Back after an afternoon of heavy hiking to Castle Boymont uphill from Schloss Korb. Great stuff.
Day 3, Morning Session on Macromolecular Interactions: P-P, P-NA, NA-Light
Sara Linse of Lund report on her group’s work on Protein Interactions, Association and Fibrillation. Systems Chemistry is the study of molecules acting collectively, she proposes. Her focus of course is on proteins interacting and she show some micro array assays for protein association studies (and I learned another buzz word: Interactome :-)). The second part of her talk is dedicated to studies of the effect of nano particles on protein fibrillation. The nano particles she studies where about 200 nm in diameter, compared to about 70 nm for a typical protein in study. Her conclusions are quite alarming in that there are clear effect of nanoparticles on protein association, because of their small size nano particles can enter the organism by various mechanism – yet, because of the fact that many nano particles are made from known and risk-assessed materials, there no *new* risk assessments done accounting for the new properties that arise from the small size. It should be noted of course, that there is awareness for the new risks arising from nano particles and discussions are going on.
Michele Vendruscolo of Cambridge talked about “Life on the Edge: Proteins are close to their Solubility Limits”. He shows an incredibly crowded picture of a yeast cell. Yet, a protein can visit most locations in a cell in a fraction of a second. Interestingly, the life time of a protein in a cell is only in the order of about 1 hour, after which it is recycled. He talks about the folding process of a protein and that dispite a well-defined folding funnel there can be many more states being adopted by a protein, potentially leading fibrilles. Michele shows a model to predict aggregation rates of proteins from the sequence. He concludes by giving another definitions of Systems chemistry being a strategy based on chemical principles to make predictions about cellular processes.
Alexander Heckel of Frankfurt speaks about “Shedding Light on Nucleic Acids and DNA under Construction”. He shows examples from his research on light-induced transcription and light-induced RNA interference. In his second part he talks about DNA constructions. Alexander shows a very impressive animation of ATP synthase that I need to get my hands on.
The morning session closes with a talk by Justin Roberts from Riverside, CA, USA, on High-Throughput Analysis of Nucleoside- and Nucleotide-binding by Proteins.
Day 3, Afternoon session on Chemical Spaces and Molecular Design
Joseph Lehár of Cambridge, MA, USA, starts the afternoon talks with the topic “Systems Biology from Synergistic Chemical Combinations”. He is the first to talk about multi-drug (he calls it combination drugs). He highlights various multi-target mechanisms such as “cooperative targets”, “block compensation”, “circumvention of resistance”. His companies looks at combinations of all approved drugs and uses cell-based assays to screen them.
Holger Wallmeier, independent consultant, speaks about “A Dynamical Supramolecular System for Chemical Biology – a Step towards Contiguous Structural Spaces”.
The last research talk of the meeting is delivered by Gisbert Schneider of Frankfurt talking about “Molecular Design: Voyages to the (un)known”. He starts with musing about what Systems Chemistry is based on Darwin’s work on the Transmutation of Species. He continues with explaining different levels of abstraction for molecular representations leading to the definition of a pharmacophore space. In the following, Gisbert shows work with Self-Organising Maps (SOMs) on the discovery of pharmacophore spaces.
My summary and closing remarks: We saw an enormously diverse set of talks, most of them dedicated to the study of biological phenomena. If this workshop was really on Systems Chemistry, this indicates that System Chemistry has to do something with Biology. My theory is that we add the view on molecular details to Systems Chemstry. A lot of reports focus on understanding the parts, but there were indeed interesting insights into the properties of biological systems, such as the talk by Danchin. I enjoyed the meeting a lot and would love to see a follow-up – the problem is far from solved – with a greater emphasis on the fundamental problems of systems simulations on varying scales – dynamic scale switching, so to say. Only the application of first-principles at places where detail is required will allow us to make meaningful prediction, for example in the prediction of drug action on organisms.
The Wednesday morning session is about to start. Paul Labute chairs it.
