Summer 2016 Newsletter
Welcome to the Summer 2016 Newsletter from CompChem Solutions Limited.
Well, they say a week is a long time in politics but, boy, this last one must surely count as one of the most dramatic episodes in living memory for most of us. What will happen next? When will some new normality condense from the fall-out? We may not know the answer to these, and may other key questions, for some time yet, but we kick off this time with a synopsis of how the vote has thus far affected our area of science, and what impacts the vote could have for us going forward. Prior to the vote, the Cresset European User Group Meeting was held near Cambridge, and here we have penned a personal perspective on the key highlights of what was an excellent meeting. Further to the strides which have been widely reported recently in the Alzheimer’s field, we feature an article from Christina Elliott of the Killick group at KCL, who reports on the emerging role of inflammation in the condition, and how this may be a key area for development of therapeutics towards this devastating condition. In other developments a new science park is planned around the theme of “big data” at Downham Market – evidence of the Cambridge effect spilling out into the surrounding region perhaps? Do refer to our listings of some upcoming events and jobs which may be of interest to our readers as well as our In Brief section for a brief round-up of news items from CompChem Solutions. But we end this time on a rather sad note, paying tribute to the great Mike Tute who sadly passed away at the end of June.
- We’re delighted to be helping Cresset alpha and beta test their new protein modelling applications.
- Need to outsource chemistry? We can link you up with high quality, cost-effective offshore chemistry resource which can be project managed by UK-based medicinal chemists with extensive experience in the area. Contact us for more information.
- IOTA Pharmaceuticals are seeking a computational chemist for an 18-month posting based in Cambridge. Do contact us if interested.
Brexit & Pharma
Susan M Boyd, CompChem Solutions Ltd
Perhaps surprisingly, in the wake of the recent leave vote, pharmaceutical shares appear to have risen rather than plummeted – somewhat against the general trend. Certainly investors are looking for industries where profit reliance is beyond our immediate doorstep, and they seem to have put the pharma industry into that basket. But will this last? The ABPI warned immediately after the result was announced that the industry faces “immediate challenges”. Regulation of new drugs and access to the single market are, of course, key issues, but more fundamentally the level of EU funding & investment which feeds our industry is in jeopardy. We employ many people from EU countries, and currently UK employees can be easily seconded to overseas posts within the EU, but all of this will be more difficult in the future. Most of the leaders of our industry supported the Remain campaign and warned of the risks of Brexit. A very nice review of some specific aspects of the probable effects can be found here. Going forward, we must prepare for a lengthy period of uncertainty for our industry, and hope that jobs will not be put at risk.
Susan M Boyd, CompChem Solutions Ltd
At the end of June month I enjoyed the Cresset User Group Meeting at Granta Park, Cambridge. The well-attended meeting was competing with the England-Wales football match which was being broadcast simultaneously, but remarkably few attendees were visibly checking portable devices during the meeting – howzat for a testament to the interesting talks presented! There were too many great talks to go through all in depth, but here are my personal highlights from the meeting:
- Cresset protein modelling tools unveiled: Cresset has been recognised as a leader in the field of ligand-based modelling for some time, but they are now developing pioneering approaches to apply their field-based technology to explore protein-ligand interactions. The initial application allows visualisation of protein-ligand interactions from a field-based perspective to aid structure-based design, plus calculation of electrostatics and looking at the “happiness” of placed waters with 3D-RISM. Their collaboration with BioMolTech will allow them to link the LeadFinder docking tool into their application and initial results look very positive. It is hoped that their protein application will be available for release in March 2017, following on from a and b-testing by experienced Cresset users. CompChem Solutions is delighted to be helping with this testing phase over the coming months.
- Spark case studies: Cresset described how the ensemble of databases supplied with Spark has been expanded to include new databases such as the eMolecules reagent database and the CSD fragment database. Some inventive uses of the tool were also described, illustrating how it can be used in fragment growing, linking, macro-cyclisation and water replacement.
