April 2012 Newsletter

Welcome to the latest newsletter from CompChem Solutions. In this edition we shine the spotlight on how computational approaches can assist in translational research and introduce our exciting new range of “fixed-fee” services. We have listed some of the latest meetings and job vacancies and our news section has information on forthcoming publications from CompChem Solutions. Finally, do check out the latest special offers for those involved in translational research, and some fixed-fee bundles open to all!

Fixed-Fee Bundles

Following on from some very successful pilot projects, CompChem Solutions is delighted to be able to offer a range of “fixed fee” bundles for discrete packages of computational chemistry services consisting of a number of predetermined elements of work. With these bundles, you’ll know exactly how much the project will cost from the outset, removing any budgetary uncertainty. Fixed fee bundles are available for:

  • Virtual screening
  • Homology model creation
  • Target tractability assessment
  • Library design/assessment
  • Scaffold hopping
  • Analogue-by-catalogue similarity/substructure searches
  • Lead optimisation/structure-based design tasks
  • Physchem/ADMET/structural property calculation
  • Design of crystallographic constructs
  • Pharmacophore creation and searching
  • Bespoke applications – ask us about your project

For each bundle, a set of pre-defined tasks and deliverables will be agreed up-front, and offered at a fixed rate which will not change, regardless of any unforeseen obstacles to project success. Contact us for more information, for prices or to receive a full proposal.

Computational Methods in Translational Research

With the increasing drive towards open innovation in pharmaceutical R&D, many academic groups are now actively involved in drug discovery research. Computational chemistry and computational biology can be valuable tools in helping to convert discoveries and ideas into new therapies with real application to disease and illness. At MRCT, for example, Dr Andy Merritt’s computational chemistry group focus much of their effort on support of internal medicinal chemistry projects through use of structure-based design methods and SAR-rationalisation, but they also contribute significantly to design of the MRCT proprietary screening collection, the design of 3D fragments, and to supporting early stage academic structural biology projects. They also outsource specific computational chemistry tasks in situations where particular expertise or software are most appropriate.

Senescence

Naturally, much early discovery work is centred around discovery and validation of potentially interesting new targets, which are often identified by cell-based screening approaches. Computational chemistry & biology approaches can be used to help identify a range of possible therapeutic applications of such targets, and can assess the likely druggability/ligandability of the targets. In one example, CompChem Solutions has contributed to a “highly-accessed” paper on senescence scoring from the CRUK-funded Beatson Laboratories, whereby the concept of “senescence profiling” was explored to examine the levels of senescence signals in various tumours. The senescence scores were based on expression profiles of senescence biomarkers from phenotypic data. The correlation of senescence scores with growth inhibition in response to around 1500 compounds which had been screened for toxicity was explored using a binary decision tree algorithm which predicted likely activities of the 1500 compounds. From the study it appears that senescence scores may predict cellular therapeutic sensitivities, as differing subsets of the dataset (as defined by differing senescence signatures) appear to be enriched in different pharmacophoric elements predictive of gene family propensity.

Similar or related approaches could also be used to predict off-target effects of compounds, to explore drug repositioning opportunities or simply to assess target tractability for small molecule approaches.

Construct design is a key component of protein crystallography programmes, and computational methods can be of great benefit to design by identifying similar structures/sequences and using these to predict likely insert/deletion regions and to identify domain boundaries.

Of course, more traditional computational methods can also be applied to support medicinal chemistry programmes, including hit finding, scaffold hopping and lead optimisation projects.

Translational research is often funded by grant awarding bodies/charities, requiring researchers to devote considerable energy and time to develop grant applications. CompChem Solutions can support organisations throughout and beyond the grant application process, acting as a partner to provide medicinal chemistry, computational chemistry/biology and other drug discovery skills to complement in-house scientific expertise

News – New Publications from CompChem Solutions

Susan Boyd of CompChem Solutions has recently co-authored two reviews on fragment-based drug discovery, both of which are now accepted and “in press”. Watch this space for “Fragment library design considerations” by S. M. Boyd, A. P. Turnbull and B. Walse, to be published in WIREs Computational Molecular Science and “Targeting cancer using fragment based drug discovery”, by A. P. Turnbull and S. M. Boyd to be published in Anti-Cancer Agents in Medicinal Chemistry.

Spring Special Offers

To support the efforts of ACADEMICS and TECHNOLOGY TRANSFER OFFICES involved in translational research, we will be offering a free initial consultation followed by up to 0.5 day of free computational services during April and May 2012 to assess the value of in silico approaches to their particular projects.

Upcoming Meetings

Spring Meeting of the UK QSAR & Chemoinformatics Group, 25th April 2012, Novartis, Horsham,http://www.ukqsar.org/2011/07/14/spring-2012/

MGMS Cutting-edge approaches to drug design, 2012, 26th April 2012, London,http://www.mgms.org/CEADD2012/index.html

SCI Protein kinase 2012, 21-22 May 2012, Accelrys, Cambridge, UK, http://www.soci.org/General-Pages/Display-Event?EventCode=FCHEM119

19th EuroQSAR: Knowledge-enabled ligand design, 26-30 August 2012, Vienna, Austria,http://www.euroqsar2012.org/

MGMS A practical introduction to chemoinformatics, 12-15 June 2012, Sheffield, UK, http://cisrg.shef.ac.uk/chemcourse/

15th International Workshop on Quantitative Structure-Activity Relationships in Environmental and Health Sciences, 18-22 June 2012, Tallinn, Estonia, http://qsar2012.ut.ee

MM2012: Discovery through biomolecular simulation, 30 Aug – 1 Sept 2012, Queenstown, NZ,http://www.mm2012.org.nz

The above list is not exhaustive, but constitutes a set of meetings which may be of interest to computational chemists and chemoinformaticians. If you have an upcoming meeting you’d like us to include in our spring newsletter please contact Susan Boyd.

Positions Open

Computational Chemist, Drug Discovery Unit, University of Dundee, Scotland, http://www.dundee.ac.uk/jobs

Application support specialist, Schrodinger, Germany,//tbe.taleo.net/NA2/ats/careers/requisition.jsp;jsessionid=3642319BE164A143801C5DB9E09309EE.NA2_primary_jvm?org=SCHRODINGER&cws=1&rid=68

Pfizer computational chemistry software developer, Groton, CT, USA, http://www.pfizercareers.com, job id 961898

Pre-Sales Scientific Support Specialist (e-Lab Notebooks), Accelrys Europe. May be located at Cambridge, Basel or Cologne, http://accelrys.com/about/careers/europe.html

Computational chemist, Biofocus, Saffron Walden, Essex, UK, http://biofocus.com/careers/ComputationalChemistCRP-427.htm

The above list is not exhaustive, but constitutes a set of positions which may be of interest to computational chemists & chemoinformaticians. CompChem Solutions takes no responsibility for the accuracy of any listing above or the availability of the positions. If you have a vacancy you’d like us to include in our spring newsletter please contact Susan Boyd.

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