Tom Blundell of Cambridge starts with “Exploring Biological and Chemical Space with High-Throughput Crystallographic, Biophysical and Computational Methods: The new Dimensions of Drug Discovery”. Tom starts with a view on a cell, stating its complicatedness or complexity. He points out the large number of crystal structures of drug targets and a lack of success of the pharma industry to make drugs fast and at reasonable cost. Tom then praises high-throughput automation in his research. A large amount of information will become available from projects like the “1000 genomes”. He describes the projects of his Astex company, soaking crystals with small molecule fragments to identify binders. Essentially, the rest of the talks is on innovative approaches to screening of compound libraries against protein libraries.
Dave Winkler of Monash University, Australia, announces to talk about Complex Systems. Large molecules are brought home into the chemistry domain. He talks about properties of complex systems, such as emergent properties – unexpected properties apprearing from the interactions of many components or agents in complex systems. Dave mentions the role of networks, Gene networks, metabolic networks, protein-protein interaction networks for System Simulation . Dave states that Systems chemistry might simply be the application of Complex Systems Science applied to Chemistry. The level of simulation is essential when modelling emergent properties of complex systems. His groups builds mesoscale models of stem cell cytokine regulatory networks.
Douglas Kell from Manchester spoke about Drugs and Xenobiotic Transport via Membrane Carriers. He emphasises the difference between a a biophysical approach vs. a mechanistic analysis. Douglas very nicely points out that a huge amount of work still lies in front of us in studying mechanistic properties of the parts to eventually put them together. He mentions ChEBI for the sake unifying chemical names, highlights the problems with literature mining. In his second part of his talk, he spoke about carrier-mediated cellular uptake vs. a lipid-only theory (logP being important here).
Tim Clark of Erlangen uses Molecular Dynamics studies to look at Signal Transduction. He mentions that when they started seven years ago they did not know if the force fields were good enough and if they could ever simulate the system for long enough to get meaningful answers. The work was on the Tetracylcine Repressor (TetR) . Tetracyline comes into a cell, comlexes with Magnesium, and then docks to the TetR, and off goes the expression of the antiporter which transports Tetracycline out of the cell. TetR can be used to switch on and off genes in eukaryotes and prokaryotes. They were able to run these TetR MD simulations on the 100 nanoseconds time scale. He showed a low-frequency mode visualization of TetR MD yielding an understanding of induction mechanism of TeTR by Tetracycline. The binding pocket properties change enormously after binding, volume for example shrinking by more than 50 percent. What does that say about docking into rigid pockets?
Wednesday afternoon is, as usual, dedicated to a hike. This time, it goes to a castle on a top of a mountain behind Schloss Korb – very nice walk – we did it in 2004 already.
I’ve been invited to deliver the summary talk for the 2008 Beilstein Symposium on Systems Chemistry in Bolzano, Italy. Being there for the fourth time in eight years (this symposium is biannual) I really always enjoy the meeting in this beautiful setting from the very first minute. The fact that the view and the food is fantastic and that Schloss Korb is a winery of course plays no role. My interest is purely scientific 🙂
Following are my notes on the various talks, hopefully helping me to put together the summary in the end. All of the talks were full of subtle, interestingly illustrated scientific details which were absolutely impossible to capture here 🙂
Tuesday morning: Life, Living Systems and their inherent properties
Martin Hicks, organizing the Beilstein workshop in Bozen in the twentieth year now, in his introduction highlights the routes between synthetic chemistry and biological systems. He also points to the different views of Chemists and Biologists on Biological Systems. And, as you will probably appreciate, 20 rabbits do not make a horse.
