Commentaries

Nobel Prize in Chemistry for Bio-Inspired Catalysts

The Nobel Prize in Chemistry in 2021 has been awarded to German Benjamin List and British David MacMillan.
Prof Stefan Howorka from the ISMB at UCL Chemistry explains: ‘The two researchers have developed a new class of catalysts that are inspired by Nature. Enzymes are widely used in biology as they initiate and specifically control biochemical reactions to achieve the desired stereochemistry while limiting the creation of undesirable by-products. Reconstructing these catalytic functions with smaller and cheaper synthetic units is of considerable scientific and industrial interest. Ideally, synthetic catalysts should also avoid precious metals such as platinum which are not environmentally friendly.
List and MacMillan succeeded independently of each other in developing efficient biomimetic and “green” catalysts. In the late 1990s, List wondered whether amino acids found in the enzymes’ active site would also be able to achieve part of the same catalytic role if added in isolation. As proof-of-principle, List tested the catalytic properties of proline and related compounds in an aldol reaction. The specific question was whether the use of a chiral proline would control the stereochemical outcome of the reaction. Indeed, the chirality of the catalyst controlled which enantiomer of the aldol products was formed.
MacMillan was working in the same field. MacMillan was motivated to develop new catalysts that avoid the widely used metals. Rather, he focused on environmentally harmless and inexpensive organic frameworks that contain -in addition to carbon- oxygen, nitrogen, sulphur or phosphorous. Similar to List, MacMillan also tested chiral versions of his organic catalysts but with a different reaction, the Diels-Alder cycloaddition. The reaction was successful as enantiopure products formed depending on the chirality of the catalysts.
Reflecting the catalysts’ composition and enantioselective control, MacMillan coined the term ‘asymmetric organocatalysis’ This new field has grown dramatically and develops simple, easy-to-manufacture and environmentally friendly catalyst. This has a huge impact in science and industry to produce new pharmaceuticals or molecules that can capture light in solar cells. This year’s Nobel prize and the Nobel prize given in 2018 for ‘the directed evolution of enzymes’ underscore the importance of developing new catalytic tools, Prof Howorka concludes.

References:
J. Am. Chem. Soc. 2000, 122, 2395-2396; J. Am. Chem. Soc. 2000, 122, 4243-4244

Posted by ubcg49z in Commentaries, News, Uncategorised

ISMB Commentary: An unexpected role for the enzyme Glutamine Synthetase

October 2018

Prof Francesco Gervasio’s group has contributed to the discovery and clarification of an unexpected, yet fundamental, role of the enzyme glutamine synthetase.

Glutamine synthetase (GS) is an enzyme that converts glutamate and ammonia to glutamine.  GS is expressed in endothelial cells, fundamentally regulating vascular development. However, a group of scientists led by Prof Peter Carmeliet at VIB in Belgium together with Prof Francesco L. Gervasio found that it surprisingly shows little glutamine synthetizing activity in these cells. Instead, GS localizes in membranes due to an expected (and so-far, unknown) auto-palmitoylation activity. This moonlighting activity turns out to be fundamental for vessel sprouting. However, it was unclear how it happens and which residues are involved. The state-of-the art models and simulations by Prof. Gervasio’s group were able to solve the mystery, showing how palmitoyl-COA binds to the active site (see figure, left) and reacts with cysteine 209 to form a covalent bond. Site-directed mutagenesis of Cys209 later confirmed the computational prediction and validated the proposed mode of action. This new finding, published by Nature at the beginning of September, has important implications for anti-cancer drug discovery, as it might lead to new drugs blocking the vascular development in solid cancers.

 

Role of glutamine synthetase in angiogenesis beyond glutamine synthesis
Eelen, G.,…, Gervasio, F.L.,…, Carmeliet, P.
Nature (2018) 561, 63-69

Posted by ubcg49z in Commentaries, News, Publications

ISMB Commentary: Using deep learning and single cell tracking to understand competitive interactions in cell populations

June 2018

Cell competition is a quality-control mechanism through which tissues eliminate unfit cells. Cell competition can result from short-range biochemical inductions or long-range mechanical cues. However, little is known about how cell-scale interactions give rise to population shifts in tissues, due to the lack of experimental and computational tools to efficiently characterize interactions at the single-cell level. Here, we address these challenges by combining long-term automated microscopy with deep-learning image analysis to decipher how single-cell behavior determines tissue makeup during competition. Using our high-throughput analysis pipeline, we show that competitive interactions between MDCK wild-type cells and cells depleted of the polarity protein scribble are governed by differential sensitivity to local density and the cell type of each cell’s neighbors. We find that local density has a dramatic effect on the rate of division and apoptosis under competitive conditions. Strikingly, our analysis reveals that proliferation of the winner cells is up-regulated in neighborhoods mostly populated by loser cells. These data suggest that tissue-scale population shifts are strongly affected by cellular-scale tissue organization. We present a quantitative mathematical model that demonstrates the effect of neighbor cell–type dependence of apoptosis and division in determining the fitness of competing cell lines.

Dr Alan Lowe

Ref: Local cellular neighbourhood controls proliferation in cell competition
Bove, A., Gradeci, D., Fujita, Y., Banerjee, S., Charras, G., Lowe, A.R.
Mol. Biol. Cell (2017) 28: 3215-3228

This video by the Alan Lowe lab demonstrates the data acquired and software developed as part of the work.

 

Posted by ubcg49z in Commentaries, Publications