- Multidrug resistance (Mire Zloh, University of Hertforshire): Multidrug resistance is obviously a major issue in drug development. Mire described a nice approach which looks at escort molecule/efflux pump substrate complex formation as a means to attenuate efflux action. Potential escort molecules for known substrates were identified using a combination of molecular similarity searches and ligand-ligand docking studies. In a validation study 3 compounds known to act synergistically with antibiotics were identified and 2 molecules which can modulate efflux with these antibiotics were discovered.
- Prediction of cyclic peptide passive permeability (Sandeep Pal, GSK): The passive permeability of cyclic peptides is influenced by lipophilicity and intramolecular H-bonding, which has the effect of masking some polar features of the structure. For larger molecules it is harder to derive useful 2D descriptors of polarity due to the molecular complexity. Improvement in passive permeability and absorption is often linked to increased lipophilicity. Sandeep described a nice PLS-DA (Partial Least Squares Discriminant Analysis) classification model based on the ChromLogD descriptor (lipophilicity) and solvation energy which can nicely predict molecules as permeable or non-permeable in tests at GSK.
- Analysing building block diversity for DNA encoded libraries (Finton Sirockin & Nikolaus Steifl, Novartis): Finton & Nikolaus described the use of rooted 2D fingerprints and modified invariant fingerprints, combined with Cresset’s 3D field approach and attachment point vector alignment to select diverse building blocks for DNA encoded libraries. Clustering of the Cresset field-points was used to select reagents which spanned the available molecular space. The approach can be used to select reagents directed at particular protein targets, and to ensure that “islands” of similar compounds exist in a library to facilitate SAR exploration post-screening.
An emerging role of inflammation in Alzheimer’s disease
Dr Christina Elliott, King’s College London, Department of Old Age Psychiatry and Dementia, Maurice Wohl Clinical Neuroscience Institute
Alzheimer’s disease (AD) is characterised by progressive cognitive impairment arising from synaptic dysfunction and eventual neuronal loss. Most research has mainly focussed around the classic AD pathologies, the deposition of extracellular amyloid-β (Aβ) plaques, and the intracellular formation of neurofibrillary Tau tangles. However, there has been a steady accumulation of circumstantial evidence highlighting a role of immune mechanisms in the development of AD, particularly the identification of TREM2 (triggering receptor expressed on myeloid cells) and other immune components in genome wide association studies in both genetic and sporadic forms of the disease.
While this provides a smoking gun, immune activation in AD has been often dismissed as merely an unfortunate consequence of the large scale death of neurons occurring within the AD brain. However, a number of prominent papers published this year paint a more intimate picture, where immune mechanisms are closely involved in excessive synapse pruning, arguably the initial event in AD pathology.
One such mechanism is the complement cascade, a family of proteins traditionally involved in the clearance of opsonised microbes by phagocytosis. In their paper, published in the journal Science, Hong et al. demonstrate that complement proteins are crucial for removal of synapses by tagging them for destruction by microglia phagocytosis. Moreover, the authors show that exposure of neurons to Aβ can inappropriately activate this cascade leading to excessive synapse loss1. It is also of note that complement mediated synapse loss has also been demonstrated in schizophrenia2. Therefore, further elucidation of these mechanisms will be of broad significance and may provide therapeutic benefit to a number diseases underpinned by synaptic dysfunction.
Another strategy to attenuate immune mediated synapse loss is by the use of anti-inflammatory cytokines such as interleukin-33 (IL-33) as described by Fu et al. in PNAS. In a mouse model of AD the authors show that administration of IL-33 can skew microglia towards an anti-inflammatory phenotype leading to preservation of cognition and a reduced amyloid plaque burden3.
It must be noted that the anti-inflammatory action of IL-33 has identified previously in Multiple Sclerosis (MS), a neurological disease where the immune component contributing to disease pathology has been formally demonstrated. In fact a number of immune modulating drugs approved for the treatment of MS have been proposed to be of benefit in AD. One such example is FTY720/Fingolimod, which has been shown to be protective against Aβ induced cognition loss in rodents4.
