2014: Big science @ a small company

2014: Big science @ a small company

The pleasant fact is that our activities cannot be summarised in a single blog entry any more! That is why we had to write two entries for 2014, this is the second one

In this part we wanted to bring up the exciting science at SARomics Biostructures.  Our experience has shown that running our own research and discovery projects both inside and outside the company is a prerequisite for the success of our CRO activity. While some of us are entirely focused on customers’ projects, on internal discovery projects and development of the technology platform, others combine company-related work with academic projects at Lund University, where they have PhD students and post-docs. All this together creates an exciting combination of science and business at the company.

Going back to 2014, one of the absolute highlights was getting the BIOCASCADE project funded by the EU. Within this project 11 early-stage researchers (normally called PhD students!) will investigate the development of sustainable chemo-enzymatic cascade reactions for the synthesis of optically pure amines and aminoalcohols as pharmaceutical ingredients. The project combines different techniques such as biocatalysis, transition-metal catalysis, compartmentalization, protein engineering and reaction engineering, in order to develop commercially viable and environmentally benign chemo-enzymatic reactions. SARomics Biostructures will participate in the consortium, together with 11 other partners, and contribute to the structure-based enzyme engineering part of the project. This will be our first commercial move into the field of industrial enzymology and we feel very excited about this new opportunity. Among the participants in the consortium are three SMEs (EntreChem, ENZYMICALS, ViaZym), seven university laboratories (Ruhr University Bochum and Greifswald University; Royal Institute of Technology, Stockholm; University of Oviedo; University of Amsterdam; Bielefeld University and Graz University of Technology) and DSM, a leading European chemical company.

Additional research highlights from 2014 include two publications co-authored by SARomics Biostructures staff, one by von Schantz et al. (2014) in which the recognition of xyloglucan by the carbohydrate binding module was studied. The second paper by Badarau et al. (2014) presented a study of heterodimer formation and receptor binding by the Staphylococcus aureus bi-component toxin LukGH. And of course we should not forget the review by Turnbull, Boyd and Walse on fragment-based discovery in targeting protein-protein interactions, which was highlighted in the Practical Fragments blog. For several reasons drug discovery efforts are increasingly turning to the area of protein-protein interactions, and the question of how fragment libraries should be designed for targeting PPI in the most optimal way is central for future progress in this direction. Luckily the review was published online just in time for the FBLD2014 meeting that took place in Basel in the end of September.

Coming back to the meeting-theme of the previous blog, the absolute highlight of our activities last autumn was the trip to Yokohama for the Bio-Japan partnering meeting in October. This is Japan’s primary event involving the global biotechnology industry. We participated in the Scandinavian pavilion organized by Business Sweden, Invest in Denmark and Medicon Valley Alliance. At the huge partnering event we met with several Japanese pharmaceutical companies and also made a presentation during the Scandinavian session within the conference programme. The trip to japan was not entirely devoted to the Bio-Japan meeting. Prior to the meeting SARomics was presented at a matchmaking seminar at the Danish Embassy in Tokyo for special invited guests. While being in Japan we also took the opportunity to make site visits to collaborators and to meet potential customers. Thus, it was both an exciting and productive trip.

We should also mention the PSDI (Protein Structure Determination in Industry) conference held from 2-5 November. The meeting was held in Portugal and nicely covered topics ranging from fragment based drug design to protein-protein complexes. A range of biophysical methods to study protein-ligand interactions were described, including recently developed techniques such as microscale capillary thermophoresis, but also more established methods like NMR, SPR and the Thermofluor technique that we use extensively in the lab. Interestingly, the Thermofluor technique seems to show good predictability for obtaining protein-ligand complex structures, which is something that we have also observed. 


von Schantz L, Håkansson M, Logan DT, Nordberg Karlsson E & Ohlin M (2014) Polar interactions with branching xyloses and CH-π interactions define carbohydrate binding module recognition of xyloglucan. Proteins, published online 10 Oct 2014, doi:10.1002/prot.24700

Badarau A, Rouha H, Malafa S, Logan DT, Håkansson M, Stulik L, Dolezilkova I, Teubenbacher A, Gross K, Maierhofer B, Weber S, Jägerhofer M, Hoffman D & Nagy E (2014) Structure-function analysis of heterodimer formation, oligomerization and receptor binding of the Staphylococcus aureus bi-component toxin LukGH. J. Biol. Chem., published online 3 Nov 2014, doi: 10.1074/jbc.M114.598110

Turnbull, A.P, Boyd, S.M. and Walse, B. (2014) Fragment-based drug discovery and protein-protein interactions. Research and Reports in Biochemistry, 4, 13-26.


SARomics Biostructures: Hamburg, Berlin, Zurich, Basel, Turin, San Diego and new FastLane structures!

The cities in the title may remind you of the way some shops market themselves, telling us in which great places we may have the pleasure to purchase their products. In our case the list gives an indication of some of the places you would have been able to meet us during the first half of 2014.  Although “new FastLane structures” does not quite fit into that picture, the further development of our list has been an important part of our activities during that period. Here follow some of the highlights from last year.