Günter von Kiedrowski, in “Systems Chemistry and the Origin of Life”, puts the understanding of the origin of life in the centre of interest of Systems Chemistry. Showing a picture of earth from space he points out the number of events necessary to form life on earth, including formation of the hydrosphere, cometary impacts, formation of the RNA world, as well as an DNA-Protein world: Prebiotic chemistry. He calls it “Origin of Life” research and acknowledges Jean-Marie Lehn, Albert Eschenmoser and Manfred Eigen as pioneers. Günter mentions Craig Venter’s minimal Cell and works on Minimal Self-Replicating System: Keypoint is a product inhibition preventing exponential growth of the system. He further shows basic structural and dynamic prerequisites for self-replicating system. My impression was that the kinetic rules for a minimal replicator are well understood. In the last slide, he sites the NASA exobiology program: “Life: A self-sustaining chemical system capable of undergoing Darwinian evolution”
The second speaker, well-known Hans V. Westerhoff from Amsterdam in “Chemistry in Three Dimensions: How Systems’s Biology may Regulate its System’s Chemsitry”, looks at chemistry from a systems biology view point. He points out that the European Science Foundation has declared Systems Biology a Grand Challenge with implications for the understanding and fight against disease. His talk focused on some fundamental properties of chemical and biological systems which I mostly missed. Mentions plan to make the virtual human in the next 30 years.
Antoine Danchin started of by talking about using Synthetic Biology (SB) for constructing a synthetic cell . The first aim of SB is to reconstruct life. He introduces the idea that the cell might be Turing machine. Life as a combination of a program running on a cell processor. He points out that while the machines reproduces, the program replicates. Replication accumulates errors. An interesting fact: One fifth of bacterial genomes comes from “outside”, a hint of the separation of program and hardware, kind of an organic open source software exchange. Antoine also introduces the notions of the Paleome, part of the genome responsible for replication and maintenance, and the Cenome , managing Life in context, sensing, etc.
Tuesday afternoon: Catalysis and Chemical Tools for Exploring Biology (Chemical Biology)
The afternoon session of the first day was opened by Benjamin List, who talked about “New Concepts for Catalysis”. Benjamin highlights progress in the understanding of catalytic properties of small organic molecules without involvement of metals as part of the catalytic principle.
Steve Ley of Cambridge presented on”New Tools for Molecule Maker: Emerging Technologies”. His main interest is in making molecules, and making these with some goal in mind, such as curing a disease. He starts off with asking how good we really are as organic chemists. A slide with examples of synthesized, quite complicated natural products his lab had synthesized in the past. Pretty impressive, but he points out the limitations: Less severe are lack of reproducibility, scale-up issues, problems with low temperature, material economy. Really bad: Current cost of organic chemistry, time consumption, wastage of man power and questions of sustainability. The solution are flow reactors and lab-on-a-chip devices. Steve shows the synthesis of Epothilones on beads, requiring no washing, no isolation, no chromatography. Flow mode chemistry, combined with the beads concept makes synthesis even more efficient. Like the following speaker, Steve shows a continuous flow reactor chip (lab-on-a-chip), coupled to collectors, HPLC and a recycling loop, pointing out that the whole dynamics of a reaction change (as in “enormous speed-up”) when going from flasks to flow reactors. The close-loop-operation of these devices allow for rapid, even on-the-fly changes and improvements of reaction conditions. An interesting point was that chemists are awfully bad in achieving proper mixing of reaction mixtures and that the ability to pump reaction mixtures back and forth in flow reactors significantly changes the rules of the games, dramatically increasing the reaction rates. These things can then be made in amounts to up to 15 kg in the Ley lab!
Peter Seeberger of ETH Zürich , who has just accepted a call to become a director of a Max-Planck-Institute near Berlin, also talked about “Microreactors as Tools for Organic Synthesis”. He points out, underpinned by pictures from MIT labs through the ages, that the chemistry lab has not changed much in the last hundred years. Besides advantages also pointed out by Steve Ley, Peter emphasizes the positive safety behaviour of flow-through reactors. The flow reactors that he describes are silicon-based with the advantage that the production process for these reactor is very well understood (think “chip industry”). Like Steve, Peter points out that flow reactors allows a coworker in his lab to run a couple of hundred reactions under different conditions in a few afternoons. Besides making things faster and more efficient, you even make things that don’t work otherwise. He exemplifies this with the synthesis of a particular tetrapeptide, where I missed the point why this was not possible without flow devices.
