in auxin-induced degradation rates for AID-Plk1 cells. Taken together, our work provides a roadmap for the application of AID technology as a general strategy for the kinome-wide discovery of kinase-substrate relationships.

Mechanism-based design of bioactive cyclopropanated sugars

<p>Carbohydrates are important feed stocks in synthesis of natural products and so attract the interest of many organic researchers throughout the world, most notably in the last 10 years. The work described within explores the manipulation of the glucose-derived glucal. The addition of a reactive substituted cyclopropane across the alkene has been employed synthetically for many years, the subsequent ring breaking/expansion has been identified in the lab as slow and needing the support of catalysts. We ask the question, “Will cyclopropanated carbohydrates undergo the slow ring breaking/expansion in the presence of proteins, and are we able to identify which of the two types of mechanisms the reaction is going through?” The cyclopropane will act as a warhead to bind to proteins through Ferrier like rearrangements, resulting in irreversible inhibition. To identify the potential of such compounds, a combination of techniques are used to identify potential pathways, protein targets and reactivity through structure activity relationships. The key steps involved in finding out the potential of cyclopropanated carbohydrates are to determine biological activities through bio-assays, structure activity relationships, selective binding, chemical genetics and chemical proteomics. The bio-assays together with structure activity relationships provides evidence on which chemical mechanism is occurring when the biological target is interacting with the bioactive cyclopropanated carbohydrates. The most active compound, benzose (7), was subjected to chemical genetic analysis to determine the pathways and processes that are involved with the mode of action. The chemical genetic analysis was complimented by chemical proteomics to identify the direct biological target. Analogues of benzose were synthesised by the addition of azide groups to undergo a Huisgen Cyclisation within a cell lysate to facilitate binding to an alkyne-substituted matrix.</p>

Mechanism-based design of bioactive cyclopropanated sugars

<p>Carbohydrates are important feed stocks in synthesis of natural products and so attract the interest of many organic researchers throughout the world, most notably in the last 10 years. The work described within explores the manipulation of the glucose-derived glucal. The addition of a reactive substituted cyclopropane across the alkene has been employed synthetically for many years, the subsequent ring breaking/expansion has been identified in the lab as slow and needing the support of catalysts. We ask the question, “Will cyclopropanated carbohydrates undergo the slow ring breaking/expansion in the presence of proteins, and are we able to identify which of the two types of mechanisms the reaction is going through?” The cyclopropane will act as a warhead to bind to proteins through Ferrier like rearrangements, resulting in irreversible inhibition. To identify the potential of such compounds, a combination of techniques are used to identify potential pathways, protein targets and reactivity through structure activity relationships. The key steps involved in finding out the potential of cyclopropanated carbohydrates are to determine biological activities through bio-assays, structure activity relationships, selective binding, chemical genetics and chemical proteomics. The bio-assays together with structure activity relationships provides evidence on which chemical mechanism is occurring when the biological target is interacting with the bioactive cyclopropanated carbohydrates. The most active compound, benzose (7), was subjected to chemical genetic analysis to determine the pathways and processes that are involved with the mode of action. The chemical genetic analysis was complimented by chemical proteomics to identify the direct biological target. Analogues of benzose were synthesised by the addition of azide groups to undergo a Huisgen Cyclisation within a cell lysate to facilitate binding to an alkyne-substituted matrix.</p>