Early in 2014 we entered a strategic partnership with the Stockholm-based company Xbrane Bioscience. Xbrane offers protein
production and bacterial expression strain development services that are tailored around each individual target and based on the needs of the customer. Xbrane’s unique bacterial expression platforms ensure high success rates in a shorter time for each project. This speed is essential for us, since having a synchrotron beamline within walking distance, we need to have all other stages of the process optimized to be able to draw maximum benefit from this. The second highlight of the first half of the year was the start of the collaboration with the Basel-based company BioVersys within the Eurostars-financed project SARTRIC. The project is aimed at targeting multidrug-resistant bacterial infections. We all know that antimicrobial resistance represents a major threat to public health worldwide and is far from being adequately addressed today. The SARTRIC project aims at restoring antibiotic activity by blocking the transcriptional activation of resistance genes with small molecules. This way the efficacy of already known antibiotics may be restored. This was also our 3rd successful EU application. The first two, the KINOMED and the TAKTIC projects, were highlighted in earlier blog posts.

When looking back now it is also exciting to see how much we travelled during the first half of 2014. In February SARomics Biostructures was represented at two meetings: The 8th Swiss-Scandinavian Bio-Business Seminar in Zurich, Switzerland, and the Science Link meeting at DESY, Hamburg.  Science Link is a EU-funded project aimed at bringing more industrial users, especially from the materials science area, to the European synchrotrons. Several synchrotrons collaborate with local business-promoting agencies within this project. Although we are not part of that project, we were invited to share our experience in serving as a bridge between the MAX-lab synchrotron on one hand and the biotech industry and academic groups on the other.

In March we were present at the BIO-Europe Spring 2014 in Turin, Italy. A great meeting, growing larger and larger each year. In 2014 there were 2083 registered participants representing 1209 companies from 42 countries! More than 70% of the delegates were at senior management level. We also managed to organize TAKTIC consortium meeting immediately after the Bio-Europe gathering. One of the consortium members, Marco Lolli, works at the University of Turin (see previous blog entry).

In May SARomics attended the two parallel conferences on Drug Design & Medicinal Chemistry and Protein Kinases in Drug Discovery in Berlin. These two events were tremendously informative and inspirational regarding the latest developments in both fields, although hopping between the two conferences (held in adjacent rooms) to catch the best of everything was a major logistics exercise! The seeds were sown for new partnerships and our collaborator Prof. Gisbert Schneider of ETH Zürich even took the opportunity during his presentation to advertise a new strategic alliance between SARomics and his company Insili.com.

In June SARomics Biostructures participated in the 2014 BIO International Convention in San Diego in order to identify in-licensing partners for their internal projects and technology, meet with strategic R&D partners and with local companies and research institutions in San Diego. Björn Walse, CEO of SARomics Biostructures noted that “we had a great BIO and identified a number of promising business partners, with whom we are in an ongoing dialogue”. Sten Sörensen, Executive Chairman of the company, added: “Participating in the BIO Partnering Conferences held annually in the US and Europe is an essential and effective strategy for a growth company such as SARomics. The Scandinavian Pavilion and Reception served us well in reaching our objectives in San Diego”.

You may think this is a lot, but that was only the first half of 2014, the second part to be published soon… 

Coordinating TAKTIC (and surviving the first year)

A year has passed since the start of the TAKTIC project (Translational Kinase Tumour Inhibitor discovery Consortium). A year can be rather short, but it may also be long - all depends on how much you manage to squeeze into it. In my experience, having an EU project to coordinate makes it very long, at least when I look back. On the other hand, when it was time to prepare our first 9-month report, the feeling was that time was running faster and faster, mercilessly eating up the dark December working hours. 
At the start of 2013 we were on our way to finishing negotiations with the Commission. Probably the most important part of the negotiation process, which started in October, was the signature of the Consortium Agreement by all partners. Time after time I had to explain to the Technology Transfer Offices of our academic partners the specificity of the program we entered, called "Research for the benefit of SMEs", which demanded that all IP generated within the project had to be kept by the SME partners. Eventually they accepted this and by the end of January the signed agreement could be sent to the Commission. The official start of the project was set to the 1st of February. However, the Grant Agreement (GA) with the EU was signed much later, on 13th of March (the same day the new Pope was elected in the Vatican). Unfortunately this meant that the funds would arrive at best by the end of April, which meant that we had to work for some time using own funds. For some reason we were impatient to start the project, but if I would do this again I would start the project in April. 
It was exciting, we were all moving into an unknown territory - we had 3 challenging kinases as targets and we did not have much experience in running a project across Europe with this number of partners (apart from SARomics Biostructures, the project includes ProQinasePrestwick Chemical, the Israel Structural Proteomics Centre at the Weizmann Institute of Science, two groups from the University of Turin – the Depts. of Science and Drug Technology and Medicine and Experimental Oncology, and finally the TechMedILL platform at the University of Strasbourg). We needed to work out the details of the organization of the project, put in place the mechanisms of interactions between the partners, learn to communicate with each other, help partners when needed with various administrative questions, set up the experimental work, etc., etc. Everybody knows that there are always a huge number of questions that need to be answered when a new project is about to start. I should say that all partners made a brilliant contribution during these first months, to the extent that when we met in June in Lund at our first project review meeting, we already had real results to discuss! The first library screens had already resulted in some hits, the chemistry program and compound modifications were starting to reveal new results (some of them quite unexpected and will be published in the near future!), proteins were produced and delivered for biochemical activity assays and the cell-based assay program was in place and running! 
The next bunch of results came already after the summer - the compounds, which were identified in the in silico screen against one of the targets, were either purchased or synthesized and their biochemical and cell-based tests started. When our second project review meeting took place in Strasbourg at Prestwick Chemical at the end of October, we already had nice hits for two of the targets. Based on the results, it was decided to focus the work on these two kinases. This step was part of the project plan, which takes into account the rather short project period we have (two years). 
Shortly after the Strasbourg meeting we had to start the work on the 9-month report. I immediately started to discover what I could have done much better. For example, the so-called deliverables could have been reported already at the time of their delivery. Each of the deliverables needs to be reported by the responsible partner, describing the aims of the task, the work performed and the results, as well as the time spent on the task and the material costs. I also discovered that the report had to be submitted directly through the electronic submission system. Avoiding having to deal with paper copies felt like a relief, also taking into account that a decent number of deliverables reports had to be prepared and submitted. On top of that was the famous Form C - the financial report. Now-days this also needs to be filled in and submitted electronically, which is a huge improvement compared to the old way, when forms had to be filled in and sent as paper copies. Each small mistake could provoke a new cycle of corrections, signatures and FedEx shipping. Now this has become much easier. Any missed numbers, details, etc, can be easily corrected when the financial officer asks for it. When all that was done, I had to prepare the actual scientific report, as well as dissemination and management reports. Preparing a dissemination report was a pleasure - as a company we are obviously interested in all forms of publicity and we did a lot to make the project known to a wide public. The management report was not a problem, but the scientific report required time to compose. Also submitting it took quite some time, as a lot of information had to be provided electronically.