Eric Meggers, University of Marburg and Wistar Institute, Philadelphia, concluded the afternoon session, with a talk on “Chemical Biology with Organometallics”. Why is Nature synthesizing complicated secondary metabolites, is his starting question, while drugs, for example, often look so much simpler. He exemplifies by showing how nicely Geldamycin fits into its target pocket – an example already answering his question. The target pocket is flat and wide and Geldamycin adopts a bulky globular shape with all functional groups nicely presented on its surface. No smaller or less complicated molecule could have this function. He then introduced a recipe for morphing indolocarbazole alkaloids into simple and easily accessible metal complexes, leading to potent inhibitors of protein kinases.
I’ll send this off now, because the reception this evening will be in the local wine cellar. No more sensible content to be expected.
I was invited to give my views on some new chemistry in European Bioinformatics at a Meeting held by the CICAG group of the Royal Society, held at Burlington House, London.
Peter Murray-Rust set the scene by emphasising the importance for Open Data. He showed some fantastic work on data extraction by OSCAR from theses, where his group had parsed a synthetic chemistry thesis into an interactive graph of a reaction network. He also showed an SVG animation of this graph as a reaction sequence, all automatically generated from an OSCAR run. Peter pointed out in the subsequent discussion that data cannot be copyrighted, which was acknowledged by all publishers in the audience. The reality is different, however, because publisher’s licenses often prevent downloading of more than few articles in a row. Detection of a robotic download for text mining comes with the danger of the whole university being disconnected. It is unclear to me how robotically parsing papers and extracting data would damage the bushiness model of publishers. It could, of course, lower the number of subscriptions from
Ian RusselL of ALPSP presented on Open Access models and how those of uses by ALPSP members. He pointed out that a lot of long-tail publishers publish only two or three journals, quite in contrast to ACS and RSC, for example. He stated that making profit is good, because it can be reinvested into innovation. I’m not sure if I’ve seen much innovation in the publishing business before the emergence of the Open Access model. He further commented on self-archiving stating that only pre-peer-review manuscripts can be self-archived without permission from the publisher. A librarian in the audience pointed out that duplication of costs by mixed read-pays and author-pays models have significantly increased the libraries expenses and Ian Russell comment was that there are no cost-savings in Open Access. Not sure if this helps. My impression is that it is not in the interest of publishers to resolve this conflict. [Editorial Note after Submission: Ian has replied to this part – See comments. ]
Robert Kiley, Wellcome Trust, summarized the Trust’s OA policy, where Trust-funded research needs to be put into pubmedcentral six month after publication. If I remember right, the Trust funds more than 90% of Biomedical research in Britain. The NIH now has a similar policy, and so has European Research Council; Robert mentioned that most text mining so far is based on PubMed abstracts, but that the full text would be required for serious efforts. He further pointed out that the number-one option for researchers to comply with the Trust’s OA policy would be to publish in a true Open Access Journal (BMC, PLOS, etc.). The second-best choice would be to publish anywhere and self-archive. The least preferable choice would be to publish with the ACS (one of the very few publishers without a Wellcome-Trust complient OA policy) and try to change the copyright notice 🙂 . The Trust is in contact with publishers to make sure that authors have a wide variety of journal with open access policies to choose from. Robert highlighted the importance of OA for the long-term preservation of articles and data therein, with special emphasis on future-proofing the record of medicine. To check the compliance of authors with this new OA policy, the Trust conducted a study with 279 papers on Trust-funded research, where, if I remember right, over 90 percent of researchers were in compliance. Robert concluded his talks with mentioning UK PubMedCentral, which will be exposed for Text Mining, including Chemical Entities. The trusts next steps are to continue to work with publishers, monitor compliance of researchers, make funds available for OA and develop UkPMC
My own talk went about Chemistry at EBI and in European Bioinformatics in general.