Together these works and many others demonstrate a crucial role for neuroinflammation entwined within the heart of AD pathology. This provides a plethora of therapeutic opportunities from novel targeting of affected pathways to repurposing of licenced drugs currently in clinical use for other immune-linked disorders.
- S. Hong et al., Complement and microglia mediate early synapse loss in Alzheimer mouse models. Science 352, 712-716 (2016).
- A. Sekar et al., Schizophrenia risk from complex variation of complement component 4. Nature 530, 177-+ (2016).
- A.K. Y. Fu et al., IL-33 ameliorates Alzheimer’s disease-like pathology and cognitive decline. Proceedings of the National Academy of Sciences of the United States of America 113, E2705-E2713 (2016).
- M. Asle-Rousta, Z. Kolahdooz, S. Oryan, A. Ahmadiani, L. Dargahi, FTY720 (Fingolimod) Attenuates Beta-amyloid Peptide (A beta(42))-Induced Impairment of Spatial Learning and Memory in Rats. Journal of Molecular Neuroscience 50, 524-532 (2013).
Centre for Advanced Knowledge Engineering – coming soon to Downham Market
Susan M Boyd, CompChem Solutions Ltd
Plans are well underway for a new £350M big data campus at Downham Market after a successful open consultation meeting held recently in the Town Hall.
Big Data has become big in biotech/pharma right now, with GSK already collaborating with the EBI & the Wellcome Trust Sanger Institute on a big data project to aid target validation, and many other big players (eg AstraZeneca, Sanofi, Allergan, Roche) heavily invested in the field. Applications of big data in pharma include custom applications for specific business problems, scientific search, competitive intelligence, medical affairs and drug repositioning. A nice article from McKinsey describes how big data can “revolutionize big pharmceutical R & D”.
The Centre for Advanced Knowledge Engineering (CfAKE), would be at the former RAF Downham Market in Bexwell, and is expected to create more than 4,500 permanent jobs if planning permission is approved.
The development will include improved infrastructure including faster broadband, road improvements and a university technical college. An outline planning application for the site is being submitted this month and, if permission is granted, building is expected to begin towards the end of the year.
The project is supported by Aventa Capital, a finance group who have a successful track record in long-term value through regeneration investments in the UK that generate positive economic growth and transformational social impact.
Susan M Boyd, CompChem Solutions Ltd
It is with great sadness that I learned that Mike Tute passed away at the end of June. Mike worked at Pfizer in Sandwich for many years and I have the privilege of sharing an office with him for a short period of his “semi-retirement” during my time there. Mike was one of the true pioneers of our field, beginning his career as a medicinal chemist before becoming a founding member of the Pfizer UK computational chemistry team. Mike was an approachable, warm, and incredibly talented man with genuine enthusiasm for his science. He will be missed.
The following meetings may be of interest to our readers:
7th Joint Sheffield Chemoinformatics Meeting, 4-6th July 2016, University of Sheffield
UK QSAR & Chemoinformatics Group Autumn 2016 Meeting, 19th October 2016, ICR Sutton
21st EuroQSAR Meeting, 4-8th September 2016, Verona, Italy
Sir Simon Campbell – Science, Art & Drug Discovery, SCI lecture (free but registration necessary), 27th September 2016, London.
SCI Cheminformatics for Drug Design: Data, Models and Tools, 12th October 2016, Duxford, UK
Some current jobs being advertised…….
Experienced Computational Chemist, IOTA Pharmaceuticals Ltd, Cambridge, UK.
Senior Software Developer, Chemical Computing Group Inc, Cambridge, UK.
Application Scientist, Chemical Computing Group Inc, UK or Germany.
Senior Scientific Consultant, Cresset Discovery Services, UK.
C++ Software Engineer in Chemoinformatics, Optibrium, Cambridge, UK.