The TAKTIC consortium meting in Turin, 13/03/2014 - one year after
the start of the project!

I now know for sure that we should have started this process much earlier, and we should definitely do that when we will approach the time for the next report! Was last years experience valuable? No doubt! I have met many people who are afraid of going into the business of writing EU projects and managing them. I always respond to that by saying that to learn swimming we need to jump into the water. There is no other way, we cannot do it by reading a book! After going through almost all stages of an EU project, writing, negotiating and reporting (the final report is still ahead) I feel like I am almost an EU project "professional"! In a year time I will tell you the second part of this story, and I am sure it is going to be a story of how successful an industrial EU project can be! 

By Salam Al-Karadaghi, coordinator


2014: Celebrating 100 years of X-ray crystallography

Probably some of you know that UNESCO has proclaimed 2014 the International Year of Crystallography. Why? 100 years ago Max von Laue was awarded the Nobel Prize in physics "for his discovery of the diffraction of X-rays by crystals". A year later the father and son Sir William Henry Bragg and William Lawrence Bragg received the Physics prize "for their services in the analysis of crystal structure by means of X-rays”. The International Union of Crystallography has recently counted an astounding 28 Nobel Prizes awarded for research in one way or another related to X-ray crystallography. 
It would not be an exaggeration to claim that we are indebted to X-ray crystallography for most of our knowledge on the atomic structure of matter. This of course includes both inorganic and living matter. The contribution of X-ray crystallography to biology probably started with Rosalind Franklin’s and Maurice Wilkins’ experiments, which brought Francis Crick and James Watson to their first insights into the detailed atomic structure of a central player in the cycle of life, DNA. For this they were awarded the Nobel Prize in Physiology or Medicine in 1962. The same year Max Perutz and John Kendrew received the Chemistry prize for the determination of the first protein structure and two years later Dorothy Hodgkin was honored with the Chemistry prize "for her determinations by X-ray techniques of the structures of important biochemical substances”, that is penicillin, Vitamin B12, and insulin. 
As we all know, the spectacular achievements in structural biology based on X-ray crystallography have included many highlights, the most recent of which are the Nobel Prize of 2009 to Yonath, Ramakrishnan & Steitz for the structure of the ribosome and the 2012 Prize to Robert J. Lefkowitz and Brian K. Kobilka for the study of the structure and function of GPCRs.
Below are some unique and never published photos, showing some of the pioneers of protein crystallography and Nobel Prize winners with colleagues, both recently and many years before the prizes were awarded!

William Lawrence Bragg during his visit to Uppsala in 1965. Photo provided by Anders Liljas (in the middle on the left).

Dorothy Hodgkin at the International Union for Crystallography (IUCR) meeting in Bordeaux, France, 1990. Photo by S Al-Karadaghi.

Michael Rossmann, one of the pioneers of structural biology, in his famous basement office at Purdue University. Around 1971. Photo by Anders Liljas.

Marin van Heel (on the left, Imperial College, London) and Ada Yonath (Weizmann Institute of Science, Israel), at the Structural Aspects of Protein Synthesis meeting in Tällberg, Sweden, September 1997. Photo by S Al-Karadaghi.

Ada Yonath with colleagues, 9th of December 2009, at the reception at the Royal Swedish Academy of Sciences on the eve prior to the Nobel Prize ceremony. Photo by S Al-Karadaghi.

Peter Moore (Yale University) & Venki Ramakrishnan (MRC Laboratory of Molecular Biology, Cambridge, UK) at the meeting Frontiers in Translation, May 1995, Victoria, Canada. Photo by S Al-Karadaghi.

Brian Kobilka (second left) together with his wife Tong Sun (first on the left) and staff members from the Department of Biochemistry and Structural Biology in Lund, December 2012 (from left: Cecilia Hägerhäll, Per Kjellbom and Ingemar Andre). The Kobilka couple visited Lund during the traditional Chemistry Nobel Prize winners’ trip around Sweden. Photo by S Al-Karadaghi.