Simon Coles, University of Southampton, talked about building repositories to preserve chemical data and publications. His view is that of an active crystallographer and he pointed out that this community could serve as a paradigm for other areas of chemistry. He pointed out that spectra are often published as inaccessible supplemental information without proper guidelines for representation. A great chance for capturing and publishing data in the very beginning are movements like OpenWetWare and Open Notebook Science which are catching and publishing laboratory experiments as they are done, and not 9 month after, when published and filtered. Simon mentioned that less than a quarter of cystral structures determined are actually published – a lot of data is just lost. This is certainly true for NMR data, an area of interest of my own research. The crystallographic community has made a step to increase the number of published crystal structures by creating Acta Cryst E (now open access) where publications just consist of the crystal structure it self and a few additional remarks. They just publish the crystal structure!!! In CIF format, computer-readable and harvestable. This would be a great step for NMR – publish structure and spectral evidence, semantically enriched, in a short communication. Simon further reported that Southampton has build the eCrystals Data Repository software based on the eGrid project, where crystallographic data can be easily deposited, supported by authoring tools, and serving as a laboratory archive. An embargo mechanism is implemented but once published, data can be harvested and analysed. The whole, funded study was really about preservation of research data, exemplified on Crystallographic data. To scale this up, Simon suggested (does is exist already?) to have a Federation of Crystallographic Data Repositories. He further mused about how that could be transferred to less well organized disciplines such as NMR, synthesis, etc. Long tail science is extremely fractioned, unorganised stuff sitting on Laptops, unorganised, inaccessible. A new kind of electronic lab notebook, the “Smart Tea Project“, can actually be taken into the lab, using mobile input devices. Analysis and discussion of on-the-fly captured data can then be published in the workgroup, between collaborators in the world, using blog-technology. Some software can enable machines and sensors to blog their results – a sensor for room temperature and or air flow in the lab for example can then be correlated with outcome of NMR experiments using time stamps.
Diana Leitch, University of Manchester, gave “the academic librarian’s perspective, in a unique way of just talking and *not* showing any slides 🙂 How relieving.
I had to miss the two talks by Chris Leonhard from BMC, whose title seems to indicate growing support for Open Access and by by David Hool from the Nature Publishing Group, because I had to catch my flight from Stansted, which I also almost missed because the fantastically reliable British rail system – all trains from London to Stansted were cancelled, we were advised to take a local train to a small station in the middle of nowhere instead, where of course there was nothing like a connection to Stansted. I was one of the lucky few to get the last available taxi, driven in snail speed by an old lady 🙂 Could have been very funny as a movie. Well, I made it to the gate in time, where “the machine was otherwise fully boarded and awaiting and an on-time departure” (Those of you travelling with Ryan Air regularly know what I’m referring to). I will never again be arrogant toward people showing up in Stansted sweating and on the very last minute. The all come from central London.
So, what it the bottom line from this meeting? The important message is perhaps that OA publishing has not yet quite reached chemistry but that there are grass-root movements which are going to revolutionize the way in which we publish science and scientific data, starting at the very first moment when research is performed in the lab.
… with a reasonably small footprint … and we’ll soon have one that is actually usable.
Well, with the JChemPaint applet, as used in NMRShiftDB, we do have an open source structure drawing applet available but we (as in “the makers”) have to admit that it still has a pretty big foot print. If you look at Peter Ertl’s famous editor in action or the new ChemWriter editor by Rich Apodaca’s MetaMolecular, you see how fast loading improves your user experience. Our ChEBI database’s new structure search still uses a ChemAxon Marvin Sketch applet, but since we promise the world a full open source version of ChEBI, we’ll be in need for a free (as in speech) replacement.
Egon has built on work done by Niels Out in a Dutch Summer of Code project last year. Niels had produced both the beautiful Java 2D based renderer as well as a provisional controller.