The technique of macromolecular X-ray crystallography has of course been evolving throughout the years. Probably the first big change was triggered by the use of synchrotron radiation at the end of the 1980s-beginning of the 1990s. This was followed by the structural genomics initiatives, which brought us new technologies and thousands of new structures. But it did not stop there. Last September I had the privilege to attend two meetings with a focus on current developments in structural biology. The first one was Synchrotron Radiation in Biology, in Hamburg, and the second was the MAX IV Laboratory users meeting in Lund. The MAX-lab meeting included two workshops, one dedicated to the future free electron laser project in Lund while the second to the future MicroMax beamline. MicroMax is going to be the second protein crystallography beamline at the new MAX IV synchrotron in Lund. If I would summarize my general impression from these two meetings in few words, those would be "the new revolution in structural biology". Just a few years ago nobody was talking about “serial crystallography”, and definitely not about collecting a whole data set within a few seconds! Micro-crystallography has made all this possible by targeting crystals with a size of just a few microns and it is essentially driving a fundamental change in the way protein crystallography experiments are run. New technologies in sample handling, data collection and data processing are emerging. This includes, for example, the ability to collect diffraction data directly from crystals in their growth environment, i.e. the crystallization drop. Developments in scanning techniques also allow a quick identification of a single-crystal region in a multi-crystal sample or a well-diffracting region in an imperfect crystal. All this opens up new possibilities for projects where only extremely small crystals can be obtained. The success of the GPCR project, which was awarded the 2012 Nobel Prize, was only possible thanks to the developments in micro-crystallography. 
We are entering an exciting new era in structural biology. To this we could of course add the expectations we have in Lund - in two years time we will essentially be walking with our samples to the most advanced synchrotron in the world, MAX IV!

The image below shows the state of the building in December 2013.

By Salam Al-Karadaghi, Director Business Development



Impressions from Boston by Björn Walse, CEO, SARomics Biostructures

I had the great pleasure to visit Boston the last two weeks of September. The reason for the trip was to participate in BioPharm America 2013 (#BPA13) and Discovery on Target 2013 (#DOTBoston13). This blog is about my impressions from the last of these meetings and from my stay in the area. 

After three intensive days packed with excellent talks about epigenetics readers, writers and erasers I am completely astonished at how fast this field is moving forward. For example, the lysine methylase LSD1 was only discovered 10 years ago, but both Oryzon and GSK will soon enter phase I with their inhibitors targeting this target. At the conference particularly GSK made a massive impression with several good talks. The conference was also dominated by presentations by the Structural Genomics Consortium (SGC). It is just amazing to see how well their approach to provide fundamental understanding of human biology works. In addition, as they have this position at the forefront of science everybody is collaborating with them, not only many academic groups but also big pharma companies like GSK and Pfizer. It is a shame that Sweden lost its SGC node. I really hope the people in charge at Karolinska Institute regret what probably is their biggest mistake.

There were over 800 attendees at this years DOT conference, which was a record in itself. According to the size of the audiences at this multitrack conference, the track about BET reader domains (or bromodomains) was by far the most popular. That is not surprising, as data were presented showing that complete shutdown of oncogenes can be achieved by inhibiting these acetyllysine binding proteins. Furthermore, the epigenetics proteins provide a multitude of druggable targets which enable target driven drug discovery campaigns utilizing rational approaches such as SBDD and FBLD. It is obvious that the biotech industry and the research community today are so much more mature compared to ten years ago. New targets are validated at an unprecedented speed and new drugs are developed in record time. I guess the advancements in science and the investments in research infrastructure are finally paying off. A lot has been learnt from the kinase field, and now epigenetics drug discovery is speeding ahead maybe twice or three times as fast.

After having spent nearly two weeks in the Boston area by far my overall largest impression was the frequent construction of new mega hubs for big pharma companies in Cambridge. Dominating them all were Novartis, who already have a huge structure close to Massachusetts Avenue. Now construction is ongoing of an even bigger structure across the street close to MIT and the Broad Institute. The rest were not bad either. Amgen, Biogen, J&J and Pfizer all have huge buildings close to Kendall Square. During the week I was there Sanofi inaugurated a huge cancer research hub close to Charles River despite the fact that Genzyme already has a distinct presence close to Kendall square. In addition, Ipsen announced on my last day in the city that they will also move into a large facility next door to Kendall Square. It makes so much more sense to conduct research here and not in a field in New Jersey or Pennsylvania. I just wonder were the other big players are? When will they relocate? When I was waiting in the reception at the Cambridge Innovation Centre at One Broadway I overheard a conversation of a desperate man from MSD talking to the receptionist. He was looking for some offices to rent. MSD has their own building close to Boston’s Childrens Hospital across the river, but he told the receptionist that he is never there. He was running around in the area around Kendal Square all day and needed a closer place to work at. 

Just imagine if that could be the situation here in Lund. What will it take to get big pharma to establish offices or research facilities close to Lund University and Medicon Village? Maybe it will be the new world-leading MAX IV synchrotron or the European Spallation Source (ESS) that will attract them? A foolproof way in the right direction would be to locate a SGC node in Science Village right between the two facilities. Now that would be something!

Mega hubs in Cambridge. From top left: Genzyme, Novartis and Sanofi. From bottom left: Amgen, Millenium (Takeda), Biogen-Idec.


How to get a million – a story of an EU project

Similarly to any other happening, a project has its own story, which is often the result of many small coincidences and events.

The TAKTIC project, which we recently started, probably originates from a meeting (in Brussels) between Professor Anders Liljas, who at the time was Chairman of the Board of SARomics Biostructures, and Professor Joel Sussman, Director of the Israel Structural Proteomics Center (ISPC). That must have been in early 2010. Anders and Joel discussed possible collaboration between SARomics Biostructures and ISPC. After the meeting Anders sent us an e-mail and suggested we try to find a way to establish collaboration with ISPC, taking into account their advanced capacity for high-throughput protein production and crystallization. At the same time we had just received the results of the positive evaluation of our Eurostars application, which meant that we were about to start the KINOMED project. By other words, it was just the right time to start thinking of the next possible EU-funded project. It was also apparent that the new project should take us to the next level and should be bigger than KINOMED, which meant FP7. When checking out the FP7 program I arrived at the program called “Research for the Benefit of SMEs”. This program seemed to be the most suitable for our initial aim, establishing collaboration with ISPC, which is an academic group. It would also fit our general strategy, directed towards establishing collaboration with academia. Many large Pharmaceutical companies are doing just this, and for SARomics Biostructures it is quite natural, since we have extensive contact network within academia. 

Around the same time, I received an e-mail from Marco (at that time he was still Dr. Marco Lolli) from the Department of Science and Drug Technologies at the University of Turin. Marco suggested a drug design collaboration (also involving Marco Piccinini from the Department of Oncology) on dihydroorotate dehydrogenase (DHODH), a protein we earlier worked on together with the company Active Biotech in Lund. After some discussions with Marco we arrived at the idea of looking for some EU funds to initiate the collaboration. Small pieces of the jigsaw puzzle started to come together. I contacted Professor Sussman and suggested that we meet and discuss possible collaboration, we decided a date (June 2010) when the Israeli Crystallography Association had its annual meeting, at which I was invited to give a talk. That gave me a good opportunity to visit the Weizmann Institute and get an idea of the setup at the ISPC. However, I felt it was still too early to go for the application: we needed to formulate the idea of the project in a better way. During autumn 2010 and winter-spring 2011 our contacts and discussions with Marco continued. Our academic collaboration on DHODH started (and is still going on). In the meantime we were still discussing how to approach the FP7 program, when we somehow arrived at the idea to target kinases, which eventually became the core of the TAKTIC project. I think the major reason for arriving at kinases was that we were already working on other kinases within the KINOMED project. In June 2011 Marco visited Lund. The discussions during those couple of days created the basis for the TAKTIC project. 

The next step was finding two other SME partners, since the program requires three SME partners from three different EU countries. This was probably the most difficult part. Although Prestwick Chemical agreed immediately to join the project after some contacts between Björn Walse (our CEO) and Paul Bikard (COO / CFO at Prestwick), we still needed a third partner. Directly after the summer vacation we started to contact potential partners. We had discussions with several companies, time was running out (the deadline for submitting the application was 6th December) and we still did not have the third partner. Closer to the end of September I was getting rather desperate and was more or less prepared to give up the whole idea and go back to my daily activities, which had been pretty much set aside. At that critical moment an encouraging e-mail from Marco managed to bring me up on my feet again. It is amazing what a few words from a friend can do to us! A Friday afternoon I got an idea: I announced in all LinkedIn groups I was a member of that we were looking for a company to join an EU kinase project. We were immediately contacted by a number of interested companies, but which did not really fit. But then came that e-mail from Michael Kubbutat from ProQinase (Michael is Head of Biochemical Drug Discovery & Head of Drug Development)! We had not had any contact with ProQinase before that and did not know each other. However, people at ProQinase and Prestwick did know each other well, and in addition they are geographically located close to each other, in Freiburg and Strasbourg. Around the middle of October we had our first meeting in Freiburg with all partners present. All the major details of the project were discussed, work packages were put together, the roles of the different partners were clearly defined, and we started the work on the actual text of the application. It took more than two months of work until we could have a party in Lund in December 2011, celebrating the submission of the application –a hard days night!

The TAKTIC team at the kick-off meeting at the Weizmann Institute

And as we know today, it was worth it! Eventually we received the much-awaited letter with the invitation to start the grant negotiations! Finally, on 13th March 2013 the Grant Agreement between the European Commission and SARomics Biostructures was signed and the Translational Kinase Tumor Inhibitor Discovery Consortium (TAKTIC) was officially born. In the evening the same day the new Pope was elected in the Vatican. Habemus TAKTIC!

By Salam Al-Karadaghi, project coordinator.


Impressions from the meeting “Fragments 2013”