The first user workshop of the European Bioinformatics Institute’s (EBI) database and ontology of Chemical Entities of Biological Interest (ChEBI) is over. We had about 30 participants from industry, universities and research institutions. The user workshop started with three talks by ChEBI users reporting on their particular use of our resource. Colin Bachelor from the Royal Society of Chemistry described text mining efforts at the RSC Publishing Department and how the ChEBI ontology could be improved to better serve their purposes. He pointed out, for example, surplus overloading of ChEBI’s ‘is_a’ relationship and how this can be overcome. We’ll work on it.
Ulrike Wittig of EML Research in Heidelberg talked about ChEBI and their SABIO-RK database, which contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. Here, ChEBI helps to match lists of compound names from different databases via its synonyms feature.
Giles Weaver from Unilever presented a talk on the construction of Genome Scale Metabolic Networks and how ChEBI aids as a small molecule hub to genomic and other information.
The workshop continued with ChEBI group coordinator Paula de Matos presenting the “ChEBI story so far”, as well as new developments such our recently introduced substructure and similarity search and future plans. The following open discussion focused on the ChEBI ontology, its potential improvements and how a discussion with experts from OBO Foundry Ontologies would help in making the ChEBI ontology more useful them. Such a meeting is now projected as a parasitic meeting of the OBO Foundry Meeting here at EBI in July.
Kirill Degtyarenko started the second day explaining how the ChEBI curation process works and what we consider to be good annotation practice, followed by Janna Hastings giving a hand-on training on ChEBI. A lively discussion originated in the end, covering question on database growth, having an automatically annotated buffer database and cooperation/crosslinking with other resources.
The ChEBI team feel thoroughly enjoyed the feedback and thinks that the workshop was a great success. The analysis of questionnaires returned by our participants unanimously point into the same direction. The results and the feedback from this workshop will help us to shape the development strategies for the upcoming month and year.
We gratefully acknowledge the sponsoring of the ChEBI user workshop by the EBI Industry Programme.
The Royal Society of Chemistry organizes a meeting on Open Access in Chemistry. It will happen on May 22nd in London. The programme is here: RSC Open Access Meeting Programme. Topics will be questions like “why do we need it?”, existing open resources, OA Publishing (with talks from Chemistry Central journal and Nature Publishing Group), and more.
The NMRShiftDB server network is currently undertaking major reconstruction. We have physically moved the server previously running at CUBIC to its new location in the NMR labs of the University of Mainz, run by Heinz Kolshorn, where the machine is now running as http://nmrshiftdb.chemie.uni-mainz.de.
The two servers impersonating nmrshiftdb.org, running at the Max-Planck-Institute for Chemical Ecology in Jena, will have their operating system moved from SUSE to Debian and will be reinstalled afterwards. We do not expect things to be overly shaky but you never know.
it has been a pleasure to serve on your thesis committee and to attack you with nifty questions during the defence. It was also great to see you wearing a dress coat and a bow tie. For everyone reading this, I can recommend attending a Dutch thesis defence. In Germany, we have thrown overboard after 1968 all these nice traditions of professors wearing gown and having a master of ceremony https://puttygen.in , who comes in at the end of the defence and exclaims "Hora est!". Well, it was very nice to see all this. The doctorate certificate had the size of a piece of wall paper. I have fun imagining you making a copy of it to send it to future employers 🙂
Congratulations for your well deserved doktor title and for your well written thesis.
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary and ontology of molecular entities focused on ‘small’ chemical compounds hosted and maintained by the European Bioinformatics Institute (EBI). The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.
The ChEBI team is now pleased to announce the first ChEBI user day to be held at the EBI on May 19th/20th 2008. The programme as well as registration information can be found here. The user day will have talks by the user community on their use of the database and ontology, followed by ChEBI team talks on latest developments, the curation process and hands-on training. Open discussions on how ChEBI should be further developed will round out the programme. And off you go to register … 🙂
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