Early last week the 4th RSC-BMCS Fragment-based Drug Discovery meeting was held at STFC Rutherford Appleton Laboratory, Oxfordshire, UK (view the poster, which was presented at the meeting). The meeting started with an introductory course for those new to the field. This was followed by several seminars that covered library design, screening methodologies, examples of fragment based applications and success stories.
Fragment-based drug discovery is based on the fact that it is (in a relative sense!) easier to use small molecules as starting points in drug discovery projects. As the molecules are small and have low binding affinity, the efficacy of a fragment has to be assessed at high concentrations. A library of just 100 suitably selected small molecules may give several weak hits as starting points. The trick is then to gradually increase the size of the fragments and their affinity to the target protein. The method relies heavily on X-ray crystallography, as one has to know where the molecules bind and how the fragments can be extended and perhaps also linked together. 
Orthogonal screening methods often need to be applied in order to confirm initial fragment hits. Ideally the hits should show both binding to target and functional effect (e.g. inhibition), although this is not always the case. 
Ligand efficiency is a concept used throughout the meeting. The ligand efficiency measure offers an approximate way to compare target affinity for different-size fragments during the optimization process. Sometimes it is difficult to extend the molecules without losing much of the ligand efficiency. Several presenters discussed the application of tethering to develop fragments to larger molecules that bind to more than one “hot spot”. 
One can get a feeling by considering a fragment with 11 atoms (a molecular weight around 150) that has a LE of 0.3. This corresponds to a Ki around 0.04 M-1. As binding affinity is weak, fragments have to be screened at high concentrations and thus a robust biochemical assay is needed. Another aspect is that fragments must have much higher solubility than compounds applied in high-throughput screening. Unfortunately solubility is a difficult parameter to predict, and it was pointed out that our intuition may fail when the solubility of the fragments is considered. For instance correlation between solubility and lipophilicity as estimated by logP can be quite low. 
Statistics also show that, on average, leads obtained from fragment based approaches were significantly smaller, less lipophilic and had higher ligand efficiency than those from high throughput screening. Perhaps this should come as no surprise, but I consider this to be valuable change in the right direction. However, it is important to select the fragment library with care. The fragments should be sufficiently soluble, not too reactive, not too symmetric and perhaps also obey the “rule of three”. Different methods to improve library design were suggested. For example shape-based approaches were used to investigate library coverage of 3D space and several posters examined improvements obtained by using sp3-rich fragment libraries.
An interesting alternative approach to navigation in kinase-ligand interaction space was presented at the meeting in a poster by Oscar van Linden and colleagues from the Netherlands. They systematically analysed ligand binding regions around the catalytic sites of more than 1200 human kinase-ligand structures present in the Protein Data Bank. The analysis was made in terms of ligand interaction fingerprints, and the method gave insights into conserved and selective interaction hot spots. With the ever-increasing number of protein-ligand structures, such methodologies may offer new rational approaches to drug design. 
It is my feeling that fragment based drug discovery has matured in the recent years. It is now seen both as an alternative and a complement to high throughput screening. At the beginning of this year 25 compounds developed using fragment-based methods had reached the clinical stages, and one has been approved (Vemurafenib). I am already looking forward to the next meeting in 2015!

By Bo Svensson, Director in silico discovery


Off-the shelf structures: Next generation

“Off-the-shelf” structures are a concept whereby a service provider offers the crystal structures of a protein purified and crystallized by the service provider itself. In addition the protein in question is stored and ready to be crystallized with customer’s compounds. One of the advantages for the customer is speed, since they do not themselves need to purify the protein for crystallization. Another advantage is the lower risk level - proteins may sometimes behave in an unpredictable way and a new purification may not necessarily behave exactly the same way as the previous one. In other words, there is a chance that the protein will not crystallize the same way it did earlier. Of course not all proteins can be stored in a frozen state before crystallization; sometimes they has to be freshly made prior to setting up crystallization trials. 

Our new off-the-shelf “platinum” concept: Drug Seeds
We have taken the off-the-shelf concept to the next level and currently offer two protein kinases - PIM1 and CK2 - in complex with small-molecule fragments ready to enter the next stage in a drug discovery pipeline. 
Small-molecule fragments with identified binding modes determined by X-ray crystallography provide a good starting point for iterative structure-based drug design, generating crucial information in lead identification, lead optimization and subsequent preclinical development (reviewed in 1). We have used fragment-based drug design to identify small-molecule fragments that bind and inhibit the activity of two kinases, PIM1 and CK2. These two kinases play important roles in activities related to cell growth and survival (2, 3). Elevated CK2 and PIM1 levels have been associated with malignant transformation and tumor growth and they have thus emerged as attractive molecular targets for drug design (4, 5). Most importantly, the insight that dual PIM1 and CK2 inhibitors may provide a special advantage has prompted our search for fragments which would bind to both kinases.
We have purified PIM1 and CK2 and determined their structures using X-ray data collected from crystals grown by us. The first fragments with a potential to bind to PIM1 were identified using in silico screening and the newly-designed Global Kinase Library, which was in turn selected from the IOTA1500 library and from commercial sources and is based on the following criteria: 

PIM1-specific fragments:
25 target the ATP site 
25 target the Type III site (see figure for kinase inhibitor sub-sites)

CK2-specific fragments:
15 target the ATP site 
35 target the Type III site 
General kinase fragments:
80 target the ATP site 
120 target the Type III site 

Soaking crystals of PIM1 with the first 3 fragments (initially identified by in silico screening) showed that two of the fragments were bound to the protein (an example structure shown below).

In addition, CK2 and PIM1 were also screened against a small-molecule fragment library consisting of 1040 fragments from the IOTA1500 library at a concentration of 100 μM. Based on IC50 data, the most potent fragment hits were co-crystallized with both PIM1 and CK2, resulting in several new fragment complexes, and establishing good starting points for the development of new human kinase inhibitors. These complexes with proprietary fragments are currently offered to our customers. In addition, inspired by the recent work by Cylene Therapeutics (reviewed in 5), which suggested that inhibitors with dual PIM1 and CK2 activity may offer particular advantages for cancer therapy, we were able to identify fragments with dual-specificity to CK2 and Pim1. Complexes of one of these fragments with the kinases were also obtained.
More structures of therapeutically relevant kinases are currently being added to our off-the-shelf library, which will be launched within the next few weeks. Structures either in complex with customers’ compounds or with our proprietary fragments will be offered.

1- Boyd SM, Turnbull AP, Walse B, 2012. Fragment library design considerations, WIREs Comput. Mol. Sci., doi:10.1002/wcms.1098
2- Trembley JH, Wang G, Unger G, Slaton J, Ahmed K, 2009. Protein kinase CK2 in health and disease: CK2: a key player in cancer biology. Cell Mol Life Sci. 66, 1858-67. 
3- Brault L, Gasser C, Bracher F, Huber K, Knapp S, Schwaller J, 2010. PIM serine/threonine kinases in the pathogenesis and therapy of hematologic malignancies and solid cancers, Haematologica, 95, 1004–1015 
4- Ermakova I, Boldyreff B, Issinger OG, Niefind K, 2003. Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit. J Mol Biol. 330, 925-34
5- Drygin D, Haddach M, Pierre F Ryckman DM, 2012. Potential Use of Selective and Nonselective Pim Kinase Inhibitors for Cancer Therapy. J Med Chem. 55, 8199-208.

KINOMED is a program coordinated by SARomics Biostructures created with the aim of offering off-the-shelf protein kinase structures and fragment complexes to the pharmaceutical and biotech industries. Our mission is to offer strategic starting points that can act to jump-start your kinase inhibitor drug design projects.
P.S. Recently about 50 kinases were added to our FastLane library Premium: Kinases ready to be expressed, purified and crystallized according to established protocols.


2012: A year unlike any other

SARomics Biostructures is entering 2013 with new owners and with significant new progress in establishing the company on the market as one of the major providers of structural biology and drug discovery services. The year started with our move to the new premises at Medicon Village, the former AstraZeneca site in Lund. The site has been converted to a joint academic-commercial research center with a primary focus on biomedicine. At MV we currently have at our disposal state-of-the-art laboratories well-equipped for protein purification and characterization, although the crystallization robotics and other related equipment are still in the lab next to the beamlines at the MAX-lab synchrotron. A big advantage of course is that the new protein lab and our new offices are just a few hundred meters from the synchrotron. 
In May we welcomed Dr Martin Welin (Martin's profile on LinkedIn), our new employee, who has moved to Lund from Stockholm after several years of work at the Structural Genomics Consortium. Together with our other staff members, Martin has already made substantial contributions to the ongoing customer projects, as well as adding new members to our growing library of structures available for quick co-crystallization with customer’s compounds (off-the-shelf) and to our premium off-the-shelf product: fragment complexes of the PIM1 and CK2 kinases.
For the first time this year SARomics Biostructures brought in new owners - Lund University and the Swedish investment agencyInnovationsbron. With Lund University as a co-owner, and in collaboration with MAX-lab, our strategic planning for future commercial use of the new MAX IV synchrotron will be taken to a new level (see press release). It is indeed very exciting to know that just in 3 years we will have one of the world’s very best synchrotrons within walking distance! 
Another highlight of 2012 was the establishment of a partnership between SARomics Biostructures and Red Glead. Red Glead Discoveryoffers research services for drug discovery and possesses in-house laboratory capabilities for medicinal chemistry, biology, analytical chemistry and ADME. Their expert area is the generation of chemical starting points for drug targets and their development into patentable lead compounds with drug-like properties and low risk profile. In other words, a perfect match for the structural biology capabilities of our company. The two companies have decided to focus on drug development within the area of epigenetic disorders (see press release). The announcement of the partnership has received much attention, and was for example, featured in the December issue of US-based Drug Discovery News.
In addition to our commercial activities, we are committed to taking forward research related to the filed of structure-based drug design. Thus, Björn Walse, our CEO, participated and presented a poster at the Fragment-Based Lead Discovery Conference in San Francisco. In addition, our CSO Derek Logan made a presentation at the PSDI 2012 (Protein Structure Determination in Industry) meeting in Paris, France (photo below). 


We should also mention the article on the industrially important omega-transaminase structures determined by SARomics Biostructures, which was selected for the May 2012 Virtual Issue of FEBS Journal on Molecular Enzymology.
As said, a year unlike any other. We are now looking forward for the New Year, to fill it again with success stories we can tell you about in exactly one year time! 
Happy New Year!

By Salam Al-Karadaghi, Director, Business Development


SARomics Biostructures is represented in Almedalen, Swedish policy makers meeting

SARomics Biostructures is represented in Almedalen, Swedish policy makers meeting

As CSO for SARomics Biostructures I yesterday had the great pleasure of taking part in a panel debate that was part of Almedal Week, in Visby, Gotland. Almedal Week started way back in 1968 when Olof Palme, Swedish prime minister at that time, spoke from the back of a lorry, but is now a gathering point for literally thousands of representatives for every sector of Swedish society. The purpose of the debate was to highlight the world-leading scientific possibilities offered by the two new major research facilities that are coming to Lund in the next few years, i.e. MAX IV and the European Spallation Source (ESS). The other industry representative was Tomas Lundqvist, Director of Cell, Protein and Structural Sciences at AstraZeneca. Together the panel members emphasized the enormous competitive advantage that access to these world-class facilities will give Swedish and Nordic life science in both industry and academia, as well as the role the novel innovative environments such as Medicon Village, where SARomics has its operational base, have for the future of life science in Sweden.

Derek Logan, CSO 


SARomics Biostructures determines structures of an industrially important ω-transaminase

SARomics Biostructures recently published an article in FEBS Journal describing four crystal structures of an industrially important enzyme in different conformational states. The work was the result of a collaboration with researchers at the Royal Institute of Technology (KTH) in Stockholm and AstraZeneca in Södertälje. The collaboration was financed by the Swedish Innovation Agency VINNOVA through theBIO-AMINES grant.
The enzyme whose structure was revealed is an ω-transaminase that transfers amino groups between molecules. This group of enzymes has received quite some industrial attention due to their ability to accept inexpensive amines, such as isopropylamine, as amino donors, in combination with a capacity to produce highly enantiomerically pure chiral amino compounds, which are important both as pharmaceuticals and as key chiral intermediates for the agrochemical, chemical and pharmaceutical industries.
The structures give insight into the conformational changes associated with binding of the enzyme’s cofactor PLP. Unexpectedly large conformational changes in three loops were seen, apparently driven by binding of the PLP molecule’s phosphate group. The enzyme was captured in a state without PLP, in another with PLP, and finally in a form where some the molecules in the crystal were in a mixture of the two states. Most importantly, the structures pave the way for further complexes with appropriate ligands and an exploration of the enzyme’s enantiomeric preference, with a view to enhancing it even further.


SARomics Biostructures contributes to fundamental understanding of ligand and water binding to a protein

SARomics Biostructures recently contributed to an exciting article in Biochemistry where ultra-high resolution X-ray crystallography was combined with a plethora of complementary biophysical and theoretical techniques such as NMR, ITC and molecular dynamics simulations to probe the nature of water binding and hydrogen bonding in the active site of the medically important carbohydrate binding protein galectin-3. The results showed that the ligand binding site of Gal3C is highly pre-organized to recognize a sugar-like framework of oxygen atoms, but that the water molecules in the binding site are highly dynamic, none of them staying in place for more than about 1 nanosecond. The results are important for drug design, where one of the major unsolved problems in the prediction of absolute free energies of binding is the treatment of ligand and solvent entropy.
One of the structures, a complex of galectin-3 with lactose, broke the current resolution record for data collected at the MAX-lab synchrotron in Lund, with data stretching all the way to 0.86 Å. At this resolution it begins to be possible to see the hydrogen atoms in the binding site and thus to analyze hydrogen bonding patterns in detail, an aspect that is ambiguous in X-ray structures at more typical resolutions. The academic groups with whom SARomics collaborated on this project are now taking the analysis one step further by using neutron diffraction to study unambiguously the positions of the protons.
This is the second publication on Gal3C to which SARomics has contributed. The collaboration reflects SARomics interest in the fundamental aspects of ligand recognition, which feeds into our commercial experimental and in silico offerings.
Saraboji K, Håkansson M, Genheden S, Diehl C, Qvist J, Weininger U, Nilsson UJ, Leffler H, Ryde U, Akke M & Logan DT (2011) The carbohydrate-binding site in galectin-3 is pre-organized to recognize a sugar-like framework of oxygens: ultra-high resolution structures and water dynamics. Biochemistry, Article ASAP.


Report from XIXth Protein Structure Determination in Industry Meeting or PSDI 2011


Date: Nov. 13-15, 2011
Place: Stenungsbaden Yacht Club, Gothenburg area, Sweden
Narrator: Maria Håkansson, Senior scientist at SARomics Biostructures
It is quite simple to say that I utterly enjoyed the PSDI 2011 meeting and leave it like that.
Going into details then; what is it that separates a good meeting from a great one? Is it the mixture of people, old friends and new acquaintances, sharing a common interest and the latest news in the field? Is it the topics of the lectures covering drug ability, fragment screening and structures of GPCRs in complex with antagonists or agonists? The simplest reminder of these complexes you get every time you drink a coke or take a cup of coffee since caffeine is inhibiting one of them (Adenosine A2A). Is it the presentation of biophysical methods, which technique freaks like me embrace? The most used techniques seems to be the one’s below: 

Thermal shift assays by QPCR
Surface plasmon resonance
Isothermal titration calorimetry

Also one entirely new technique was presented called ”Thermophoresis”. As the name implies it makes use of differences in diffusion at different temperatures for fluorescence labelled proteins and protein-ligand complexes very much like standard electrophoresis. I don’t see the immediate use of it but it is always a comfort to know that there are people thinking outside the box.
With these methods in combination with biological assays and X-ray crystallography it is possible to develop fragments into high affinity ligands and potential drug candidates. Don’t you believe me? Go to the next PSDI 2012 meeting. 


New publication with a structure contributed by SARomics Biostructures

Recent work by SARomics Biostructures' Co-founder Mikael Akke, and a structure contributed by the company has been selected for the latest issue of JACS Select.
"Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3",
Carl Diehl, Olof Engström, Tamara Delaine, Maria Håkansson, Samuel Genheden, Kristofer Modig, Hakon Leffler, Ulf Ryde, Ulf J. Nilsson, and Mikael Akke. J. Am. Chem. Soc. (2010) 132, 14577-89.
About JACS Select: In order to both highlight and further explain topics of interest to a diverse audience, the Journal of the American Chemical Society has launched JACS Select, an online feature conceived and designed to showcase significant recent publications. Articles are selected based on their high scientific quality and broad appeal.